You can also try waiting for the alert to appear and then accepting it.

Below is the code for that (after the upload button is clicked):

try{

   //Wait 10 seconds till alert is present

   WebDriverWait wait = new WebDriverWait(driver, 10);

   Alert alert = wait.until(ExpectedConditions.alertIsPresent());



   //Accepting alert.

   alert.accept();

   System.out.println(Accepted the alert successfully.);

}catch(Throwable e){

   System.err.println(Error came while waiting for the alert popup. +e.getMessage());

}