Refactor parsed file field

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

@@ -136,6 +136,7 @@
 import org.jabref.model.entry.event.EntryEventSource;
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.model.entry.specialfields.SpecialFieldValue;
+import org.jabref.model.util.FileHelper;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreviewPreferences;
 import org.jabref.shared.DBMSSynchronizer;
@@ -522,11 +523,11 @@ public void update() {
         actions.put(Actions.OPEN_EXTERNAL_FILE, (BaseAction) () -> openExternalFile());
 
         actions.put(Actions.OPEN_FOLDER, (BaseAction) () -> JabRefExecutorService.INSTANCE.execute(() -> {
-            final List<File> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(),
+            final List<Path> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(),
                     bibDatabaseContext.getFileDirectories(Globals.prefs.getFileDirectoryPreferences()));
-            for (final File f : files) {
+            for (final Path f : files) {
                 try {
-                    JabRefDesktop.openFolderAndSelectFile(f.getAbsolutePath());
+                    JabRefDesktop.openFolderAndSelectFile(f.toAbsolutePath());
                 } catch (IOException e) {
                     LOGGER.info("Could not open folder", e);
                 }
@@ -2119,7 +2120,7 @@ public Optional<String> searchAndOpen() {
                 final List<File> res = result.get(entry);
                 if (!res.isEmpty()) {
                     final String filepath = res.get(0).getPath();
-                    final Optional<String> extension = FileUtil.getFileExtension(filepath);
+                    final Optional<String> extension = FileHelper.getFileExtension(filepath);
                     if (extension.isPresent()) {
                         Optional<ExternalFileType> type = ExternalFileTypes.getInstance()
                                 .getExternalFileTypeByExt(extension.get());

src/main/java/org/jabref/gui/desktop/JabRefDesktop.java

@@ -2,6 +2,9 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -31,12 +34,12 @@
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
-import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.identifier.DOI;
 import org.jabref.model.entry.identifier.Eprint;
+import org.jabref.model.util.FileHelper;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.apache.commons.logging.Log;
@@ -66,16 +69,16 @@ public static void openExternalViewer(BibDatabaseContext databaseContext, String
             // Find the default directory for this field type:
             List<String> dir = databaseContext.getFileDirectories(fieldName, Globals.prefs.getFileDirectoryPreferences());
 
-            Optional<File> file = FileUtil.expandFilename(link, dir);
+            Optional<Path> file = FileHelper.expandFilename(link, dir);
 
             // Check that the file exists:
-            if (!file.isPresent() || !file.get().exists()) {
+            if (!file.isPresent() || !Files.exists(file.get())) {
                 throw new IOException("File not found (" + fieldName + "): '" + link + "'.");
             }
-            link = file.get().getCanonicalPath();
+            link = file.get().toAbsolutePath().toString();
 
             // Use the correct viewer even if pdf and ps are mixed up:
-            String[] split = file.get().getName().split("\\.");
+            String[] split = file.get().getFileName().toString().split("\\.");
             if (split.length >= 2) {
                 if ("pdf".equalsIgnoreCase(split[split.length - 1])) {
                     fieldName = FieldName.PDF;
@@ -138,20 +141,19 @@ public static boolean openExternalFileAnyFormat(final BibDatabaseContext databas
         }
 
         // For other platforms we'll try to find the file type:
-        File file = new File(link);
-
+        Path file = Paths.get(link);
         if (!httpLink) {
-            Optional<File> tmp = FileUtil.expandFilename(databaseContext, link,
+            Optional<Path> tmp = FileHelper.expandFilename(databaseContext, link,
                     Globals.prefs.getFileDirectoryPreferences());
             if (tmp.isPresent()) {
                 file = tmp.get();
             }
         }
 
