Merge branch 'main' into floating-mode

CHANGELOG.md

@@ -28,9 +28,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Fixed
 
-- We fixed an issue where the 'Check for updates' preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
+- We fixed an issue where the "Check for updates" preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
-- We fixed an issue where a new unsaved library was not marked with an asterisk [#11519](https://github.com/JabRef/jabref/pull/11519)
+- We fixed an issue with colors in the search bar when dark theme is enabled. [#11569](https://github.com/JabRef/jabref/issues/11569)
+- We fixed an issue where a new unsaved library was not marked with an asterisk. [#11519](https://github.com/JabRef/jabref/pull/11519)
 - We fixed an issue where JabRef starts without window decorations. [#11440](https://github.com/JabRef/jabref/pull/11440)
 
 ### Removed

settings.gradle

@@ -19,7 +19,7 @@ pluginManagement {
 }
 
 plugins {
-  id("org.gradle.toolchains.foojay-resolver-convention") version "0.8.0"
+    id("org.gradle.toolchains.foojay-resolver-convention") version "0.8.0"
 }
 
 rootProject.name = "JabRef"

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

@@ -149,7 +149,7 @@ public void initialize() {
         Injector.setModelOrService(DialogService.class, dialogService);
 
         JabRefGUI.clipBoardManager = new ClipBoardManager();
-        Injector.setModelOrService(TaskExecutor.class, taskExecutor);
+        Injector.setModelOrService(ClipBoardManager.class, clipBoardManager);
     }
 
     private void setupProxy() {
@@ -181,29 +181,33 @@ private void openWindow() {
         LOGGER.debug("Initializing frame");
 
         GuiPreferences guiPreferences = preferencesService.getGuiPreferences();
+        LOGGER.debug("Reading from prefs: isMaximized {}", guiPreferences.isWindowMaximised());
 
-        mainStage.setMinHeight(330);
         mainStage.setMinWidth(580);
+        mainStage.setMinHeight(330);
+
         // maximized target state is stored, because "saveWindowState" saves x and y only if not maximized
         boolean windowMaximised = guiPreferences.isWindowMaximised();
 
         LOGGER.debug("Screens: {}", Screen.getScreens());
         debugLogWindowState(mainStage);
 
-        if (isWindowPositionOutOfBounds()) {
-            LOGGER.debug("The JabRef window is outside of screen bounds. Position and size will be corrected. Main screen will be used.");
-            Rectangle2D bounds = Screen.getPrimary().getBounds();
-            mainStage.setX(bounds.getMinX());
-            mainStage.setY(bounds.getMinY());
-            mainStage.setHeight(Math.min(bounds.getHeight(), 786.0));
-            mainStage.setWidth(Math.min(bounds.getWidth(), 1024.0));
-            saveWindowState();
-        } else {
+        if (isWindowPositionInBounds()) {
             LOGGER.debug("The JabRef window is inside screen bounds.");
             mainStage.setX(guiPreferences.getPositionX());
             mainStage.setY(guiPreferences.getPositionY());
             mainStage.setWidth(guiPreferences.getSizeX());
             mainStage.setHeight(guiPreferences.getSizeY());
+            LOGGER.debug("NOT saving window positions");
+        } else {
+            LOGGER.info("The JabRef window is outside of screen bounds. Position and size will be corrected to 1024x768. Primary screen will be used.");
+            Rectangle2D bounds = Screen.getPrimary().getBounds();
+            mainStage.setX(bounds.getMinX());
+            mainStage.setY(bounds.getMinY());
+            mainStage.setWidth(Math.min(bounds.getWidth(), 1024.0));
+            mainStage.setHeight(Math.min(bounds.getHeight(), 786.0));
+            LOGGER.debug("Saving window positions");
+            saveWindowState();
         }
         // after calling "saveWindowState" the maximized state can be set
         mainStage.setMaximized(windowMaximised);
@@ -264,32 +268,56 @@ private void saveWindowState() {
     }
 
     /**
-     * outprints the Data from the Screen (only in debug mode)
+     * prints the data from the screen (only in debug mode)
      *
-     * @param mainStage JabRefs stage
+     * @param mainStage JabRef's stage
      */
     private void debugLogWindowState(Stage mainStage) {
-        if (LOGGER.isDebugEnabled()) {
-            String debugLogString = "SCREEN DATA:" +
-                    "mainStage.WINDOW_MAXIMISED: " + mainStage.isMaximized() + "\n" +
-                    "mainStage.POS_X: " + mainStage.getX() + "\n" +
-                    "mainStage.POS_Y: " + mainStage.getY() + "\n" +
-                    "mainStage.SIZE_X: " + mainStage.getWidth() + "\n" +
-                    "mainStages.SIZE_Y: " + mainStage.getHeight() + "\n";
-            LOGGER.debug(debugLogString);
-        }
+        LOGGER.debug("""
+                        screen data:
+                          mainStage.WINDOW_MAXIMISED: {}
+                          mainStage.POS_X: {}
+                          mainStage.POS_Y: {}
+                          mainStage.SIZE_X: {}
+                          mainStage.SIZE_Y: {}
+                        """,
+                mainStage.isMaximized(), mainStage.getX(), mainStage.getY(), mainStage.getWidth(), mainStage.getHeight());
     }
 
