Fixes #6357: File directory (#6377)

* Fixes #6357: File directory

Bug was introduced in 1b03f03.

* Fix tests

* Replace Paths.get

* Fix code style

Author: tobiasdiez

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

@@ -3,7 +3,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -111,9 +110,9 @@ private static Optional<ParserResult> importFile(String argument) {
             }
         } else {
             if (OS.WINDOWS) {
-                file = Paths.get(address);
+                file = Path.of(address);
             } else {
-                file = Paths.get(address.replace("~", System.getProperty("user.home")));
+                file = Path.of(address.replace("~", System.getProperty("user.home")));
             }
         }
 
@@ -280,7 +279,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
                 // We have an TemplateExporter instance:
                 try {
                     System.out.println(Localization.lang("Exporting") + ": " + data[1]);
-                    exporter.get().export(databaseContext, Paths.get(data[1]),
+                    exporter.get().export(databaseContext, Path.of(data[1]),
                             databaseContext.getMetaData().getEncoding().orElse(Globals.prefs.getDefaultEncoding()),
                             matches);
                 } catch (Exception ex) {
@@ -389,7 +388,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
         try {
             System.out.println(Localization.lang("Saving") + ": " + subName);
             SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
-            AtomicFileWriter fileWriter = new AtomicFileWriter(Paths.get(subName), prefs.getEncoding());
+            AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), prefs.getEncoding());
             BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs, Globals.entryTypesManager);
             databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
 
@@ -441,7 +440,7 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
             } else {
                 // We have an exporter:
                 try {
-                    exporter.get().export(pr.getDatabaseContext(), Paths.get(data[0]),
+                    exporter.get().export(pr.getDatabaseContext(), Path.of(data[0]),
                             pr.getDatabaseContext().getMetaData().getEncoding()
                                     .orElse(Globals.prefs.getDefaultEncoding()),
                             pr.getDatabaseContext().getDatabase().getEntries());

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

@@ -1,6 +1,6 @@
 package org.jabref.cli;
 
-import java.nio.file.Paths;
+import java.nio.file.Path;
 
 import org.jabref.gui.auximport.AuxParserResultViewModel;
 import org.jabref.logic.auxparser.DefaultAuxParser;
@@ -23,7 +23,7 @@ public BibDatabase perform() {
 
         if (!auxFile.isEmpty() && (database != null)) {
             AuxParser auxParser = new DefaultAuxParser(database);
-            AuxParserResult result = auxParser.parse(Paths.get(auxFile));
+            AuxParserResult result = auxParser.parse(Path.of(auxFile));
             subDatabase = result.getGeneratedBibDatabase();
             // print statistics
             System.out.println(new AuxParserResultViewModel(result).getInformation(true));

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

@@ -2,7 +2,6 @@
 
 import java.io.File;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -320,7 +319,7 @@ public void setWindowTitle() {
      * The MacAdapter calls this method when a "BIB" file has been double-clicked from the Finder.
      */
     public void openAction(String filePath) {
-        Path file = Paths.get(filePath);
+        Path file = Path.of(filePath);
         // all the logic is done in openIt. Even raising an existing panel
         getOpenDatabaseAction().openFile(file, true);
     }

src/main/java/org/jabref/gui/actions/ActionHelper.java

@@ -47,7 +47,7 @@ public static BooleanExpression isFilePresentForSelectedEntry(StateManager state
         return Bindings.createBooleanBinding(() -> {
                     List<LinkedFile> files = stateManager.getSelectedEntries().get(0).getFiles();
                     if ((files.size() > 0) && stateManager.getActiveDatabase().isPresent()) {
-                        Optional<Path> filename = FileHelper.expandFilename(
+                        Optional<Path> filename = FileHelper.find(
                                 stateManager.getActiveDatabase().get(),
                                 files.get(0).getLink(),
                                 preferencesService.getFilePreferences());

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

@@ -1,6 +1,6 @@
 package org.jabref.gui.auximport;
 
-import java.nio.file.Paths;
+import java.nio.file.Path;
 
 import javafx.fxml.FXML;
 import javafx.scene.control.Button;
@@ -36,7 +36,7 @@ public class FromAuxDialog extends BaseDialog<Void> {
     private final DialogService dialogService;
     private final BasePanel basePanel;
     @FXML private ButtonType generateButtonType;
-    private Button generateButton;
+    private final Button generateButton;
     @FXML private TextField auxFileField;
     @FXML private ListView<String> notFoundList;
 
@@ -74,7 +74,7 @@ private void parseActionPerformed() {
 
         if ((auxName != null) && (refBase != null) && !auxName.isEmpty()) {
             AuxParser auxParser = new DefaultAuxParser(refBase);
-            auxParserResult = auxParser.parse(Paths.get(auxName));
+            auxParserResult = auxParser.parse(Path.of(auxName));
             notFoundList.getItems().setAll(auxParserResult.getUnresolvedKeys());
             statusInfos.setText(new AuxParserResultViewModel(auxParserResult).getInformation(false));
 

src/main/java/org/jabref/gui/copyfiles/CopyFilesAction.java

@@ -1,7 +1,6 @@
 package org.jabref.gui.copyfiles;
 
