Merge remote-tracking branch 'upstream/main' into searchColPrefs

* upstream/main: Observable Preferences H (WorkingDir, getUser, NameFormatter, Version, SpecialFields) (#8260) Bump checkstyle from 9.0.1 to 9.1 (#8266) Bump mockito-core from 4.0.0 to 4.1.0 (#8267) Bump classgraph from 4.8.130 to 4.8.135 (#8268) Fix some fetcher tests (#8258) Clicking a DOI link in the preview pane no longer crashes (#8255)
JabRef · Nov 22, 2021 · e367b1e · e367b1e
2 parents c1282f9 + ab13b2a
commit e367b1e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -66,6 +66,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The default directory of the "LaTeX Citations" tab is now the directory of the currently opened database (and not the directory chosen at the last open file dialog or the last database save) [koppor#538](https://github.com/koppor/jabref/issues/538)
 - We fixed an issue where right-clicking on a tab and selecting close will close the focused tab even if it is not the tab we right-clicked [#8193](https://github.com/JabRef/jabref/pull/8193)
 - We fixed an issue where selecting a citation style in the preferences would sometimes produce an exception [#7860](https://github.com/JabRef/jabref/issues/7860)
+- We fixed an issue where an exception would occur when clicking on a DOI link in the preview pane [#7706](https://github.com/JabRef/jabref/issues/7706)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -207,14 +207,14 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.130'
+    testImplementation 'io.github.classgraph:classgraph:4.8.135'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.1'
 
     testImplementation 'net.bytebuddy:byte-buddy-parent:1.12.1'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:4.0.0'
+    testImplementation 'org.mockito:mockito-core:4.1.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.3'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.3'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
@@ -223,7 +223,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:9.0.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:9.1'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
 }
 

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -310,28 +310,28 @@ private void writeMetadatatoPDFsOfEntry(BibDatabaseContext databaseContext, Stri
         try {
             if (writeXMP) {
                 if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
-                    System.out.println(String.format("Successfully written XMP metadata on at least one linked file of %s", citeKey));
+                    System.out.printf("Successfully written XMP metadata on at least one linked file of %s%n", citeKey);
                 } else {
-                    System.err.println(String.format("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+                    System.err.printf("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
                 }
             }
             if (embeddBibfile) {
                 if (embeddedBibFilePdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
-                    System.out.println(String.format("Successfully embedded metadata on at least one linked file of %s", citeKey));
+                    System.out.printf("Successfully embedded metadata on at least one linked file of %s%n", citeKey);
                 } else {
-                    System.out.println(String.format("Cannot embedd metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+                    System.out.printf("Cannot embedd metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
                 }
             }
         } catch (Exception e) {
-            LOGGER.error(String.format("Failed writing metadata on a linked file of %s.", citeKey));
+            LOGGER.error("Failed writing metadata on a linked file of {}.", citeKey);
         }
     }
 
     private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         for (String citeKey : citeKeys) {
             List<BibEntry> bibEntryList = dataBase.getEntriesByCitationKey(citeKey);
             if (bibEntryList.isEmpty()) {
-                System.err.println(String.format("Skipped - Cannot find %s in library.", citeKey));
+                System.err.printf("Skipped - Cannot find %s in library.%n", citeKey);
                 continue;
             }
             for (BibEntry entry : bibEntryList) {
@@ -350,25 +350,25 @@ private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, B
                 try {
                     if (writeXMP) {
                         if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
-                            System.out.println(String.format("Successfully written XMP metadata of at least one entry to %s", fileName));
+                            System.out.printf("Successfully written XMP metadata of at least one entry to %s%n", fileName);
                         } else {
-                            System.out.println(String.format("File %s is not linked to any entry in database.", fileName));
+                            System.out.printf("File %s is not linked to any entry in database.%n", fileName);
                         }
                     }
                     if (embeddBibfile) {
                         if (embeddedBibFilePdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
-                            System.out.println(String.format("Successfully embedded XMP metadata of at least one entry to %s", fileName));
+                            System.out.printf("Successfully embedded XMP metadata of at least one entry to %s%n", fileName);
                         } else {
-                            System.out.println(String.format("File %s is not linked to any entry in database.", fileName));
+                            System.out.printf("File %s is not linked to any entry in database.%n", fileName);
                         }
                     }
                 } catch (IOException e) {
                     LOGGER.error("Error accessing file '{}'.", fileName);
                 } catch (Exception e) {
-                    LOGGER.error(String.format("Error writing entry to %s.", fileName));
+                    LOGGER.error("Error writing entry to {}.", fileName);
                 }
             } else {
-                LOGGER.error(String.format("Skipped - PDF %s does not exist", fileName));
+                LOGGER.error("Skipped - PDF {} does not exist", fileName);
             }
         }
     }

