Fixes #6357: File directory

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/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/fieldeditors/LinkedFileViewModel.java

@@ -101,7 +101,7 @@ public LinkedFileViewModel(LinkedFile linkedFile,
                     if (linkedFile.isOnlineLink()) {
                         return true;
                     } else {
-                        Optional<Path> path = FileHelper.expandFilename(databaseContext, link, filePreferences);
+                        Optional<Path> path = FileHelper.find(databaseContext, link, filePreferences);
                         return path.isPresent() && Files.exists(path.get());
                     }
                 },
@@ -192,7 +192,7 @@ public void open() {
     public void openFolder() {
         try {
             if (!linkedFile.isOnlineLink()) {
-                Optional<Path> resolvedPath = FileHelper.expandFilename(
+                Optional<Path> resolvedPath = FileHelper.find(
                         databaseContext,
                         linkedFile.getLink(),
                         filePreferences);

src/main/java/org/jabref/gui/filelist/LinkedFilesEditDialogViewModel.java

@@ -70,7 +70,7 @@ private void setExternalFileTypeByExtension(String link) {
     public void openBrowseDialog() {
         String fileText = link.get();
 
-        Optional<Path> file = FileHelper.expandFilename(database, fileText, preferences.getFilePreferences());
+        Optional<Path> file = FileHelper.find(database, fileText, preferences.getFilePreferences());
 
         Path workingDir = file.orElse(preferences.getWorkingDir());
         String fileName = Paths.get(fileText).getFileName().toString();

src/main/java/org/jabref/gui/preferences/FileTabViewModel.java

@@ -19,8 +19,6 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.field.StandardField;
-import org.jabref.model.metadata.FilePreferences;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.NewLineSeparator;
 
@@ -87,7 +85,7 @@ public void setValues() {
         selectedNewLineSeparatorProperty.setValue(preferences.getNewLineSeparator());
         alwaysReformatBibProperty.setValue(preferences.getBoolean(JabRefPreferences.REFORMAT_FILE_ON_SAVE_AND_EXPORT));
 
-        mainFileDirProperty.setValue(preferences.getAsOptional(StandardField.FILE.getName() + FilePreferences.DIR_SUFFIX).orElse(""));
+        mainFileDirProperty.setValue(preferences.getAsOptional(JabRefPreferences.MAIN_FILE_DIRECTORY).orElse(""));
         useBibLocationAsPrimaryProperty.setValue(preferences.getBoolean(JabRefPreferences.BIB_LOC_AS_PRIMARY_DIR));
         if (preferences.getBoolean(JabRefPreferences.AUTOLINK_USE_REG_EXP_SEARCH_KEY)) { // Flipped around
             autolinkUseRegexProperty.setValue(true);
@@ -118,7 +116,7 @@ public void storeSettings() {
         preferences.setNewLineSeparator(selectedNewLineSeparatorProperty.getValue());
         preferences.putBoolean(JabRefPreferences.REFORMAT_FILE_ON_SAVE_AND_EXPORT, alwaysReformatBibProperty.getValue());
 
-        preferences.put(StandardField.FILE.getName() + FilePreferences.DIR_SUFFIX, mainFileDirProperty.getValue());
+        preferences.put(JabRefPreferences.MAIN_FILE_DIRECTORY, mainFileDirProperty.getValue());
         preferences.putBoolean(JabRefPreferences.BIB_LOC_AS_PRIMARY_DIR, useBibLocationAsPrimaryProperty.getValue());
         preferences.putBoolean(JabRefPreferences.AUTOLINK_USE_REG_EXP_SEARCH_KEY, autolinkUseRegexProperty.getValue());
         preferences.putBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY, autolinkFileExactBibtexProperty.getValue());

src/main/java/org/jabref/logic/layout/format/FileLink.java

@@ -1,6 +1,7 @@
 package org.jabref.logic.layout.format;
 
 import java.nio.file.Paths;
+import java.util.Collections;
 import java.util.List;
 import java.util.stream.Collectors;
 
@@ -55,7 +56,7 @@ public String format(String field) {
         // ugly hack, the export routine has set a global variable before
         // starting the export, which contains the database's file directory:
         if (prefs.getFileDirForDatabase() == null) {
-            dirs = prefs.getGeneratedDirForDatabase();
+            dirs = Collections.singletonList(prefs.getMainFileDirectory());
         } else {
             dirs = prefs.getFileDirForDatabase();
         }

src/main/java/org/jabref/logic/layout/format/FileLinkPreferences.java

@@ -4,15 +4,16 @@
 
 public class FileLinkPreferences {
 
-    private final List<String> generatedDirForDatabase;
+    private final String mainFileDirectory;
     private final List<String> fileDirForDatabase;
-    public FileLinkPreferences(List<String> generatedDirForDatabase, List<String> fileDirForDatabase) {
-        this.generatedDirForDatabase = generatedDirForDatabase;
+
+    public FileLinkPreferences(String mainFileDirectory, List<String> fileDirForDatabase) {
+        this.mainFileDirectory = mainFileDirectory;
         this.fileDirForDatabase = fileDirForDatabase;
     }
 