         // Check if we have arrived at a file type, and either an http link or an existing file:
-        if ((httpLink || file.exists()) && (type.isPresent())) {
+        if (httpLink || Files.exists(file) && (type.isPresent())) {
             // Open the file:
-            String filePath = httpLink ? link : file.getPath();
+            String filePath = httpLink ? link : file.toString();
             openExternalFilePlatformIndependent(type, filePath);
             return true;
         } else {
@@ -253,7 +255,7 @@ public static boolean openExternalFileUnknown(JabRefFrame frame, BibEntry entry,
      * @param fileLink the location of the file
      * @throws IOException
      */
-    public static void openFolderAndSelectFile(String fileLink) throws IOException {
+    public static void openFolderAndSelectFile(Path fileLink) throws IOException {
         NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
     }
 

src/main/java/org/jabref/gui/desktop/os/DefaultDesktop.java

@@ -4,7 +4,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.List;
 
 import org.apache.commons.logging.Log;
@@ -24,8 +23,8 @@ public void openFileWithApplication(String filePath, String application) throws
     }
 
     @Override
-    public void openFolderAndSelectFile(String filePath) throws IOException {
-        File file = Paths.get(filePath).toAbsolutePath().getParent().toFile();
+    public void openFolderAndSelectFile(Path filePath) throws IOException {
+        File file = filePath.toAbsolutePath().getParent().toFile();
         Desktop.getDesktop().open(file);
     }
 

src/main/java/org/jabref/gui/desktop/os/Linux.java

@@ -50,7 +50,7 @@ public void openFileWithApplication(String filePath, String application) throws
     }
 
     @Override
-    public void openFolderAndSelectFile(String filePath) throws IOException {
+    public void openFolderAndSelectFile(Path filePath) throws IOException {
         String desktopSession = System.getenv("DESKTOP_SESSION").toLowerCase(Locale.ROOT);
 
         String cmd;
@@ -60,7 +60,7 @@ public void openFolderAndSelectFile(String filePath) throws IOException {
         } else if (desktopSession.contains("kde")) {
             cmd = "dolphin --select " + filePath;
         } else {
-            cmd = "xdg-open " + Paths.get(filePath).toAbsolutePath().getParent().toString();
+            cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString();
         }
 
         Runtime.getRuntime().exec(cmd);

src/main/java/org/jabref/gui/desktop/os/NativeDesktop.java

@@ -17,7 +17,7 @@ public interface NativeDesktop {
      */
     void openFileWithApplication(String filePath, String application) throws IOException;
 
-    void openFolderAndSelectFile(String filePath) throws IOException;
+    void openFolderAndSelectFile(Path file) throws IOException;
 
     void openConsole(String absolutePath) throws IOException;
 

src/main/java/org/jabref/gui/desktop/os/OSX.java

@@ -33,9 +33,8 @@ public void openFileWithApplication(String filePath, String application) throws
     }
 
     @Override
-    public void openFolderAndSelectFile(String filePath) throws IOException {
-        File file = new File(filePath);
-        Desktop.getDesktop().open(file.getParentFile());
+    public void openFolderAndSelectFile(Path file) throws IOException {
+        Desktop.getDesktop().open(file.getParent().toFile());
     }
 
     @Override

src/main/java/org/jabref/gui/desktop/os/Windows.java

@@ -59,8 +59,8 @@ public void openFileWithApplication(String filePath, String application) throws
     }
 
     @Override
-    public void openFolderAndSelectFile(String filePath) throws IOException {
-        new ProcessBuilder("explorer.exe", "/select,", filePath).start();
+    public void openFolderAndSelectFile(Path filePath) throws IOException {
+        new ProcessBuilder("explorer.exe", "/select,", filePath.toString()).start();
     }
 
     @Override

src/main/java/org/jabref/gui/documentviewer/DocumentViewerController.java

@@ -16,12 +16,12 @@
 import org.jabref.gui.util.OnlyIntegerFormatter;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.gui.util.ViewModelListCellFactory;
-import org.jabref.model.entry.ParsedFileField;
+import org.jabref.model.entry.LinkedFile;
 
 public class DocumentViewerController extends AbstractController<DocumentViewerViewModel> {
 
