Merge branch 'fix-arch2' of github.com:JabRef/jabref into fix-arch2

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

@@ -32,6 +32,7 @@
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.server.RemoteListenerServerManager;
 import org.jabref.logic.util.BuildInfo;
+import org.jabref.logic.util.FallbackExceptionHandler;
 import org.jabref.logic.util.HeadlessExecutorService;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.logic.util.WebViewStore;
@@ -87,7 +88,12 @@ public static void setup(List<UiCommand> uiCommands,
     public void start(Stage stage) {
         this.mainStage = stage;
 
-        FallbackExceptionHandler.installExceptionHandler();
+        FallbackExceptionHandler.installExceptionHandler((exception, thread) -> {
+            UiTaskExecutor.runInJavaFXThread(() -> {
+                DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
+                dialogService.showErrorDialogAndWait("Uncaught exception occurred in " + thread, exception);
+            });
+        });
 
         initialize();
 

src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java

@@ -23,7 +23,6 @@
 
 public class DuplicateResolverDialog extends BaseDialog<DuplicateResolverResult> {
 
-    private final BibDatabaseContext database;
     private final StateManager stateManager;
 
     public enum DuplicateResolverType {
@@ -72,7 +71,6 @@ public DuplicateResolverDialog(BibEntry one,
                                    DialogService dialogService,
                                    PreferencesService preferencesService) {
         this.setTitle(Localization.lang("Possible duplicate entries"));
-        this.database = database;
         this.stateManager = stateManager;
         this.dialogService = dialogService;
         this.preferencesService = preferencesService;

src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java

@@ -148,7 +148,7 @@ private void onSuccess(Path targetDirectory, Path downloadedFile) {
         boolean isDuplicate;
         boolean isHtml;
         try {
-            isDuplicate = FileNameUniqueness.isDuplicatedFile(targetDirectory, downloadedFile.getFileName(), dialogService);
+            isDuplicate = FileNameUniqueness.isDuplicatedFile(targetDirectory, downloadedFile.getFileName(), dialogService::notify);
         } catch (IOException e) {
             LOGGER.error("FileNameUniqueness.isDuplicatedFile failed", e);
             return;

src/main/java/org/jabref/gui/util/UiTaskExecutor.java

@@ -183,7 +183,8 @@ public static <V> Task<V> getJavaFXTask(BackgroundTask<V> task) {
             }
 
             @Override
-            public V call() throws Exception {
+            protected V call() throws Exception {
+                // this requires that background task call is public as it's in another package
                 return task.call();
             }
         };

src/main/java/org/jabref/logic/search/indexing/BibFieldsIndexer.java

@@ -36,7 +36,7 @@ public class BibFieldsIndexer implements LuceneIndexer {
 
     public BibFieldsIndexer(BibDatabaseContext databaseContext) {
         this.databaseContext = databaseContext;
-        this.libraryName = databaseContext.getDatabasePath().map(path -> path.getFileName().toString()).orElseGet(() -> "unsaved");
+        this.libraryName = databaseContext.getDatabasePath().map(path -> path.getFileName().toString()).orElse("unsaved");
 
         IndexWriterConfig config = new IndexWriterConfig(SearchFieldConstants.LATEX_AWARE_NGRAM_ANALYZER);
 

src/main/java/org/jabref/logic/util/FallbackExceptionHandler.java

@@ -0,0 +1,36 @@
+package org.jabref.logic.util;
+
+import java.util.function.BiConsumer;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Catch and log any unhandled exceptions.
+ */
+public class FallbackExceptionHandler implements Thread.UncaughtExceptionHandler {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(FallbackExceptionHandler.class);
+
+    private final BiConsumer<Throwable, Thread> onException;
+
+    public FallbackExceptionHandler(BiConsumer<Throwable, Thread> onException) {
+        this.onException = onException;
+    }
+
+    public FallbackExceptionHandler() {
+        this(null);
+    }
+
+    public static void installExceptionHandler(BiConsumer<Throwable, Thread> onException) {
+        Thread.setDefaultUncaughtExceptionHandler(new FallbackExceptionHandler(onException));
+    }
+
+    @Override
+    public void uncaughtException(Thread thread, Throwable exception) {
+        LOGGER.error("Uncaught exception occurred in {}", thread, exception);
+        if (this.onException != null) {
+            this.onException.accept(exception, thread);
+        }
+    }
+}

src/main/java/org/jabref/logic/util/HeadlessExecutorService.java

@@ -14,16 +14,13 @@
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 
-import org.jabref.gui.FallbackExceptionHandler;
-import org.jabref.gui.util.UiTaskExecutor;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
  * Responsible for managing of all threads (<em>except</em> GUI threads) in JabRef.
  * <p>
- * GUI background tasks should run in {@link UiTaskExecutor}.
+ * GUI background tasks should run in {@link org.jabref.gui.util.UiTaskExecutor}.
  * <p>
  * This is a wrapper around {@link ExecutorService}
  * <p>

src/main/java/org/jabref/logic/util/io/FileNameUniqueness.java

@@ -5,10 +5,10 @@
 import java.nio.file.Path;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.function.Consumer;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.jabref.gui.DialogService;
 import org.jabref.logic.l10n.Localization;
 