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -754,19 +754,20 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(stateManager, dialogService, undoManager))
         );
 
-        if (prefs.getSpecialFieldsPreferences().isSpecialFieldsEnabled()) {
-            edit.getItems().addAll(
-                    new SeparatorMenuItem(),
-                    // ToDo: SpecialField needs the active BasePanel to mark it as changed.
-                    //  Refactor BasePanel, should mark the BibDatabaseContext or the UndoManager as dirty instead!
-                    SpecialFieldMenuItemFactory.createSpecialFieldMenu(SpecialField.RANKING, factory, this, dialogService, prefs, undoManager, stateManager),
-                    SpecialFieldMenuItemFactory.getSpecialFieldSingleItem(SpecialField.RELEVANCE, factory, this, dialogService, prefs, undoManager, stateManager),
-                    SpecialFieldMenuItemFactory.getSpecialFieldSingleItem(SpecialField.QUALITY, factory, this, dialogService, prefs, undoManager, stateManager),
-                    SpecialFieldMenuItemFactory.getSpecialFieldSingleItem(SpecialField.PRINTED, factory, this, dialogService, prefs, undoManager, stateManager),
-                    SpecialFieldMenuItemFactory.createSpecialFieldMenu(SpecialField.PRIORITY, factory, this, dialogService, prefs, undoManager, stateManager),
-                    SpecialFieldMenuItemFactory.createSpecialFieldMenu(SpecialField.READ_STATUS, factory, this, dialogService, prefs, undoManager, stateManager)
-            );
-        }
+        SeparatorMenuItem specialFieldsSeparator = new SeparatorMenuItem();
+        specialFieldsSeparator.visibleProperty().bind(prefs.getSpecialFieldsPreferences().specialFieldsEnabledProperty());
+
+        edit.getItems().addAll(
+                specialFieldsSeparator,
+                // ToDo: SpecialField needs the active BasePanel to mark it as changed.
+                //  Refactor BasePanel, should mark the BibDatabaseContext or the UndoManager as dirty instead!
+                SpecialFieldMenuItemFactory.createSpecialFieldMenu(SpecialField.RANKING, factory, this, dialogService, prefs, undoManager, stateManager),
+                SpecialFieldMenuItemFactory.getSpecialFieldSingleItem(SpecialField.RELEVANCE, factory, this, dialogService, prefs, undoManager, stateManager),
+                SpecialFieldMenuItemFactory.getSpecialFieldSingleItem(SpecialField.QUALITY, factory, this, dialogService, prefs, undoManager, stateManager),
+                SpecialFieldMenuItemFactory.getSpecialFieldSingleItem(SpecialField.PRINTED, factory, this, dialogService, prefs, undoManager, stateManager),
+                SpecialFieldMenuItemFactory.createSpecialFieldMenu(SpecialField.PRIORITY, factory, this, dialogService, prefs, undoManager, stateManager),
+                SpecialFieldMenuItemFactory.createSpecialFieldMenu(SpecialField.READ_STATUS, factory, this, dialogService, prefs, undoManager, stateManager)
+        );
 
