Fix that "Rename and move file" throws file not found exception

Fixes #4307. Moreover, I refactored a bit how files are renamed/moved to the default file directory. This should make it easier to reuse the code.
JabRef · Sep 4, 2018 · dafd614 · dafd614
1 parent b39ed7b
commit dafd614
Show file tree

Hide file tree

Showing 64 changed files with 544 additions and 728 deletions.
diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -454,7 +454,7 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
             BibDatabaseContext databaseContext = pr.getDatabaseContext();
             databaseContext.setDatabaseFile(theFile);
             Globals.prefs.fileDirForDatabase = databaseContext
-                    .getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
+                    .getFileDirectories(Globals.prefs.getFilePreferences());
             System.out.println(Localization.lang("Exporting") + ": " + data[0]);
             Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(data[1]);
             if (!exporter.isPresent()) {

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -193,7 +193,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         this.tableModel = new MainTableDataModel(getBibDatabaseContext());
 
         citationStyleCache = new CitationStyleCache(bibDatabaseContext);
-        annotationCache = new FileAnnotationCache(bibDatabaseContext, Globals.prefs.getFileDirectoryPreferences());
+        annotationCache = new FileAnnotationCache(bibDatabaseContext, Globals.prefs.getFilePreferences());
 
         setupMainPanel();
 
@@ -370,7 +370,7 @@ private void setupActions() {
         actions.put(Actions.OPEN_EXTERNAL_FILE, this::openExternalFile);
 
         actions.put(Actions.OPEN_FOLDER, () -> JabRefExecutorService.INSTANCE.execute(() -> {
-            final List<Path> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(), bibDatabaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences()));
+            final List<Path> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(), bibDatabaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()));
             for (final Path f : files) {
                 try {
                     JabRefDesktop.openFolderAndSelectFile(f.toAbsolutePath());
@@ -1458,7 +1458,7 @@ public void searchAndOpen() {
             }
 
             final Set<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
-            final List<Path> dirs = basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences());
+            final List<Path> dirs = basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
             final List<String> extensions = types.stream().map(ExternalFileType::getExtension).collect(Collectors.toList());
 
             // Run the search operation:

diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -41,7 +41,6 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.event.FieldChangedEvent;
-import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreviewPreferences;
 
 import com.google.common.eventbus.Subscribe;
@@ -89,12 +88,10 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
         this.keyBindingRepository = keyBindingRepository;
 
         fileHandler = new NewDroppedFileHandler(dialogService, databaseContext, externalFileTypes,
-                                                Globals.prefs.getFileDirectoryPreferences(),
-                                                Globals.prefs.getCleanupPreferences(Globals.journalAbbreviationLoader).getFileDirPattern(),
+                Globals.prefs.getFilePreferences(),
                                                 Globals.prefs.getImportFormatPreferences(),
                                                 Globals.prefs.getUpdateFieldPreferences(),
-                                                Globals.getFileUpdateMonitor(),
-                                                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
+                Globals.getFileUpdateMonitor());
 
         // Set up scroll pane for preview pane
         setFitToHeight(true);

diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -74,8 +74,6 @@ private void doCleanup(CleanupPreset preset, BibEntry entry, NamedCompound ce) {
                 Globals.journalAbbreviationLoader));
         List<FieldChange> changes = cleaner.cleanup(preset, entry);
 
-        unsuccessfulRenames = cleaner.getUnsuccessfulRenames();
-
         if (changes.isEmpty()) {
             return;
         }
@@ -90,11 +88,7 @@ private void showResults() {
         if (isCanceled) {
             return;
         }
-        if (unsuccessfulRenames > 0) { //Rename failed for at least one entry
-            dialogService.showErrorDialogAndWait(
-                    Localization.lang("Autogenerate PDF Names"),
-                    Localization.lang("File rename failed for %0 entries.", Integer.toString(unsuccessfulRenames)));
-        }
+
         if (modifiedEntriesCount > 0) {
             panel.updateEntryEditorIfShowing();
             panel.markBaseChanged();

