FULL PRODUCT VERSION :
java version  " 1.7.0_25 " 
Java(TM) SE Runtime Environment (build 1.7.0_25-b16)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Windows 7 Professional, 64-bit

A DESCRIPTION OF THE PROBLEM :
XML signature validation code that functions in jre170_21 and earlier, breaks in the latest release. This pertains to signatures for manifest items, referenced by xmldsig:id attributes in the XML document.

The XML signature validation source code is available here:
https://raw.github.com/joval/jOVAL/master/src/org/joval/xml/SignatureValidator.java

A Java keystore file containing the NIST certificate is available here:
https://github.com/joval/jOVAL/raw/master/components/jovaldi/rsrc/security/cacerts.jks

I am attempting to validate the XML documents contained here (specifically scap_gov.nist_USGCB-Windows-7.xml):
http://usgcb.nist.gov/usgcb/content/scap/oval510/Win7-510-1.2.7.1.zip


REGRESSION.  Last worked in version 6u45

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Instantiate an org.joval.xml.SignatureValidator with the XML file and keystore backed by the file I referenced above, and invoke the validate() method.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The method should return true.
ACTUAL -
An XMLSignatureException is thrown.

ERROR MESSAGES/STACK TRACES THAT OCCUR :
2013.06.19 22:46:16.588 - INFO - Verifying XML digital signature: ..\..\..\..\content\scap12\scap_gov.nist_USGCB-Windows-7.xml
2013.06.19 22:46:17.334 - SEVERE - javax.xml.crypto.dsig.XMLSignatureException: javax.xml.crypto.URIReferenceException: com.sun.org.apache.xml.internal.security.utils.resolver.ResourceResolverException: Cannot resolve element with ID scap_gov.nist_datastream_USGCB-Windows-7-1.2.3.1.zip
    org.jcp.xml.dsig.internal.dom.DOMReference.dereference(DOMReference.java:412)
    org.jcp.xml.dsig.internal.dom.DOMReference.validate(DOMReference.java:371)
    org.jcp.xml.dsig.internal.dom.DOMXMLSignature.validate(DOMXMLSignature.java:265)
    org.joval.xml.SignatureValidator.validate(SignatureValidator.java:104)
    org.joval.scap.xccdf.engine.XPERT.main(XPERT.java:283)
caused by:
javax.xml.crypto.URIReferenceException: com.sun.org.apache.xml.internal.security.utils.resolver.ResourceResolverException: Cannot resolve element with ID scap_gov.nist_datastream_USGCB-Windows-7-1.2.3.1.zip
    org.jcp.xml.dsig.internal.dom.DOMURIDereferencer.dereference(DOMURIDereferencer.java:124)
    org.jcp.xml.dsig.internal.dom.DOMReference.dereference(DOMReference.java:404)
    org.jcp.xml.dsig.internal.dom.DOMReference.validate(DOMReference.java:371)
    org.jcp.xml.dsig.internal.dom.DOMXMLSignature.validate(DOMXMLSignature.java:265)
    org.joval.xml.SignatureValidator.validate(SignatureValidator.java:104)
    org.joval.scap.xccdf.engine.XPERT.main(XPERT.java:283)
caused by:
com.sun.org.apache.xml.internal.security.utils.resolver.ResourceResolverException: Cannot resolve element with ID scap_gov.nist_datastream_USGCB-Windows-7-1.2.3.1.zip
    com.sun.org.apache.xml.internal.security.utils.resolver.implementations.ResolverFragment.engineResolve(ResolverFragment.java:90)
    com.sun.org.apache.xml.internal.security.utils.resolver.ResourceResolver.resolve(ResourceResolver.java:283)
    org.jcp.xml.dsig.internal.dom.DOMURIDereferencer.dereference(DOMURIDereferencer.java:117)
    org.jcp.xml.dsig.internal.dom.DOMReference.dereference(DOMReference.java:404)
    org.jcp.xml.dsig.internal.dom.DOMReference.validate(DOMReference.java:371)
    org.jcp.xml.dsig.internal.dom.DOMXMLSignature.validate(DOMXMLSignature.java:265)
    org.joval.xml.SignatureValidator.validate(SignatureValidator.java:104)
    org.joval.scap.xccdf.engine.XPERT.main(XPERT.java:283)


REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
// Copyright (C) 2012 jOVAL.org.  All rights reserved.
// This software is licensed under the AGPL 3.0 license available at http://www.joval.org/agpl_v3.txt

package org.joval.xml;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Enumeration;
import java.util.NoSuchElementException;
import java.security.Key;
import java.security.KeyException;
import java.security.KeyStore;
import java.security.KeyStoreException;
import java.security.PublicKey;
import java.security.cert.Certificate;
import java.security.cert.CertificateFactory;
import java.security.cert.CertSelector;
import java.security.cert.X509Certificate;
import java.security.cert.X509CertSelector;
import javax.security.auth.x500.X500Principal;
import javax.xml.XMLConstants;
import javax.xml.crypto.AlgorithmMethod;
import javax.xml.crypto.KeySelector;
import javax.xml.crypto.KeySelectorException;
import javax.xml.crypto.KeySelectorResult;
import javax.xml.crypto.MarshalException;
import javax.xml.crypto.NoSuchMechanismException;
import javax.xml.crypto.NodeSetData;
import javax.xml.crypto.OctetStreamData;
import javax.xml.crypto.XMLCryptoContext;
import javax.xml.crypto.XMLStructure;
import javax.xml.crypto.dsig.SignatureMethod;
import javax.xml.crypto.dsig.XMLSignature;
import javax.xml.crypto.dsig.XMLSignatureException;
import javax.xml.crypto.dsig.XMLSignatureFactory;
import javax.xml.crypto.dsig.dom.DOMValidateContext;
import javax.xml.crypto.dsig.keyinfo.KeyInfo;
import javax.xml.crypto.dsig.keyinfo.KeyName;
import javax.xml.crypto.dsig.keyinfo.KeyValue;
import javax.xml.crypto.dsig.keyinfo.RetrievalMethod;
import javax.xml.crypto.dsig.keyinfo.X509Data;
import javax.xml.crypto.dsig.keyinfo.X509IssuerSerial;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.FactoryConfigurationError;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.Source;
import javax.xml.transform.dom.DOMSource;
import org.xml.sax.SAXException;
import org.w3c.dom.Document;
import org.w3c.dom.NodeList;

/**
 * Utility class for validating XML digital signatures.
 * @see http://docs.oracle.com/cd/E17802_01/webservices/webservices/docs/1.6/tutorial/doc/XMLDigitalSignatureAPI8.html
 *
 * @author David A. Solin
 * @version %I% %G%
 */
public class SignatureValidator {
    private Document doc;
    private NodeList signatures;
    private KeyStore keyStore;

    /**
     * Create a new validator for the specified XML file using the specified KeyStore.
     */
    public SignatureValidator(File f, KeyStore keyStore)
throws FactoryConfigurationError, ParserConfigurationException, SAXException, IOException {

DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
dbf.setNamespaceAware(true);
doc = dbf.newDocumentBuilder().parse(f);
signatures = doc.getElementsByTagNameNS(XMLSignature.XMLNS,  " Signature " );
this.keyStore = keyStore;
    }

    /**
     * Assign a specific KeyStore to be used for validation.
     */
    public void setKeyStore(KeyStore keyStore) {
this.keyStore = keyStore;
    }

    /**
     * Returns whether or not there is an XML signature node in the document.
     */
    public boolean containsSignature() {
return signatures.getLength() > 0;
    }

    /**
     * Validate the document's XML digital signature.
     */
    public boolean validate() throws XMLSignatureException {
int len = signatures.getLength();
if (len == 0) {
    throw new XMLSignatureException( " Cannot find Signature element " );
} else {
    try {
for (int i=0; i < len; i++) {
    DOMValidateContext ctx = new DOMValidateContext(new X509KeySelector(), signatures.item(i));
    XMLSignature signature = XMLSignatureFactory.getInstance().unmarshalXMLSignature(ctx);
    if (!signature.validate(ctx)) {
return false;
    }
}
return true;
    } catch (NoSuchMechanismException e) {
throw new XMLSignatureException(e);
    } catch (ClassCastException e) {
throw new XMLSignatureException(e);
    } catch (MarshalException e) {
throw new XMLSignatureException(e);
    }
}
    }

