Merge remote-tracking branch 'upstream/master' into storeColumnSortOrder

* upstream/master: Fix that web search pane steals input (#4335) Fix entry editor field display (#4333) Convert update worker to BackgroundTask (#4334) Fix that "Rename and move file" throws file not found exception (#4317)
JabRef · Sep 12, 2018 · 5aad511 · 5aad511
2 parents 6e9a564 + 7775e05
commit 5aad511
Show file tree

Hide file tree

Showing 79 changed files with 711 additions and 895 deletions.
diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
@@ -15,18 +15,17 @@
 import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.dialogs.BackupUIManager;
+import org.jabref.gui.help.VersionWorker;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.importer.ParserResultWarningDialog;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.shared.SharedDatabaseUIManager;
-import org.jabref.gui.worker.VersionWorker;
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.shared.exception.InvalidDBMSConnectionPropertiesException;
 import org.jabref.logic.shared.exception.NotASharedDatabaseException;
-import org.jabref.logic.util.Version;
 import org.jabref.model.database.shared.DatabaseNotSupportedException;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -60,13 +59,8 @@ public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBl
                                     .orElse(Globals.prefs.get(JabRefPreferences.LAST_FOCUSED));
 
         openWindow(mainStage);
-        JabRefGUI.checkForNewVersion(false);
-    }
-
-    public static void checkForNewVersion(boolean manualExecution) {
-        Version toBeIgnored = Globals.prefs.getVersionPreferences().getIgnoredVersion();
-        Version currentVersion = Globals.BUILD_INFO.getVersion();
-        new VersionWorker(JabRefGUI.getMainFrame(), manualExecution, currentVersion, toBeIgnored).execute();
+        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), JabRefGUI.getMainFrame().getDialogService(), Globals.TASK_EXECUTOR)
+                .checkForNewVersionAsync(false);
     }
 
     private void openWindow(Stage mainStage) {

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
@@ -191,7 +191,7 @@ 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();
 
@@ -368,7 +368,7 @@ 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());
@@ -1398,7 +1398,7 @@ 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/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -954,7 +954,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SEARCH_FOR_UPDATES, new SearchForUpdateAction()),
+                factory.createMenuItem(StandardActions.SEARCH_FOR_UPDATES, new SearchForUpdateAction(Globals.BUILD_INFO, prefs.getVersionPreferences(), dialogService, Globals.TASK_EXECUTOR)),
                 factory.createSubMenu(StandardActions.WEB_MENU,
                         factory.createMenuItem(StandardActions.OPEN_WEBPAGE, new OpenBrowserAction("https://jabref.org/")),
                         factory.createMenuItem(StandardActions.OPEN_BLOG, new OpenBrowserAction("https://blog.jabref.org/")),

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);
@@ -153,8 +150,7 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
         });
 
         createKeyBindings();
-        updateLayout(preferences);
-
+        updateLayout(preferences, true);
     }
 
     private void createKeyBindings() {
@@ -211,6 +207,10 @@ public void setBasePanel(BasePanel basePanel) {
     }
 
     public void updateLayout(PreviewPreferences previewPreferences) {
+        updateLayout(previewPreferences, false);
+    }
+
+    private void updateLayout(PreviewPreferences previewPreferences, boolean init) {
         if (fixedLayout) {
             LOGGER.debug("cannot change the layout because the layout is fixed");
             return;
@@ -223,12 +223,16 @@ public void updateLayout(PreviewPreferences previewPreferences) {
                 CitationStyle.createCitationStyleFromFile(style)
                              .ifPresent(citationStyle -> {
                                  basePanel.get().getCitationStyleCache().setCitationStyle(citationStyle);
-                                 basePanel.get().output(Localization.lang("Preview style changed to: %0", citationStyle.getTitle()));
+                                 if (!init) {
+                                     basePanel.get().output(Localization.lang("Preview style changed to: %0", citationStyle.getTitle()));
+                                 }
                              });
             }
         } else {
             updatePreviewLayout(previewPreferences.getPreviewStyle(), previewPreferences.getLayoutFormatterPreferences());
-            basePanel.ifPresent(panel -> panel.output(Localization.lang("Preview style changed to: %0", Localization.lang("Preview"))));
+            if (!init) {
+                basePanel.ifPresent(panel -> panel.output(Localization.lang("Preview style changed to: %0", Localization.lang("Preview"))));
+            }
         }
 
         update();

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/SearchForUpdateAction.java b/src/main/java/org/jabref/gui/actions/SearchForUpdateAction.java
@@ -1,11 +1,28 @@
 package org.jabref.gui.actions;
 
-import org.jabref.JabRefGUI;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.help.VersionWorker;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.util.BuildInfo;
+import org.jabref.preferences.VersionPreferences;
 
 public class SearchForUpdateAction extends SimpleCommand {
 
+    private final BuildInfo buildInfo;
+    private final VersionPreferences versionPreferences;
+    private final DialogService dialogService;
+    private final TaskExecutor taskExecutor;
+
+    public SearchForUpdateAction(BuildInfo buildInfo, VersionPreferences versionPreferences, DialogService dialogService, TaskExecutor taskExecutor) {
+        this.buildInfo = buildInfo;
+        this.versionPreferences = versionPreferences;
+        this.dialogService = dialogService;
+        this.taskExecutor = taskExecutor;
+    }
+
     @Override
     public void execute() {
-        JabRefGUI.checkForNewVersion(true);
+        new VersionWorker(buildInfo.getVersion(), versionPreferences.getIgnoredVersion(), dialogService, taskExecutor)
+                .checkForNewVersionAsync(true);
     }
 }
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;