-    public List<String> getGeneratedDirForDatabase() {
-        return generatedDirForDatabase;
+    public String getMainFileDirectory() {
+        return mainFileDirectory;
     }
 
     public List<String> getFileDirForDatabase() {

src/main/java/org/jabref/logic/layout/format/WrapFileLinks.java

@@ -2,6 +2,7 @@
 
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -201,7 +202,7 @@ public String format(String field) {
                             // ugly hack, the export routine has set a global variable before
                             // starting the export, which contains the database's file directory:
                             if ((prefs.getFileDirForDatabase() == null) || prefs.getFileDirForDatabase().isEmpty()) {
-                                dirs = prefs.getGeneratedDirForDatabase();
+                                dirs = Collections.singletonList(prefs.getMainFileDirectory());
                             } else {
                                 dirs = prefs.getFileDirForDatabase();
                             }

src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -1,6 +1,5 @@
 package org.jabref.model.database;
 
-import java.io.File;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -14,8 +13,6 @@
 import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.database.shared.DatabaseSynchronizer;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.field.Field;
-import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.metadata.MetaData;
 
@@ -107,63 +104,34 @@ public boolean isBiblatexMode() {
         return getMode() == BibDatabaseMode.BIBLATEX;
     }
 
-    public List<Path> getFileDirectoriesAsPaths(FilePreferences preferences) {
-        // Filter for empty string, as this would be expanded to the jar-directory with Paths.get()
-        return getFileDirectories(preferences).stream()
-                                              .filter(s -> !s.isEmpty())
-                                              .map(Paths::get)
-                                              .map(Path::toAbsolutePath)
-                                              .map(Path::normalize)
-                                              .collect(Collectors.toList());
-    }
-
     /**
-     * @deprecated use {@link #getFileDirectoriesAsPaths(FilePreferences)} instead
-     */
-    @Deprecated
-    public List<String> getFileDirectories(FilePreferences preferences) {
-        return getFileDirectories(StandardField.FILE, preferences);
-    }
-
-    /**
-     * Returns the first existing file directory from  {@link #getFileDirectories(FilePreferences)}
-     *
-     * @param preferences The FilePreferences
-     * @return Optional of Path
-     */
-    public Optional<Path> getFirstExistingFileDir(FilePreferences preferences) {
-        return getFileDirectoriesAsPaths(preferences).stream().filter(Files::exists).findFirst();
-    }
-
-    /**
-     * Look up the directories set up for the given field type for this database. If no directory is set up, return that
-     * defined in global preferences. There can be up to three directory definitions for these files: the database's
-     * metadata can specify a general directory and/or a user-specific directory or the preferences can specify one. <p>
-     * The settings are prioritized in the following order and the first defined setting is used:
+     * Look up the directories set up for this database.
+     * There can be up to three directory definitions for these files: the database's
+     * metadata can specify a general directory and/or a user-specific directory, or the preferences can specify one.
+     * <p>
+     * The settings are prioritized in the following order, and the first defined setting is used:
      * <ol>
-     *     <li>metadata</li>
-     *     <li>user-specific directory</li>
+     *     <li>user-specific metadata directory</li>
+     *     <li>general metadata directory</li>
      *     <li>preferences directory</li>
      *     <li>BIB file directory</li>
      * </ol>
      *
-     * @param field       The field
      * @param preferences The fileDirectory preferences
-     * @return The default directory for this field type.
      */
-    public List<String> getFileDirectories(Field field, FilePreferences preferences) {
-        List<String> fileDirs = new ArrayList<>();
+    public List<Path> getFileDirectoriesAsPaths(FilePreferences preferences) {
+        List<Path> fileDirs = new ArrayList<>();
 
-        // 1. metadata user-specific directory
+        // 1. Metadata user-specific directory
         metaData.getUserFileDirectory(preferences.getUser())
                 .ifPresent(userFileDirectory -> fileDirs.add(getFileDirectoryPath(userFileDirectory)));
 