     @FXML private ScrollBar scrollBar;
-    @FXML private ComboBox<ParsedFileField> fileChoice;
+    @FXML private ComboBox<LinkedFile> fileChoice;
     @FXML private BorderPane mainPane;
     @FXML private ToggleButton modeLive;
     @FXML private TextField currentPage;
@@ -59,8 +59,8 @@ private void setupPageControls() {
     }
 
     private void setupFileChoice() {
-        ViewModelListCellFactory<ParsedFileField> cellFactory = new ViewModelListCellFactory<ParsedFileField>()
-                .withText(ParsedFileField::getLink);
+        ViewModelListCellFactory<LinkedFile> cellFactory = new ViewModelListCellFactory<LinkedFile>()
+                .withText(LinkedFile::getLink);
         fileChoice.setButtonCell(cellFactory.call(null));
         fileChoice.setCellFactory(cellFactory);
         fileChoice.getSelectionModel().selectedItemProperty().addListener(

src/main/java/org/jabref/gui/documentviewer/DocumentViewerViewModel.java

@@ -19,10 +19,8 @@
 import org.jabref.Globals;
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.StateManager;
-import org.jabref.logic.TypedBibEntry;
-import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.ParsedFileField;
+import org.jabref.model.entry.LinkedFile;
 
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.fxmisc.easybind.EasyBind;
@@ -31,7 +29,7 @@ public class DocumentViewerViewModel extends AbstractViewModel {
 
     private StateManager stateManager;
     private ObjectProperty<DocumentViewModel> currentDocument = new SimpleObjectProperty<>();
-    private ListProperty<ParsedFileField> files = new SimpleListProperty<>();
+    private ListProperty<LinkedFile> files = new SimpleListProperty<>();
     private BooleanProperty liveMode = new SimpleBooleanProperty();
     private ObjectProperty<Integer> currentPage = new SimpleObjectProperty<>();
     private IntegerProperty maxPages = new SimpleIntegerProperty();
@@ -79,7 +77,7 @@ public ObjectProperty<DocumentViewModel> currentDocumentProperty() {
         return currentDocument;
     }
 
-    public ListProperty<ParsedFileField> filesProperty() {
+    public ListProperty<LinkedFile> filesProperty() {
         return files;
     }
 
@@ -90,10 +88,9 @@ private void setCurrentEntries(List<BibEntry> entries) {
         }
     }
 
-    private void setCurrentEntry(BibEntry rawEntry) {
+    private void setCurrentEntry(BibEntry entry) {
         stateManager.getActiveDatabase().ifPresent(database -> {
-            TypedBibEntry entry = new TypedBibEntry(rawEntry, database);
-            List<ParsedFileField> linkedFiles = entry.getFiles();
+            List<LinkedFile> linkedFiles = entry.getFiles();
             // We don't need to switch to the first file, this is done automatically in the UI part
             files.setValue(FXCollections.observableArrayList(linkedFiles));
         });
@@ -107,10 +104,10 @@ private void setCurrentDocument(Path path) {
         }
     }
 
-    public void switchToFile(ParsedFileField file) {
+    public void switchToFile(LinkedFile file) {
         if (file != null) {
             stateManager.getActiveDatabase().ifPresent(database ->
-                    FileUtil.toPath(file, database, Globals.prefs.getFileDirectoryPreferences())
+                    file.findIn(database, Globals.prefs.getFileDirectoryPreferences())
                             .ifPresent(this::setCurrentDocument));
         }
     }

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

@@ -35,6 +35,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.util.FileHelper;
 import org.jabref.preferences.JabRefPreferences;
 
 public class AutoSetLinks {
@@ -149,7 +150,7 @@ public void run() {
                         if (!alreadyHas) {
                             foundAny = true;
                             Optional<ExternalFileType> type;
-                            Optional<String> extension = FileUtil.getFileExtension(f);
+                            Optional<String> extension = FileHelper.getFileExtension(f);
                             if (extension.isPresent()) {
                                 type = ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension.get());
                             } else {