         // @formatter:off
         library.getItems().addAll(
@@ -1192,7 +1193,7 @@ private Boolean confirmEmptyEntry(LibraryTab libraryTab, BibDatabaseContext cont
         if (response.isPresent() && response.get().equals(deleteEmptyEntries)) {
             // The user wants to delete.
             try {
-                for (BibEntry currentEntry : new ArrayList<BibEntry>(context.getEntries())) {
+                for (BibEntry currentEntry : new ArrayList<>(context.getEntries())) {
                     if (currentEntry.getFields().isEmpty()) {
                         context.getDatabase().removeEntries(Collections.singletonList(currentEntry));
                     }

diff --git a/src/main/java/org/jabref/gui/JabRefGUI.java b/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -59,9 +59,9 @@ public JabRefGUI(Stage mainStage, List<ParserResult> databases, boolean isBlank,
         openWindow(mainStage);
 
         new VersionWorker(Globals.BUILD_INFO.version,
-                preferencesService.getVersionPreferences().getIgnoredVersion(),
                 mainFrame.getDialogService(),
-                Globals.TASK_EXECUTOR)
+                Globals.TASK_EXECUTOR,
+                preferencesService.getVersionPreferences())
                 .checkForNewVersionDelayed();
     }
 

diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/src/main/java/org/jabref/gui/LibraryTab.java
@@ -31,7 +31,6 @@
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.maintable.MainTable;
 import org.jabref.gui.maintable.MainTableDataModel;
-import org.jabref.gui.specialfields.SpecialFieldDatabaseChangeListener;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
@@ -465,8 +464,6 @@ public void editEntryAndFocusField(BibEntry entry, Field field) {
     }
 
     private void createMainTable() {
-        bibDatabaseContext.getDatabase().registerListener(SpecialFieldDatabaseChangeListener.INSTANCE);
-
         mainTable = new MainTable(tableModel,
                 this,
                 bibDatabaseContext,

diff --git a/src/main/java/org/jabref/gui/auximport/FromAuxDialog.java b/src/main/java/org/jabref/gui/auximport/FromAuxDialog.java
@@ -93,7 +93,7 @@ private void browseButtonClicked() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .addExtensionFilter(StandardFileType.AUX)
                 .withDefaultExtension(StandardFileType.AUX)
-                .withInitialDirectory(preferences.getWorkingDir()).build();
+                .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory()).build();
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> auxFileField.setText(file.toAbsolutePath().toString()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/copyfiles/CopySingleFileAction.java b/src/main/java/org/jabref/gui/copyfiles/CopySingleFileAction.java
@@ -14,40 +14,40 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.util.OptionalUtil;
-import org.jabref.preferences.PreferencesService;
+import org.jabref.preferences.FilePreferences;
 
 public class CopySingleFileAction extends SimpleCommand {
 
     private final LinkedFile linkedFile;
     private final DialogService dialogService;
     private final BibDatabaseContext databaseContext;
-    private final PreferencesService preferencesService;
+    private final FilePreferences filePreferences;
 
     private final BiFunction<Path, Path, Path> resolvePathFilename = (path, file) -> path.resolve(file.getFileName());
 
-    public CopySingleFileAction(LinkedFile linkedFile, DialogService dialogService, BibDatabaseContext databaseContext, PreferencesService preferencesService) {
+    public CopySingleFileAction(LinkedFile linkedFile, DialogService dialogService, BibDatabaseContext databaseContext, FilePreferences filePreferences) {
         this.linkedFile = linkedFile;
         this.dialogService = dialogService;
         this.databaseContext = databaseContext;
-        this.preferencesService = preferencesService;
+        this.filePreferences = filePreferences;
 
         this.executable.bind(Bindings.createBooleanBinding(
                 () -> !linkedFile.isOnlineLink()
-                        && linkedFile.findIn(databaseContext, preferencesService.getFilePreferences()).isPresent(),
+                        && linkedFile.findIn(databaseContext, this.filePreferences).isPresent(),
                 linkedFile.linkProperty()));
     }
 