diff --git a/src/main/java/org/jabref/gui/actions/IntegrityCheckAction.java b/src/main/java/org/jabref/gui/actions/IntegrityCheckAction.java
@@ -48,7 +48,7 @@ public IntegrityCheckAction(JabRefFrame frame) {
     @Override
     public void execute() {
         IntegrityCheck check = new IntegrityCheck(frame.getCurrentBasePanel().getBibDatabaseContext(),
-                Globals.prefs.getFileDirectoryPreferences(),
+                Globals.prefs.getFilePreferences(),
                 Globals.prefs.getBibtexKeyPatternPreferences(),
                 Globals.journalAbbreviationLoader.getRepository(Globals.prefs.getJournalAbbreviationPreferences()),
                 Globals.prefs.getBoolean(JabRefPreferences.ENFORCE_LEGAL_BIBTEX_KEY));

diff --git a/src/main/java/org/jabref/gui/actions/WriteXMPAction.java b/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
@@ -111,7 +111,7 @@ private void writeXMP() {
             // Make a list of all PDFs linked from this entry:
             List<Path> files = entry.getFiles().stream()
                                     .filter(file -> file.getFileType().equalsIgnoreCase("pdf"))
-                                    .map(file -> file.findIn(basePanel.getBibDatabaseContext(), Globals.prefs.getFileDirectoryPreferences()))
+                                    .map(file -> file.findIn(basePanel.getBibDatabaseContext(), Globals.prefs.getFilePreferences()))
                                     .filter(Optional::isPresent)
                                     .map(Optional::get)
                                     .collect(Collectors.toList());

diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.java b/src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.java
@@ -53,7 +53,7 @@ private void init() {
         cleanUpISSN = new JCheckBox(Localization.lang("Reformat ISSN"));
 
         Optional<Path> firstExistingDir = databaseContext
-                .getFirstExistingFileDir(JabRefPreferences.getInstance().getFileDirectoryPreferences());
+                .getFirstExistingFileDir(JabRefPreferences.getInstance().getFilePreferences());
         if (firstExistingDir.isPresent()) {
             cleanUpMovePDF = new JCheckBox(Localization.lang("Move linked files to default file directory %0",
                     firstExistingDir.get().toString()));

diff --git a/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java b/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java
@@ -74,7 +74,7 @@ protected List<CopyFilesResultItemViewModel> call() throws InterruptedException,
 
                     LinkedFile fileName = files.get(j);
 
-                    Optional<Path> fileToExport = fileName.findIn(databaseContext, Globals.prefs.getFileDirectoryPreferences());
+                    Optional<Path> fileToExport = fileName.findIn(databaseContext, Globals.prefs.getFilePreferences());
 
                     newPath = OptionalUtil.combine(Optional.of(exportPath), fileToExport, resolvePathFilename);
 

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -57,7 +57,7 @@ public static void openExternalViewer(BibDatabaseContext databaseContext, String
         String fieldName = initialFieldName;
         if (FieldName.PS.equals(fieldName) || FieldName.PDF.equals(fieldName)) {
             // Find the default directory for this field type:
-            List<String> dir = databaseContext.getFileDirectories(fieldName, Globals.prefs.getFileDirectoryPreferences());
+            List<String> dir = databaseContext.getFileDirectories(fieldName, Globals.prefs.getFilePreferences());
 
             Optional<Path> file = FileHelper.expandFilename(link, dir);
 
@@ -128,7 +128,7 @@ public static boolean openExternalFileAnyFormat(final BibDatabaseContext databas
             return true;
         }
 
-        Optional<Path> file = FileHelper.expandFilename(databaseContext, link, Globals.prefs.getFileDirectoryPreferences());
+        Optional<Path> file = FileHelper.expandFilename(databaseContext, link, Globals.prefs.getFilePreferences());
         if (file.isPresent() && Files.exists(file.get())) {
             // Open the file:
             String filePath = file.get().toString();

diff --git a/src/main/java/org/jabref/gui/documentviewer/DocumentViewerViewModel.java b/src/main/java/org/jabref/gui/documentviewer/DocumentViewerViewModel.java
@@ -112,8 +112,8 @@ private void setCurrentDocument(Path path) {
     public void switchToFile(LinkedFile file) {
         if (file != null) {
             stateManager.getActiveDatabase().ifPresent(database ->
-                    file.findIn(database, Globals.prefs.getFileDirectoryPreferences())
-                            .ifPresent(this::setCurrentDocument));
+                    file.findIn(database, Globals.prefs.getFilePreferences())
+                        .ifPresent(this::setCurrentDocument));
         }
     }
 

