replace most of Deprecated APIs (#12045)

* fix CONSTRAINED_RESIZE_POLICY_FLEX_LAST_COLUMN

fix CONSTRAINED_RESIZE_POLICY_FLEX_LAST_COLUMN Deprecated issue in comment

* fix override deprecated method

fix override deprecated method in IconValidationDecorator

* fix Deprecated ANTLRInputStream

replace ANTLRInputStream to CharStreams

* fix Deprecated BOMInputStream

use builder instead.

* fix wrong CharStreams method

fromFileName -> fromString

* fix requested changes

1.fix requested changes
2.add more unit test to support change in  IconValidationDecorator

* fix last Deprecated API

remove Deprecated setGroup

* remove unnecessary IOException and add comment

remove unnecessary IOException and add comment

* revert wrong change

revert wrong change with added comment

* merge from main

merge from main

* Discard changes to src/main/java/org/jabref/logic/database/DatabaseMerger.java

---------

Co-authored-by: Oliver Kopp <[email protected]>

src/main/java/org/jabref/gui/maintable/SmartConstrainedResizePolicy.java

@@ -17,6 +17,7 @@
  * This resize policy is almost the same as {@link TableView#CONSTRAINED_RESIZE_POLICY}
  * We make sure that the width of all columns sums up to the total width of the table.
  * However, in contrast to {@link TableView#CONSTRAINED_RESIZE_POLICY} we size the columns initially by their preferred width.
+ * Although {@link TableView#CONSTRAINED_RESIZE_POLICY} is deprecated, this policy maintains a similar resizing behavior.
  */
 public class SmartConstrainedResizePolicy implements Callback<TableView.ResizeFeatures, Boolean> {
 

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

@@ -31,19 +31,11 @@ public IconValidationDecorator(Pos position) {
         this.position = position;
     }
 
-    @Override
-    protected Node createErrorNode() {
-        return IconTheme.JabRefIcons.ERROR.getGraphicNode();
-    }
-
-    @Override
-    protected Node createWarningNode() {
-        return IconTheme.JabRefIcons.WARNING.getGraphicNode();
-    }
-
     @Override
     public Node createDecorationNode(ValidationMessage message) {
-        Node graphic = Severity.ERROR == message.getSeverity() ? createErrorNode() : createWarningNode();
+        Node graphic = Severity.ERROR == message.getSeverity()
+                ? IconTheme.JabRefIcons.ERROR.getGraphicNode()
+                : IconTheme.JabRefIcons.WARNING.getGraphicNode();
         graphic.getStyleClass().add(Severity.ERROR == message.getSeverity() ? "error-icon" : "warning-icon");
         Label label = new Label();
         label.setGraphic(graphic);

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

@@ -462,10 +462,11 @@ private BufferedReader getReaderFromZip(Path filePath) throws IOException {
         // 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)));
+                        new BOMInputStream.Builder()
+                            .setInputStream(Files.newInputStream(newFile, StandardOpenOption.READ))
+                            .setInclude(false)
+                            .setByteOrderMarks(ByteOrderMark.UTF_8, ByteOrderMark.UTF_16BE, ByteOrderMark.UTF_16LE, ByteOrderMark.UTF_32BE, ByteOrderMark.UTF_32LE)
+                            .get()));
     }
 
     private String clean(String input) {

src/main/java/org/jabref/model/groups/GroupTreeNode.java

@@ -58,9 +58,7 @@ public ObjectProperty<AbstractGroup> getGroupProperty() {
      * Associates the specified group with this node.
      *
      * @param newGroup the new group (has to be non-null)
-     * @deprecated use {@link #setGroup(AbstractGroup, boolean, boolean, List)}} instead
      */
-    @Deprecated
     public void setGroup(AbstractGroup newGroup) {
         this.groupProperty.set(Objects.requireNonNull(newGroup));
     }

src/test/java/org/jabref/logic/util/IconValidationDecoratorTest.java

@@ -0,0 +1,50 @@
+package org.jabref.logic.util;
+
+import javafx.scene.control.Control;
+import javafx.scene.control.Label;
+
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.util.IconValidationDecorator;
+
+import org.controlsfx.validation.Severity;
+import org.controlsfx.validation.ValidationMessage;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.testfx.framework.junit5.ApplicationExtension;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+@ExtendWith(ApplicationExtension.class)
+public class IconValidationDecoratorTest {
+    static Object[][] decorationTestData() {
+        return new Object[][]{
+                {Severity.ERROR, IconTheme.JabRefIcons.ERROR.getGraphicNode().toString()},
+                {Severity.WARNING, IconTheme.JabRefIcons.WARNING.getGraphicNode().toString()}
+        };
+    }
+
+    @ParameterizedTest
+    @MethodSource("decorationTestData")
+    public void createDecorationNodeTest(Severity severity, String expectedGraphic) {
+        IconValidationDecorator iconValidationDecorator = new IconValidationDecorator();
+        Label node = (Label) iconValidationDecorator.createDecorationNode(new ValidationMessage() {
+            @Override
+            public String getText() {
+                return "test";
+            }
+
+            @Override
+            public Severity getSeverity() {
+                return severity;
+            }
+
+            @Override
+            public Control getTarget() {
+                return null;
+            }
+        });
+
+        assertEquals(node.getGraphic().toString(), expectedGraphic);
+    }
+}