Demonstrates a JavaFX task which runs in the background reading data and, when required, pauses from reading data to prompt the user for extra input before continuing processing.

PromptingTaskDemo.java

import java.util.concurrent.*;
import javafx.application.Application;
import static javafx.application.Application.launch;
import javafx.application.Platform;
import javafx.beans.property.*;
import javafx.concurrent.Task;
import javafx.event.*;
import javafx.geometry.Pos;
import javafx.scene.*;
import javafx.scene.control.*;
import javafx.scene.layout.*;
import javafx.stage.*;

public class PromptingTaskDemo extends Application {
  private static final String[] SAMPLE_TEXT = 
    "MISSING Lorem ipsum dolor sit amet MISSING consectetur adipisicing elit sed do eiusmod tempor incididunt MISSING ut labore et dolore magna aliqua"
    .split(" ");

  @Override public void start(Stage primaryStage) {
    Label status = new Label();
    ProgressBar progress = new ProgressBar();
    
    VBox textContainer = new VBox(10);
    textContainer.setStyle("-fx-background-color: burlywood; -fx-padding: 10;");
    
    LoadTextTask task = new LoadTextTask(SAMPLE_TEXT, textContainer);
    status.textProperty().bind(task.messageProperty());
    progress.progressProperty().bind(task.progressProperty());
    
    final Thread taskThread = new Thread(task, "label-generator");
    taskThread.setDaemon(true);
    
    VBox layout = new VBox(10);
    layout.getChildren().addAll(status, progress, textContainer);
    layout.setStyle("-fx-background-color: cornsilk; -fx-padding: 10;");
    
    primaryStage.setScene(new Scene(layout, 300, 700));
    primaryStage.show();

    taskThread.start();
}
  
  public static void main(String[] args) { launch(args); }
}

class LoadTextTask extends Task<Void> {
  private final String[] lines;
  private final Pane container;
  private final IntegerProperty idx = new SimpleIntegerProperty(0);

  LoadTextTask(final String[] lines, final Pane container) {
    this.lines = lines;
    this.container = container;
  }

  @Override protected Void call() throws Exception {
    try {    
      updateProgress(0, lines.length);

      while (idx.get() < lines.length) {
        final Label nextLabel = new Label();
        final int curIdx = idx.get();
        updateMessage("Reading Line: " + curIdx);
        String nextText = lines[curIdx];

        if ("MISSING".equals(nextText)) {
          updateMessage("Prompting for missing text for line: " + curIdx);
          FutureTask<String> futureTask = new FutureTask(
            new MissingTextPrompt(
              container.getScene().getWindow()
            )
          );
          Platform.runLater(futureTask);
          nextText = futureTask.get();

          nextLabel.setStyle("-fx-background-color: palegreen;");
        }
        nextLabel.setText(nextText);

        Platform.runLater(
          new AddNodeLater(
            container, 
            curIdx, 
            nextLabel
          )
        );
        idx.set(curIdx + 1);

        updateProgress(curIdx + 1, lines.length);

        Thread.sleep(200);
      }              

      updateMessage("Loading Text Completed: " + idx.get() + " lines loaded.");
    } catch (Throwable t) {
      t.printStackTrace();
    }
    return null;
  }

  class MissingTextPrompt implements Callable<String> {
    final Window owner; 

    MissingTextPrompt(Window owner) {
      this.owner = owner;
    }

    @Override public String call() throws Exception {
      final Stage dialog = new Stage();
      dialog.setTitle("Enter Missing Text");
      dialog.initOwner(owner);
      dialog.initStyle(StageStyle.UTILITY);
      dialog.initModality(Modality.WINDOW_MODAL);

      final TextField textField = new TextField();
      final Button submitButton = new Button("Submit");
      submitButton.setDefaultButton(true);
      submitButton.setOnAction(new EventHandler<ActionEvent>() {
        @Override public void handle(ActionEvent t) {
          dialog.close();
        }
      });

      final VBox layout = new VBox(10);
      layout.setAlignment(Pos.CENTER_RIGHT);
      layout.setStyle("-fx-background-color: azure; -fx-padding: 10;");
      layout.getChildren().setAll(textField, submitButton);

      dialog.setScene(new Scene(layout));
      dialog.showAndWait();
      
      return textField.getText();
    }
  }
  
  class AddNodeLater implements Runnable {
    final Pane container;
    final Node node;
    final int idx;

    public AddNodeLater(final Pane container, final int idx, final Node node) {
      this.container = container;
      this.node = node;
      this.idx = idx;
    }

    @Override public void run() {
      container.getChildren().add(idx, node);
    }
  }  
}

Answer to the StackOverflow question => JavaFX2: Can I pause a background Task / Service?