The problem can be reproducible using the latest jdk 6.

According to the spec for org.w3c.dom.Node.setNodeValue(String):
"
void setNodeValue(String nodeValue)
                  throws DOMException
    Throws:
        DOMException - NO_MODIFICATION_ALLOWED_ERR: Raised when the node is readonly and if it is not defined to be null.
"

In the following code example, the test calls setNodeValue(String) on a read-only Entity node. The test expects the method to throw DOMException.NO_MODIFICATION_ALLOWED_ERR, but on jdk 6, it doesn't throw any exception.
===============================================================
import org.w3c.dom.*;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.xml.sax.SAXException;
import java.io.IOException;
import java.io.ByteArrayInputStream;
import java.io.InputStreamReader;
import org.xml.sax.InputSource;
import java.io.StringReader;

public class MyDomTest1 {

    public static void main(String[] args) {
    String data =
            "<?xml version=\"1.0\" ?>"
            + "<!DOCTYPE root ["
            + "<!ELEMENT root ANY>"
            + "<!ENTITY ent \"foo\">"
            + "<!NOTATION not PUBLIC \"http://xxx.xxx.xx/x.txt\">"
            + "]>"
            + "<root>"
            + "</root>";
    
    Document document = null;
    try {
        DocumentBuilderFactory docBF = DocumentBuilderFactory.newInstance();
        docBF.setNamespaceAware(true);
        DocBuilderWrapper docBuilder = new DocBuilderWrapper(docBF.newDocumentBuilder());
        document = docBuilder.parse(data);
    } catch (ParserConfigurationException e) {
        //return Status.failed(e.toString());
    } catch (IOException e) {
        //return Status.failed(e.toString());
    } catch (SAXException e) {
       // return Status.failed(e.toString());
    }

    Entity anEntity = (Entity)document.getDoctype().getEntities().item(0);
    try {
        anEntity.setNodeValue("someValue"); //on jdk 6, not even throwing exception
        
        System.out.println("Should throw DOMException: NO_MODIFICATION_ALLOWED_ERR ");
    } catch(DOMException e) {
        if (e.code == DOMException.NO_MODIFICATION_ALLOWED_ERR) {
            System.out.println("OK");
        } else {
            System.out.println("should throw DOMException.NO_MODIFICATION_ALLOWED_ERR (7). The error returned is " + e.code );
        }
    }
    }
}

class DocBuilderWrapper {

     private DocumentBuilder docBuilder;
     private final String ENCODING = "UTF-8";

     /**
      * Creates a new <code>DocBuilderWrapper</code> with the default
      * <code>DocumentBuilder</code> object.
      *
      * @throws ParserConfigurationException if a DocumentBuilder cannot be create
      */
     public DocBuilderWrapper() throws ParserConfigurationException {
         this.docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
     }

     /**
      * Creates a new <code>DocBuilderWrapper</code> with the specified
      * <code>DocumentBuilder</code> object.
      *
      * @param docBuilder the <code>DocumentBuilder</code> object, it can not be null
      * @throws IllegalArgumentException If the docBuilder is null
      */
     public DocBuilderWrapper(DocumentBuilder docBuilder) {
         setDocumentBuilder(docBuilder);
     }

     /**
      * Gets the <code>DocumentBuilder</code> object of this wrapper.
      *
      * @return the wrapped <code>DocumentBuilder</code> object
      */
     public DocumentBuilder getDocumentBuilder() {
         return docBuilder;
     }

     /**
      * Sets the <code>DocumentBuilder</code> object to wrap.
      *
      * @param docBuilder the DocumentBuilder object, it can not be null
      * @throws IllegalArgumentException If the docBuilder is null
      */
     public void setDocumentBuilder(DocumentBuilder docBuilder) {
         if (docBuilder == null) {
             new IllegalArgumentException("DocumentBuilder cannot be null");
         }
         
         this.docBuilder = docBuilder;
     }

     /**
      * Parses the content of the given String as an XML document.
      *
      * @param xmlData <code>String</code> containing the content to be parsed, it cannot be null.
      * @return A new <code>Document</code> object.
      * @throws IllegalArgumentException If the xmlData is null
      */
     public Document parse(String xmlData) throws IOException, SAXException {
         if (xmlData == null) {
             new IllegalArgumentException("String cannot be null");
         }
         
         ByteArrayInputStream bis = new ByteArrayInputStream(xmlData.getBytes(ENCODING));
         InputStreamReader isr = new InputStreamReader(bis, ENCODING);
         InputSource source = new InputSource(isr);
         return docBuilder.parse(source);
     }
 }
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