You are providing generated PDF documents on your web pages.

The PDF can only be tested in the context of the web pages. So, the input data for a test has to be entered to the browser frontend and the generated PDF has to be selected also through the web page.

Selenium provides a good way to select a PDF document from a web page. This document will be opened by PDFUnit as a Stream.

The following lines represent the main part of the test:

/**
 * When the URL of the pdf document inside an HTML page is generated dynamically,
 * you have to find the link (href) first.
 * Input data for the web page can also be typed with Selenium (not shown here).
 */
@Test
public void verifyPDF_LoadedBySeleniumWebdriver() throws Exception {
  // arrange, navigate to web site:
  String startURL = "http://www.unicode.org/charts/";
  driver.get(startURL);
  WebElement element = driver.findElement(By.linkText("Basic Latin (ASCII)"));
  String hrefValue = element.getAttribute("href");
  
  // act, load PDF web site:
  URL url = new URL(hrefValue);
  
  // assert, validate PDF:
  String expectedTitle  = "The Unicode Standard, Version 6.3";

  AssertThat.document(url)
            .hasTitle().equalsTo(expectedTitle)
  ;
  AssertThat.document(url)
            .restrictedTo(FIRST_PAGE)
            .hasText()
            .containing("0000", "007F")
  ;
}

The remaining lines are:

/**
 * This sample shows how to test a PDF document with Selenium and PDFUnit.
 * See the previous code listing for the '@Test' method. 
 *
 * @author Carsten Siedentop, March 2012
 */
public class PDFFromWebsiteTest {

  private WebDriver driver;

  @Before
  public void createDriver() throws Exception {
    driver = new HtmlUnitDriver();
    Logger htmlunitLogger = Logger.getLogger("com.gargoylesoftware.htmlunit");
    htmlunitLogger.setLevel(java.util.logging.Level.SEVERE); 
  }
  
  @After
  public void closeAll() throws Exception {
    driver.close();
  }
  
  // @Test
  // public void verifyPDF_LoadedBySeleniumWebdriver()...

}

For more information about Selenium contact the project site http://seleniumhq.org/.