     /**
-     * Tests if the window coordinates are out of the mainscreen
+     * Tests if the window coordinates are inside any screen
      */
-    private boolean isWindowPositionOutOfBounds() {
-        // The upper right corner is checked as there are most probably the window controls.
+    private boolean isWindowPositionInBounds() {
         GuiPreferences guiPreferences = preferencesService.getGuiPreferences();
-        double rightX = guiPreferences.getPositionX() + guiPreferences.getSizeX();
+
+        if (LOGGER.isDebugEnabled()) {
+            Screen.getScreens().forEach(screen -> LOGGER.debug("Screen bounds: {}", screen.getBounds()));
+        }
+
+        return lowerLeftIsInBounds(guiPreferences) && upperRightIsInBounds(guiPreferences);
+    }
+
+    private boolean lowerLeftIsInBounds(GuiPreferences guiPreferences) {
+        // Windows/PowerToys somehow removes 10 pixels to the left; they are re-added
+        double leftX = guiPreferences.getPositionX() + 10.0;
+        double bottomY = guiPreferences.getPositionY() + guiPreferences.getSizeY();
+        LOGGER.debug("left x: {}, bottom y: {}", leftX, bottomY);
+
+        boolean inBounds = Screen.getScreens().stream().anyMatch((screen -> screen.getBounds().contains(leftX, bottomY)));
+        LOGGER.debug("lower left corner is in bounds: {}", inBounds);
+        return inBounds;
+    }
+
+    private boolean upperRightIsInBounds(GuiPreferences guiPreferences) {
+        // The upper right corner is checked as there are most probably the window controls.
+        // Windows/PowerToys somehow adds 10 pixels to the right and top of the screen, they are removed
+        double rightX = guiPreferences.getPositionX() + guiPreferences.getSizeX() - 10.0;
         double topY = guiPreferences.getPositionY();
-        return Screen.getScreens().stream().noneMatch((screen -> screen.getBounds().contains(
-                rightX, topY)));
+        LOGGER.debug("right x: {}, top y: {}", rightX, topY);
+
+        boolean inBounds = Screen.getScreens().stream().anyMatch((screen -> screen.getBounds().contains(rightX, topY)));
+        LOGGER.debug("upper right corner is in bounds: {}", inBounds);
+        return inBounds;
     }
 
     // Background tasks

src/main/java/org/jabref/logic/importer/fileformat/CitaviXmlImporter.java

@@ -1,12 +1,9 @@
 package org.jabref.logic.importer.fileformat;
 
-import java.io.BufferedInputStream;
 import java.io.BufferedReader;
-import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.io.PushbackInputStream;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -55,6 +52,8 @@
 import jakarta.xml.bind.JAXBContext;
 import jakarta.xml.bind.JAXBException;
 import jakarta.xml.bind.Unmarshaller;
+import org.apache.commons.io.ByteOrderMark;
+import org.apache.commons.io.input.BOMInputStream;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -431,7 +430,7 @@ private Object unmarshallRoot(BufferedReader reader) throws XMLStreamException,
     @Override
     public ParserResult importDatabase(BufferedReader reader) throws IOException {
         Objects.requireNonNull(reader);
-        throw new UnsupportedOperationException("CitaviXmlImporter does not support importDatabase(BufferedReader reader)."
+        throw new UnsupportedOperationException("CitaviXmlImporter does not support importDatabase(BufferedReader reader). "
                                                 + "Instead use importDatabase(Path filePath, Charset defaultEncoding).");
     }
 
@@ -447,39 +446,25 @@ public List<BibEntry> parseEntries(InputStream inputStream) {
     }
 
     private BufferedReader getReaderFromZip(Path filePath) throws IOException {
-        ZipInputStream zis = new ZipInputStream(new FileInputStream(filePath.toFile()));
-        ZipEntry zipEntry = zis.getNextEntry();
-
         Path newFile = Files.createTempFile("citavicontent", ".xml");
+        newFile.toFile().deleteOnExit();
 