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.List;
 import java.util.Optional;
 
@@ -47,7 +46,7 @@ public void execute() {
         List<BibEntry> entries = stateManager.getSelectedEntries();
 
         DirectoryDialogConfiguration dirDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                .withInitialDirectory(Paths.get(Globals.prefs.get(JabRefPreferences.EXPORT_WORKING_DIRECTORY)))
+                .withInitialDirectory(Path.of(Globals.prefs.get(JabRefPreferences.EXPORT_WORKING_DIRECTORY)))
                 .build();
         Optional<Path> exportPath = dialogService.showDirectorySelectionDialog(dirDialogConfiguration);
         exportPath.ifPresent(path -> {

src/main/java/org/jabref/gui/copyfiles/CopySingleFileAction.java

@@ -1,7 +1,6 @@
 package org.jabref.gui.copyfiles;
 
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.Optional;
 import java.util.function.BiFunction;
 
@@ -17,9 +16,9 @@
 
 public class CopySingleFileAction {
 
-    private LinkedFile linkedFile;
-    private DialogService dialogService;
-    private BibDatabaseContext databaseContext;
+    private final LinkedFile linkedFile;
+    private final DialogService dialogService;
+    private final BibDatabaseContext databaseContext;
     private final BiFunction<Path, Path, Path> resolvePathFilename = (path, file) -> {
         return path.resolve(file.getFileName());
     };
@@ -32,7 +31,7 @@ public CopySingleFileAction(LinkedFile linkedFile, DialogService dialogService,
 
     public void copyFile() {
         DirectoryDialogConfiguration dirDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                                                                                                        .withInitialDirectory(Paths.get(Globals.prefs.get(JabRefPreferences.EXPORT_WORKING_DIRECTORY)))
+                                                                                                        .withInitialDirectory(Path.of(Globals.prefs.get(JabRefPreferences.EXPORT_WORKING_DIRECTORY)))
                                                                                                         .build();
         Optional<Path> exportPath = dialogService.showDirectorySelectionDialog(dirDialogConfiguration);
         exportPath.ifPresent(this::copyFileToDestination);

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

@@ -55,12 +55,12 @@ public static void openExternalViewer(BibDatabaseContext databaseContext, String
         Field field = initialField;
         if (StandardField.PS.equals(field) || StandardField.PDF.equals(field)) {
             // Find the default directory for this field type:
-            List<String> dir = databaseContext.getFileDirectories(field, Globals.prefs.getFilePreferences());
+            List<Path> directories = databaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
 
-            Optional<Path> file = FileHelper.expandFilename(link, dir);
+            Optional<Path> file = FileHelper.find(link, directories);
 
             // Check that the file exists:
-            if (!file.isPresent() || !Files.exists(file.get())) {
+            if (file.isEmpty() || !Files.exists(file.get())) {
                 throw new IOException("File not found (" + field + "): '" + link + "'.");
             }
             link = file.get().toAbsolutePath().toString();
@@ -126,21 +126,16 @@ public static boolean openExternalFileAnyFormat(final BibDatabaseContext databas
             return true;
         }
 
-        Optional<Path> file = FileHelper.expandFilename(databaseContext, link, Globals.prefs.getFilePreferences());
+        Optional<Path> file = FileHelper.find(databaseContext, link, Globals.prefs.getFilePreferences());
         if (file.isPresent() && Files.exists(file.get())) {
             // Open the file:
             String filePath = file.get().toString();
             openExternalFilePlatformIndependent(type, filePath);
-            return true;
         } else {
             // No file matched the name, try to open it directly using the given app
             openExternalFilePlatformIndependent(type, link);
-            return true;
         }
-    }
-
-    public static boolean openExternalFileAnyFormat(Path file, final BibDatabaseContext databaseContext, final Optional<ExternalFileType> type) throws IOException {
-        return openExternalFileAnyFormat(databaseContext, file.toString(), type);
+        return true;
     }
 
     private static void openExternalFilePlatformIndependent(Optional<ExternalFileType> fileType, String filePath)

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

@@ -5,7 +5,6 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.Locale;
 import java.util.Optional;
 
@@ -109,6 +108,6 @@ public String detectProgramPath(String programName, String directoryName) {
 
     @Override
     public Path getApplicationDirectory() {
-        return Paths.get("/usr/lib/");
+        return Path.of("/usr/lib/");
     }
 }

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

@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 
 public interface NativeDesktop {
     void openFile(String filePath, String fileType) throws IOException;
@@ -35,6 +34,6 @@ public interface NativeDesktop {
      * @return the path to the user directory.
      */
     default Path getUserDirectory() {
-        return Paths.get(System.getProperty("user.home"));
+        return Path.of(System.getProperty("user.home"));
     }
 }