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -48,7 +48,6 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.util.FileUpdateMonitor;
-import org.jabref.preferences.JabRefPreferences;
 
 import com.airhacks.afterburner.views.ViewLoader;
 import org.fxmisc.easybind.EasyBind;
@@ -102,12 +101,10 @@ public EntryEditor(BasePanel panel, EntryEditorPreferences preferences, FileUpda
         this.dialogService = dialogService;
 
         fileHandler = new NewDroppedFileHandler(dialogService, databaseContext, externalFileTypes,
-                                                Globals.prefs.getFileDirectoryPreferences(),
-                                                Globals.prefs.getCleanupPreferences(Globals.journalAbbreviationLoader).getFileDirPattern(),
+                Globals.prefs.getFilePreferences(),
                                                 Globals.prefs.getImportFormatPreferences(),
                                                 Globals.prefs.getUpdateFieldPreferences(),
-                                                Globals.getFileUpdateMonitor(),
-                                                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
+                Globals.getFileUpdateMonitor());
 
         ViewLoader.view(this)
                   .root(this)

diff --git a/src/main/java/org/jabref/gui/exporter/ExportCommand.java b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
@@ -86,8 +86,8 @@ private void export(Path file, FileChooser.ExtensionFilter selectedExtensionFilt
         // so formatters can resolve linked files correctly.
         // (This is an ugly hack!)
         Globals.prefs.fileDirForDatabase = frame.getCurrentBasePanel()
-                .getBibDatabaseContext()
-                .getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
+                                                .getBibDatabaseContext()
+                                                .getFileDirectories(Globals.prefs.getFilePreferences());
 
         // Make sure we remember which filter was used, to set
         // the default for next time:

diff --git a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
@@ -73,7 +73,7 @@ private String exportToClipboard(Exporter exporter) {
         // Set the global variable for this database's file directory before exporting,
         // so formatters can resolve linked files correctly.
         // (This is an ugly hack!)
-        Globals.prefs.fileDirForDatabase = panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences()).stream().map(Path::toString).collect(Collectors.toList());
+        Globals.prefs.fileDirForDatabase = panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()).stream().map(Path::toString).collect(Collectors.toList());
 
         Path tmp = null;
         try {

diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
@@ -18,7 +18,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.metadata.FileDirectoryPreferences;
+import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.util.FileHelper;
 
 import org.slf4j.Logger;
@@ -31,8 +31,8 @@ public class AutoSetFileLinksUtil {
     private AutoLinkPreferences autoLinkPreferences;
     private ExternalFileTypes externalFileTypes;
 
-    public AutoSetFileLinksUtil(BibDatabaseContext databaseContext, FileDirectoryPreferences fileDirectoryPreferences, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
-        this(databaseContext.getFileDirectoriesAsPaths(fileDirectoryPreferences), autoLinkPreferences, externalFileTypes);
+    public AutoSetFileLinksUtil(BibDatabaseContext databaseContext, FilePreferences filePreferences, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
+        this(databaseContext.getFileDirectoriesAsPaths(filePreferences), autoLinkPreferences, externalFileTypes);
     }
 
     public AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
@@ -68,7 +68,7 @@ public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOEx
                         .orElse(Optional.of(new UnknownExternalFileType("")));
 
                 String strType = type.isPresent() ? type.get().getName() : "";
-                String relativeFilePath = FileUtil.shortenFileName(foundFile, directories).toString();
+                String relativeFilePath = FileUtil.relativize(foundFile, directories).toString();
                 LinkedFile linkedFile = new LinkedFile("", relativeFilePath, strType);
                 linkedFiles.add(linkedFile);
             }

diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java
@@ -89,7 +89,7 @@ public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCom
 
