Creating a JavaFX Scene from Button click; Close the created Scene

Question

I am learning JavaFX, and creating a scene that will be created and displayed to get user input. I created a VBox that holds different textfields and a button that I want to use to close the scene that was created and then store that information to use elsewhere. I can't seem to figure out how to add functionality to the button that will close the scene.

I've tried adding a EventHandler that will do it, but I can't seem to get the program to work.

part of Controller

public void drawNewClass(ActionEvent actionEvent) throws IOException {
        ClassInstance classInstance = new ClassInstance();
        TextField classDescription = new TextField("Enter      Description");
        TextField className = new TextField("Enter Class Name");
        Button close = new Button("Submit");
        close.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent event) {
                
            }
        });
        TextField attributes = new TextField("Enter Variables (privacy type name, format)");
        VBox secondaryLayout = new VBox();
        secondaryLayout.getChildren().addAll(classDescription, className, attributes, close);
        Scene secondScene = new Scene(secondaryLayout, 230, 100);

        // New window (Stage)
        Stage newWindow = new Stage();
        newWindow.setTitle("Add Class");
        newWindow.setScene(secondScene);

        // Set position of second window, related to primary window.
        newWindow.setX(canvas.getLayoutX() + 200);
        newWindow.setY(canvas.getLayoutY() + 100);

        newWindow.showAndWait();

.FXML

<?xml version="1.0" encoding="UTF-8"?>

<?import javafx.scene.layout.VBox?>
<?import javafx.scene.layout.BorderPane?>
<?import javafx.scene.layout.HBox?>
<?import javafx.scene.control.Button?>
<?import javafx.scene.control.ScrollPane?>
<?import javafx.scene.canvas.Canvas?>
<?import javafx.scene.layout.StackPane?>
<BorderPane xmlns="http://javafx.com/javafx/17"
            xmlns:fx="http://javafx.com/fxml/1"
            fx:controller="com.diagrambuilder.csc260w2022project2.diagramBuilderController"
            prefHeight="500.0" prefWidth="500.0"
            fx:id="root">
    <top>
        <HBox>
            <Button text="Close" fx:id="closeButton" onAction="#closeApplication"/>
            <Button text="New" onAction="#newCanvas"/>
            <Button text="Save" onAction="#saveCanvas"/>
            <Button text="Save As" onAction="#saveAsCanvas"/>
            <Button text="Load" onAction="#loadCanvas"/>
            <Button text="Export as Image" onAction="#exportCanvas"/>
        </HBox>
    </top>
    <left>
        <VBox>
            <Button text="Draw New Class" fx:id="newClass" onAction="#drawNewClass"/>
            <Button text="Add New Relationship" onAction="#drawNewRelationship"/>
        </VBox>
    </left>
    <center>
        <StackPane fx:id="stackPane" style="-fx-border-color: #000; -fx-border-width: 1px"
                    maxWidth="500" maxHeight="500">
            <Canvas fx:id="canvas" width="${stackPane.width}" height="${stackPane.height}"/>
        </StackPane>
    </center>
</BorderPane>

Image of GUI