-        // 2. metadata general directory
+        // 2. Metadata general directory
         metaData.getDefaultFileDirectory()
                 .ifPresent(metaDataDirectory -> fileDirs.add(getFileDirectoryPath(metaDataDirectory)));
 
-        // 3. preferences directory
-        preferences.getFileDirectory(field).ifPresent(path -> fileDirs.add(path.toAbsolutePath().toString()));
+        // 3. Preferences directory
+        preferences.getFileDirectory().ifPresent(fileDirs::add);
 
         // 4. BIB file directory
         getDatabasePath().ifPresent(dbPath -> {
@@ -173,38 +141,47 @@ public List<String> getFileDirectories(Field field, FilePreferences preferences)
                 parentPath = Paths.get(System.getProperty("user.dir"));
             }
             Objects.requireNonNull(parentPath, "BibTeX database parent path is null");
-            String parentDir = parentPath.toAbsolutePath().toString();
+
             // Check if we should add it as primary file dir (first in the list) or not:
             if (preferences.isBibLocationAsPrimary()) {
-                fileDirs.add(0, parentDir);
+                fileDirs.add(0, parentPath);
             } else {
-                fileDirs.add(parentDir);
+                fileDirs.add(parentPath);
             }
         });
 
-        return fileDirs;
+        return fileDirs.stream().map(Path::toAbsolutePath).collect(Collectors.toList());
+    }
+
+    /**
+     * Returns the first existing file directory from  {@link #getFileDirectories(FilePreferences)}
+     *
+     * @param preferences The FilePreferences
+     * @return Optional of Path
+     */
+    public Optional<Path> getFirstExistingFileDir(FilePreferences preferences) {
+        return getFileDirectoriesAsPaths(preferences).stream().filter(Files::exists).findFirst();
     }
 
-    private String getFileDirectoryPath(String directoryName) {
-        String dir = directoryName;
+    /**
+     * @deprecated use {@link #getFileDirectoriesAsPaths(FilePreferences)} instead
+     */
+    @Deprecated
+    public List<String> getFileDirectories(FilePreferences preferences) {
+        return getFileDirectoriesAsPaths(preferences).stream()
+                                                     .map(directory -> directory.toAbsolutePath().toString())
+                                                     .collect(Collectors.toList());
+    }
+
+    private Path getFileDirectoryPath(String directoryName) {
+        Path directory = Path.of(directoryName);
         // If this directory is relative, we try to interpret it as relative to
         // the file path of this BIB file:
         Optional<Path> databaseFile = getDatabasePath();
-        if (!new File(dir).isAbsolute() && databaseFile.isPresent()) {
-            Path relDir;
-            if (".".equals(dir)) {
-                // if dir is only "current" directory, just use its parent (== real current directory) as path
-                relDir = databaseFile.get().getParent();
-            } else {
-                relDir = databaseFile.get().getParent().resolve(dir);
-            }
-            // If this directory actually exists, it is very likely that the
-            // user wants us to use it:
-            if (Files.exists(relDir)) {
-                dir = relDir.toString();
-            }
+        if (!directory.isAbsolute() && databaseFile.isPresent()) {
+            return databaseFile.get().getParent().resolve(directory).normalize();
         }
-        return dir;
+        return directory;
     }
 
     public DatabaseSynchronizer getDBMSSynchronizer() {

src/main/java/org/jabref/model/entry/LinkedFile.java

@@ -188,7 +188,7 @@ public Optional<Path> findIn(List<Path> directories) {
                     return Optional.empty();
                 }
             } else {
-                return FileHelper.expandFilenameAsPath(link.get(), directories);
+                return FileHelper.find(link.get(), directories);
             }
         } catch (InvalidPathException ex) {
             return Optional.empty();

src/main/java/org/jabref/model/groups/TexGroup.java

@@ -23,12 +23,12 @@ public class TexGroup extends AbstractGroup implements FileUpdateListener {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(TexGroup.class);
 
-    private Path filePath;
+    private final Path filePath;
     private Set<String> keysUsedInAux = null;
     private final FileUpdateMonitor fileMonitor;
-    private AuxParser auxParser;
+    private final AuxParser auxParser;
     private final MetaData metaData;
-    private String user;
+    private final String user;
 
     TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) {
         super(name, context);
@@ -126,7 +126,7 @@ private Path relativize(Path path) {
 
     private Path expandPath(Path path) {
         List<Path> fileDirectories = getFileDirectoriesAsPaths();
-        return FileHelper.expandFilenameAsPath(path.toString(), fileDirectories).orElse(path);
+        return FileHelper.find(path.toString(), fileDirectories).orElse(path);
     }
 
     private List<Path> getFileDirectoriesAsPaths() {