         Runnable r = () -> {
             boolean foundAny = false;
-            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, Globals.prefs.getFileDirectoryPreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
 
             for (BibEntry entry : entries) {
 

diff --git a/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java b/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
@@ -202,7 +202,7 @@ public void download(URL url, String mimeType, final DownloadCallback callback)
             fileType = ExternalFileTypes.getInstance().getExternalFileTypeByExt(suffix);
         }
         String suggestedName = getSuggestedFileName(suffix);
-        List<String> fDirectory = databaseContext.getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
+        List<String> fDirectory = databaseContext.getFileDirectories(Globals.prefs.getFilePreferences());
         String directory;
         if (fDirectory.isEmpty()) {
             directory = null;

diff --git a/src/main/java/org/jabref/gui/externalfiles/DroppedFileHandler.java b/src/main/java/org/jabref/gui/externalfiles/DroppedFileHandler.java
@@ -147,9 +147,9 @@ public void handleDroppedfile(String fileName, ExternalFileType fileType, BibEnt
         String destFilename;
 
         if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.shortenFileName(Paths.get(fileName),
-                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences()))
-                    .toString();
+            destFilename = FileUtil.relativize(Paths.get(fileName),
+                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()))
+                                   .toString();
         } else {
             destFilename = renameCheckBox.isSelected() ? renameToTextBox.getText() : Paths.get(fileName).toString();
             if (copyRadioButton.isSelected()) {
@@ -199,9 +199,9 @@ public void linkPdfToEntry(String fileName, BibEntry entry) {
         NamedCompound edits = new NamedCompound(Localization.lang("Drop %0", fileType.getExtension()));
 
         if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.shortenFileName(Paths.get(fileName),
-                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences()))
-                    .toString();
+            destFilename = FileUtil.relativize(Paths.get(fileName),
+                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()))
+                                   .toString();
         } else {
             destFilename = renameCheckBox.isSelected() ? renameToTextBox.getText() : new File(fileName).getName();
             if (copyRadioButton.isSelected()) {
@@ -284,9 +284,9 @@ private boolean tryXmpImport(String fileName, ExternalFileType fileType, NamedCo
         String destFilename;
 
         if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.shortenFileName(Paths.get(fileName),
-                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences()))
-                    .toString();
+            destFilename = FileUtil.relativize(Paths.get(fileName),
+                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()))
+                                   .toString();
         } else {
             if (renameCheckBox.isSelected() || (single == null)) {
                 destFilename = fileName;
@@ -325,7 +325,7 @@ private boolean showLinkMoveCopyRenameDialog(String linkFileName, ExternalFileTy
         String dialogTitle = Localization.lang("Link to file %0", linkFileName);
 
         Optional<Path> dir = panel.getBibDatabaseContext()
-                .getFirstExistingFileDir(Globals.prefs.getFileDirectoryPreferences());
+                                  .getFirstExistingFileDir(Globals.prefs.getFilePreferences());
 
         if (!dir.isPresent()) {
             destDirLabel.setText(Localization.lang("File directory is not set or does not exist!"));
@@ -416,7 +416,7 @@ private void doLink(BibEntry entry, ExternalFileType fileType, String filename,
         if (avoidDuplicate) {
             // For comparison, find the absolute filename:
             List<Path> dirs = panel.getBibDatabaseContext()
-                    .getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences());
+                                   .getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
             String absFilename;
             if (new File(filename).isAbsolute() || dirs.isEmpty()) {
                 absFilename = filename;
@@ -475,7 +475,7 @@ private void doLink(BibEntry entry, ExternalFileType fileType, String filename,
      */
     private boolean doMove(String fileName, String destFilename, NamedCompound edits) {
         Optional<Path> dir = panel.getBibDatabaseContext()
-                .getFirstExistingFileDir(Globals.prefs.getFileDirectoryPreferences());
+                                  .getFirstExistingFileDir(Globals.prefs.getFilePreferences());
 
         if (dir.isPresent()) {
             Path destFile = dir.get().resolve(destFilename);
@@ -522,7 +522,7 @@ private boolean doMove(String fileName, String destFilename, NamedCompound edits
     private boolean doCopy(String fileName, String toFile, NamedCompound edits) {
 
         List<String> dirs = panel.getBibDatabaseContext()
-                .getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
+                                 .getFileDirectories(Globals.prefs.getFilePreferences());
         int found = -1;
         for (int i = 0; i < dirs.size(); i++) {
             if (new File(dirs.get(i)).exists()) {