 import org.slf4j.Logger;
@@ -60,18 +60,17 @@ public static String getNonOverWritingFileName(Path targetDirectory, String file
      *
      * @param directory The directory which saves the files (.pdf, for example)
      * @param fileName Suggest name for the newly downloaded file
-     * @param dialogService To display the error and success message
+     * @param messageOnDeletion To display the error and success message
      * @return true when the content of the newly downloaded file is same as the file with "similar" name,
      *         false when there is no "similar" file name or the content is different from that of files with "similar" name
      * @throws IOException Fail when the file is not exist or something wrong when reading the file
      */
-    public static boolean isDuplicatedFile(Path directory, Path fileName, DialogService dialogService) throws IOException {
+    public static boolean isDuplicatedFile(Path directory, Path fileName, Consumer<String> messageOnDeletion ) throws IOException {
         Objects.requireNonNull(directory);
         Objects.requireNonNull(fileName);
-        Objects.requireNonNull(dialogService);
 
         String extensionSuffix = FileUtil.getFileExtension(fileName).orElse("");
-        extensionSuffix = "".equals(extensionSuffix) ? extensionSuffix : "." + extensionSuffix;
+        extensionSuffix = extensionSuffix.isEmpty() ? extensionSuffix : "." + extensionSuffix;
         String newFilename = FileUtil.getBaseName(fileName) + extensionSuffix;
 
         String fileNameWithoutDuplicated = eraseDuplicateMarks(FileUtil.getBaseName(fileName));
@@ -89,7 +88,7 @@ public static boolean isDuplicatedFile(Path directory, Path fileName, DialogServ
             if (com.google.common.io.Files.equal(originalFile.toFile(), duplicateFile.toFile())) {
                 try {
                     Files.delete(duplicateFile);
-                    dialogService.notify(Localization.lang("File '%1' is a duplicate of '%0'. Keeping '%0'", originalFileName, fileName));
+                    messageOnDeletion.accept(Localization.lang("File '%1' is a duplicate of '%0'. Keeping '%0'", originalFileName, fileName));
                 } catch (IOException e) {
                     LOGGER.error("File '{}' is a duplicate of '{}'. Could not delete '{}'.", fileName, originalFileName, fileName);
                 }

src/test/java/org/jabref/logic/util/io/FileNameUniquenessTest.java

@@ -5,9 +5,12 @@
 import java.nio.file.Path;
 
 import org.jabref.gui.DialogService;
+import org.jabref.gui.push.PushToTexShop;
 
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -16,6 +19,8 @@
 
 class FileNameUniquenessTest {
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(FileNameUniquenessTest.class);
+
     @TempDir
     protected Path tempDir;
 
@@ -56,21 +61,20 @@ void isDuplicatedFileWithNoSimilarNames() throws IOException {
         Path filePath1 = tempDir.resolve(filename1);
         Files.createFile(filePath1);
 
-        boolean isDuplicate = FileNameUniqueness.isDuplicatedFile(tempDir, filePath1, dialogService);
+        boolean isDuplicate = FileNameUniqueness.isDuplicatedFile(tempDir, filePath1, LOGGER::info);
         assertFalse(isDuplicate);
     }
 
     @Test
     void isDuplicatedFileWithOneSimilarNames() throws IOException {
-        DialogService dialogService = mock(DialogService.class);
         String filename1 = "file.txt";
         String filename2 = "file (1).txt";
         Path filePath1 = tempDir.resolve(filename1);
         Path filePath2 = tempDir.resolve(filename2);
         Files.createFile(filePath1);
         Files.createFile(filePath2);
 
-        boolean isDuplicate = FileNameUniqueness.isDuplicatedFile(tempDir, filePath2, dialogService);
+        boolean isDuplicate = FileNameUniqueness.isDuplicatedFile(tempDir, filePath2, LOGGER::info);
         assertTrue(isDuplicate);
     }
 
@@ -82,21 +86,21 @@ void taseDuplicateMarksReturnsOrignalFileName1() throws IOException {
     }
 
     @Test
-    void taseDuplicateMarksReturnsOrignalFileName2() throws IOException {
+    void taseDuplicateMarksReturnsOrignalFileName2() {
         String fileName1 = "abc (def) gh (1)";
         String fileName2 = FileNameUniqueness.eraseDuplicateMarks(fileName1);
         assertEquals("abc (def) gh", fileName2);
     }
 
     @Test
-    void taseDuplicateMarksReturnsSameName1() throws IOException {
+    void taseDuplicateMarksReturnsSameName1() {
         String fileName1 = "abc def (g)";
         String fileName2 = FileNameUniqueness.eraseDuplicateMarks(fileName1);
         assertEquals("abc def (g)", fileName2);
     }
 
     @Test
-    void taseDuplicateMarksReturnsSameName2() throws IOException {
+    void taseDuplicateMarksReturnsSameName2() {
         String fileName1 = "abc def";
         String fileName2 = FileNameUniqueness.eraseDuplicateMarks(fileName1);
         assertEquals("abc def", fileName2);