     @Override
     public void execute() {
         DirectoryDialogConfiguration dirDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                .withInitialDirectory(preferencesService.getWorkingDir())
+                .withInitialDirectory(filePreferences.getWorkingDirectory())
                 .build();
         Optional<Path> exportPath = dialogService.showDirectorySelectionDialog(dirDialogConfiguration);
         exportPath.ifPresent(this::copyFileToDestination);
     }
 
     private void copyFileToDestination(Path exportPath) {
-        Optional<Path> fileToExport = linkedFile.findIn(databaseContext, preferencesService.getFilePreferences());
+        Optional<Path> fileToExport = linkedFile.findIn(databaseContext, filePreferences);
         Optional<Path> newPath = OptionalUtil.combine(Optional.of(exportPath), fileToExport, resolvePathFilename);
 
         if (newPath.isPresent()) {

diff --git a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
@@ -60,14 +60,16 @@ enum Status {
     private LatexParserResult latexParserResult;
     private BibEntry currentEntry;
 
-    public LatexCitationsTabViewModel(BibDatabaseContext databaseContext, PreferencesService preferencesService,
-                                      TaskExecutor taskExecutor, DialogService dialogService) {
+    public LatexCitationsTabViewModel(BibDatabaseContext databaseContext,
+                                      PreferencesService preferencesService,
+                                      TaskExecutor taskExecutor,
+                                      DialogService dialogService) {
         this.databaseContext = databaseContext;
         this.preferencesService = preferencesService;
         this.taskExecutor = taskExecutor;
         this.dialogService = dialogService;
-        this.directory = new SimpleObjectProperty(databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
-                                                                          .orElse(FileUtil.getInitialDirectory(databaseContext, preferencesService)));
+        this.directory = new SimpleObjectProperty<>(databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getFilePreferences().getUser())
+                                                                   .orElse(FileUtil.getInitialDirectory(databaseContext, preferencesService.getFilePreferences().getWorkingDirectory())));
         this.citationList = FXCollections.observableArrayList();
         this.status = new SimpleObjectProperty<>(Status.IN_PROGRESS);
         this.searchError = new SimpleStringProperty("");
@@ -128,8 +130,8 @@ private void cancelSearch() {
 
     private Collection<Citation> searchAndParse(String citeKey) throws IOException {
         // we need to check whether the user meanwhile set the LaTeX file directory or the database changed locations
-        Path newDirectory = databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
-                                           .orElse(FileUtil.getInitialDirectory(databaseContext, preferencesService));
+        Path newDirectory = databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getFilePreferences().getUser())
+                                           .orElse(FileUtil.getInitialDirectory(databaseContext, preferencesService.getFilePreferences().getWorkingDirectory()));
 
         if (latexParserResult == null || !newDirectory.equals(directory.get())) {
             directory.set(newDirectory);
@@ -170,7 +172,7 @@ public void setLatexDirectory() {
                 .withInitialDirectory(directory.get()).build();
 
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
-                databaseContext.getMetaData().setLatexFileDirectory(preferencesService.getUser(), selectedDirectory.toAbsolutePath()));
+                databaseContext.getMetaData().setLatexFileDirectory(preferencesService.getFilePreferences().getUser(), selectedDirectory.toAbsolutePath()));
 
         init(currentEntry);
     }

diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -160,10 +160,10 @@ private Optional<Path> askForSavePath() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .addExtensionFilter(StandardFileType.BIBTEX_DB)
                 .withDefaultExtension(StandardFileType.BIBTEX_DB)
-                .withInitialDirectory(preferences.getWorkingDir())
+                .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory())
                 .build();
         Optional<Path> selectedPath = dialogService.showFileSaveDialog(fileDialogConfiguration);
-        selectedPath.ifPresent(path -> preferences.setWorkingDirectory(path.getParent()));
+        selectedPath.ifPresent(path -> preferences.getFilePreferences().setWorkingDirectory(path.getParent()));
         if (selectedPath.isPresent()) {
             Path savePath = selectedPath.get();
             // Workaround for linux systems not adding file extension