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

@@ -40,6 +40,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.IdGenerator;
+import org.jabref.model.util.FileHelper;
 import org.jabref.preferences.JabRefPreferences;
 
 import com.jgoodies.forms.builder.FormBuilder;
@@ -422,9 +423,9 @@ private void doLink(BibEntry entry, ExternalFileType fileType, String filename,
             if (new File(filename).isAbsolute() || dirs.isEmpty()) {
                 absFilename = filename;
             } else {
-                Optional<File> file = FileUtil.expandFilename(filename, dirs);
+                Optional<Path> file = FileHelper.expandFilename(filename, dirs);
                 if (file.isPresent()) {
-                    absFilename = file.get().getAbsolutePath();
+                    absFilename = file.get().toAbsolutePath().toString();
                 } else {
                     absFilename = ""; // This shouldn't happen based on the old code, so maybe one should set it something else?
                 }
@@ -435,17 +436,12 @@ private void doLink(BibEntry entry, ExternalFileType fileType, String filename,
             for (int i = 0; i < tm.getRowCount(); i++) {
                 FileListEntry flEntry = tm.getEntry(i);
                 // Find the absolute filename for this existing link:
-                String absName;
-                if (new File(flEntry.getLink()).isAbsolute() || dirs.isEmpty()) {
-                    absName = flEntry.getLink();
-                } else {
-                    Optional<File> file = FileUtil.expandFilename(flEntry.getLink(), dirs);
-                    if (file.isPresent()) {
-                        absName = file.get().getAbsolutePath();
-                    } else {
-                        absName = null;
-                    }
-                }
+                String absName = flEntry.toParsedFileField()
+                        .findIn(dirs)
+                        .map(Path::toAbsolutePath)
+                        .map(Path::toString)
+                        .orElse(null);
+
                 LOGGER.debug("absName: " + absName);
                 // If the filenames are equal, we don't need to link, so we simply return:
                 if (absFilename.equals(absName)) {

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

@@ -1,12 +1,8 @@
 package org.jabref.gui.externalfiles;
 
 import java.awt.event.ActionEvent;
-import java.io.File;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Locale;
 import java.util.Optional;
 
 import javax.swing.AbstractAction;
@@ -19,8 +15,7 @@
 import org.jabref.gui.filelist.FileListEntry;
 import org.jabref.logic.cleanup.MoveFilesCleanup;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.entry.ParsedFileField;
+import org.jabref.model.entry.LinkedFile;
 
 /**
  * Action for moving a file that is linked  from an entry in JabRef.
@@ -47,31 +42,25 @@ public void actionPerformed(ActionEvent event) {
         }
 
         FileListEntry entry = editor.getTableModel().getEntry(selected);
-        // Check if the current file exists:
-        String ln = entry.getLink();
-        ParsedFileField field = entry.toParsedFileField();
+        LinkedFile field = entry.toParsedFileField();
 
-        boolean httpLink = ln.toLowerCase(Locale.ENGLISH).startsWith("http");
-        if (httpLink) {
+        if (field.isOnlineLink()) {
             // TODO: notify that this operation cannot be done on remote links
             return;
         }
+
         // Get an absolute path representation:
-        List<String> dirs = frame.getCurrentBasePanel().getBibDatabaseContext()
-                .getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
         Optional<Path> fileDir = frame.getCurrentBasePanel().getBibDatabaseContext()
                 .getFirstExistingFileDir(Globals.prefs.getFileDirectoryPreferences());
         if (!fileDir.isPresent()) {
             JOptionPane.showMessageDialog(frame, Localization.lang("File directory is not set or does not exist!"),
                     Localization.lang("Move file"), JOptionPane.ERROR_MESSAGE);
             return;
         }
-        Path file = Paths.get(ln);
-        if (!file.isAbsolute()) {
-            file = FileUtil.expandFilename(ln, dirs).map(File::toPath).orElse(null);
-        }
 
-        if ((file != null) && Files.exists(file)) {
+        // Check if the current file exists:
+        Optional<Path> file = field.findIn(frame.getCurrentBasePanel().getBibDatabaseContext(), Globals.prefs.getFileDirectoryPreferences());
+        if ((file.isPresent()) && Files.exists(file.get())) {
 
             MoveFilesCleanup moveFiles = new MoveFilesCleanup(frame.getCurrentBasePanel().getBibDatabaseContext(),
                     Globals.prefs.getCleanupPreferences(Globals.journalAbbreviationLoader).getFileDirPattern(),