-        while (zipEntry != null) {
-            Files.copy(zis, newFile, StandardCopyOption.REPLACE_EXISTING);
-
-            zipEntry = zis.getNextEntry();
-        }
-
-        zis.closeEntry();
-
-        InputStream stream = Files.newInputStream(newFile, StandardOpenOption.READ);
-
-        // check and delete the utf-8 BOM bytes
-        InputStream newStream = checkForUtf8BOMAndDiscardIfAny(stream);
-
-        // clean up the temp file
-        Files.delete(newFile);
-
-        return new BufferedReader(new InputStreamReader(newStream, StandardCharsets.UTF_8));
-    }
-
-    private static InputStream checkForUtf8BOMAndDiscardIfAny(InputStream inputStream) throws IOException {
-        PushbackInputStream pushbackInputStream = new PushbackInputStream(new BufferedInputStream(inputStream), 3);
-        byte[] bom = new byte[3];
-        if (pushbackInputStream.read(bom) != -1) {
-            if (!((bom[0] == (byte) 0xEF) && (bom[1] == (byte) 0xBB) && (bom[2] == (byte) 0xBF))) {
-                pushbackInputStream.unread(bom);
+        try (ZipInputStream zis = new ZipInputStream(Files.newInputStream(filePath))) {
+            ZipEntry zipEntry = zis.getNextEntry();
+            while (zipEntry != null) {
+                Files.copy(zis, newFile, StandardCopyOption.REPLACE_EXISTING);
+                zipEntry = zis.getNextEntry();
             }
         }
-        return pushbackInputStream;
+
+        // Citavi XML files sometimes contains BOM markers. We just discard them.
+        // Solution inspired by https://stackoverflow.com/a/37445972/873282
+        return new BufferedReader(
+                new InputStreamReader(
+                        new BOMInputStream(
+                                Files.newInputStream(newFile, StandardOpenOption.READ),
+                                false,
+                                ByteOrderMark.UTF_8, ByteOrderMark.UTF_16BE, ByteOrderMark.UTF_16LE, ByteOrderMark.UTF_32BE, ByteOrderMark.UTF_32LE)));
     }
 
     private String clean(String input) {

src/main/java/org/jabref/preferences/GuiPreferences.java

@@ -24,14 +24,17 @@ public class GuiPreferences {
 
     private final BooleanProperty windowMaximised;
 
+    private final DoubleProperty sidePaneWidth;
+
     // the last libraries that were open when jabref closes and should be reopened on startup
     private final ObservableList<Path> lastFilesOpened;
+
     private final ObjectProperty<Path> lastFocusedFile;
+
     // observable list last files opened in the file menu
     private final FileHistory fileHistory;
 
     private final StringProperty lastSelectedIdBasedFetcher;
-    private final DoubleProperty sidePaneWidth;
 
     public GuiPreferences(double positionX,
                           double positionY,

src/main/java/org/jabref/preferences/JabRefPreferences.java

@@ -213,11 +213,11 @@ public class JabRefPreferences implements PreferencesService {
     public static final String XMP_PRIVACY_FILTERS = "xmpPrivacyFilters";
     public static final String USE_XMP_PRIVACY_FILTER = "useXmpPrivacyFilter";
     public static final String DEFAULT_SHOW_SOURCE = "defaultShowSource";
-    // Window sizes
-    public static final String SIZE_Y = "mainWindowSizeY";
-    public static final String SIZE_X = "mainWindowSizeX";
-    public static final String POS_Y = "mainWindowPosY";
-    public static final String POS_X = "mainWindowPosX";
+
+    public static final String MAIN_WINDOW_POS_X = "mainWindowPosX";
+    public static final String MAIN_WINDOW_POS_Y = "mainWindowPosY";
+    public static final String MAIN_WINDOW_WIDTH = "mainWindowSizeX";
+    public static final String MAIN_WINDOW_HEIGHT = "mainWindowSizeY";
 
     public static final String LAST_EDITED = "lastEdited";
     public static final String OPEN_LAST_EDITED = "openLastEdited";
@@ -616,12 +616,16 @@ private JabRefPreferences() {
                                         .getSslDirectory()
                                         .resolve("truststore.jks").toString());
 
-        defaults.put(POS_X, 0);
-        defaults.put(POS_Y, 0);
-        defaults.put(SIZE_X, 1024);
-        defaults.put(SIZE_Y, 768);
+        defaults.put(MAIN_WINDOW_POS_X, 0);
+        defaults.put(MAIN_WINDOW_POS_Y, 0);
+        defaults.put(MAIN_WINDOW_WIDTH, 1024);
+        defaults.put(MAIN_WINDOW_HEIGHT, 768);
+
         defaults.put(WINDOW_MAXIMISED, Boolean.TRUE);
-        defaults.put(AUTO_RESIZE_MODE, Boolean.FALSE); // By default disable "Fit table horizontally on the screen"
+
+        // By default disable "Fit table horizontally on the screen"
+        defaults.put(AUTO_RESIZE_MODE, Boolean.FALSE);
+
         defaults.put(ENTRY_EDITOR_HEIGHT, 0.65);
         defaults.put(ENTRY_EDITOR_PREVIEW_DIVIDER_POS, 0.5);
         defaults.put(NAMES_AS_IS, Boolean.FALSE); // "Show names unchanged"
@@ -2620,10 +2624,10 @@ public GuiPreferences getGuiPreferences() {
         }
 
         guiPreferences = new GuiPreferences(
-                getDouble(POS_X),
-                getDouble(POS_Y),
-                getDouble(SIZE_X),
-                getDouble(SIZE_Y),
+                getDouble(MAIN_WINDOW_POS_X),
+                getDouble(MAIN_WINDOW_POS_Y),
+                getDouble(MAIN_WINDOW_WIDTH),
+                getDouble(MAIN_WINDOW_HEIGHT),
                 getBoolean(WINDOW_MAXIMISED),
                 getStringList(LAST_EDITED).stream()
                                           .map(Path::of)
@@ -2633,11 +2637,13 @@ public GuiPreferences getGuiPreferences() {
                 get(ID_ENTRY_GENERATOR),
                 getDouble(SIDE_PANE_WIDTH));
 
-        EasyBind.listen(guiPreferences.positionXProperty(), (obs, oldValue, newValue) -> putDouble(POS_X, newValue.doubleValue()));
-        EasyBind.listen(guiPreferences.positionYProperty(), (obs, oldValue, newValue) -> putDouble(POS_Y, newValue.doubleValue()));
-        EasyBind.listen(guiPreferences.sizeXProperty(), (obs, oldValue, newValue) -> putDouble(SIZE_X, newValue.doubleValue()));
-        EasyBind.listen(guiPreferences.sizeYProperty(), (obs, oldValue, newValue) -> putDouble(SIZE_Y, newValue.doubleValue()));
+        EasyBind.listen(guiPreferences.positionXProperty(), (obs, oldValue, newValue) -> putDouble(MAIN_WINDOW_POS_X, newValue.doubleValue()));
+        EasyBind.listen(guiPreferences.positionYProperty(), (obs, oldValue, newValue) -> putDouble(MAIN_WINDOW_POS_Y, newValue.doubleValue()));
+        EasyBind.listen(guiPreferences.sizeXProperty(), (obs, oldValue, newValue) -> putDouble(MAIN_WINDOW_WIDTH, newValue.doubleValue()));
+        EasyBind.listen(guiPreferences.sizeYProperty(), (obs, oldValue, newValue) -> putDouble(MAIN_WINDOW_HEIGHT, newValue.doubleValue()));
         EasyBind.listen(guiPreferences.windowMaximisedProperty(), (obs, oldValue, newValue) -> putBoolean(WINDOW_MAXIMISED, newValue));
+        EasyBind.listen(guiPreferences.sidePaneWidthProperty(), (obs, oldValue, newValue) -> putDouble(SIDE_PANE_WIDTH, newValue.doubleValue()));
+
         guiPreferences.getLastFilesOpened().addListener((ListChangeListener<Path>) change -> {
             if (change.getList().isEmpty()) {
                 prefs.remove(LAST_EDITED);
@@ -2657,7 +2663,6 @@ public GuiPreferences getGuiPreferences() {
         });
         guiPreferences.getFileHistory().addListener((InvalidationListener) change -> storeFileHistory(guiPreferences.getFileHistory()));
         EasyBind.listen(guiPreferences.lastSelectedIdBasedFetcherProperty(), (obs, oldValue, newValue) -> put(ID_ENTRY_GENERATOR, newValue));
-        EasyBind.listen(guiPreferences.sidePaneWidthProperty(), (obs, oldValue, newValue) -> putDouble(SIDE_PANE_WIDTH, newValue.doubleValue()));
 
         return guiPreferences;
     }

src/main/resources/tinylog.properties

@@ -11,3 +11,5 @@ exception = strip: jdk.internal
 #[email protected] = debug
 
 [email protected] = debug
+
+#[email protected] = debug

src/test/java/org/jabref/logic/importer/fileformat/ImporterTestEngine.java

@@ -52,8 +52,7 @@ public static void testImportEntries(Importer importer, String fileName, String
         if (parserResult.isInvalid()) {
             throw new ImportException(parserResult.getErrorMessage());
         }
-        List<BibEntry> entries = parserResult.getDatabase()
-                                             .getEntries();
+        List<BibEntry> entries = parserResult.getDatabase().getEntries();
         BibEntryAssert.assertEquals(ImporterTestEngine.class, fileName.replaceAll(fileType, ".bib"), entries);
     }