    /**
     * Validate the document's XML digital signature using the supplied public key.
     */
    public boolean validate(Key validationKey) throws XMLSignatureException {
int len = signatures.getLength();
if (len == 0) {
    throw new XMLSignatureException( " Cannot find Signature element " );
} else {
    try {
for (int i=0; i < len; i++) {
    DOMValidateContext ctx = new DOMValidateContext(validationKey, signatures.item(i));
    XMLSignature signature = XMLSignatureFactory.getInstance().unmarshalXMLSignature(ctx);
    if (!signature.validate(ctx)) {
return false;
    }
}
return true;
    } catch (NoSuchMechanismException e) {
throw new XMLSignatureException(e);
    } catch (ClassCastException e) {
throw new XMLSignatureException(e);
    } catch (MarshalException e) {
throw new XMLSignatureException(e);
    }
}
    }

    /**
     * Obtain a Source for the document. This makes it possible to insure that the underlying data has been validated.
     */
    public Source getSource() {
return new DOMSource(doc);
    }

    // Private

    /**
     * KeySelector implementation for X.509 certificates.
     */
    class X509KeySelector extends KeySelector {
@Override
public KeySelectorResult select(KeyInfo ki, KeySelector.Purpose p, AlgorithmMethod am, XMLCryptoContext ctx)
throws KeySelectorException {

    KeySelectorResult result = null;
    SignatureMethod sm = (SignatureMethod)am;
    for (Object obj : ki.getContent()) {
XMLStructure xs = (XMLStructure)obj;
if (xs instanceof X509Data) {
    result = select((X509Data)xs, sm);
} else if (xs instanceof KeyName) {
    KeyName kn = (KeyName)xs;
    try {
Certificate cert = keyStore.getCertificate(kn.getName());
if (cert != null && equals(sm.getAlgorithm(), cert.getPublicKey().getAlgorithm())) {
    result = new SimpleKeySelectorResult(cert.getPublicKey());
}
    } catch (KeyStoreException e) {
throw new KeySelectorException(e);
    }
} else if (xs instanceof RetrievalMethod) {
    RetrievalMethod rm = (RetrievalMethod)xs;
    try {
if (rm.getType().equals(X509Data.RAW_X509_CERTIFICATE_TYPE)) {
    OctetStreamData data = (OctetStreamData)rm.dereference(ctx);
    CertificateFactory cf = CertificateFactory.getInstance( " X.509 " );
    X509Certificate cert = (X509Certificate)cf.generateCertificate(data.getOctetStream());
    result = select(cert, sm);
} else if (rm.getType().equals(X509Data.TYPE)) {
    NodeSetData nd = (NodeSetData)rm.dereference(ctx);
    System.out.println( " DAS conversion is TBD " );
}
    } catch (Exception e) {
throw new KeySelectorException(e);
    }
} else if (xs instanceof KeyValue) {
    PublicKey pk = null;
    try {
pk = ((KeyValue)xs).getPublicKey();
    } catch (KeyException ke) {
throw new KeySelectorException(ke);
    }
    if (equals(sm.getAlgorithm(), pk.getAlgorithm())) {
result = new SimpleKeySelectorResult(pk);
    }
}
if (result != null) {
    return result;
}
    }
    throw new KeySelectorException( " Key not found " );
}

// Internal

KeySelectorResult select(X509Data data, SignatureMethod sm) throws KeySelectorException {
    String oid = getOid(sm.getAlgorithm());
    KeySelectorResult result = null;
    for (Object obj : data.getContent()) {
try {
    if (obj instanceof X509Certificate) {
return select((X509Certificate)obj, sm);
    } else if (obj instanceof X509IssuerSerial) {
X509IssuerSerial xis = (X509IssuerSerial)obj;
X509CertSelector xcs = new X509CertSelector();
xcs.setSubjectPublicKeyAlgID(oid);
xcs.setSerialNumber(xis.getSerialNumber());
xcs.setIssuer(new X500Principal(xis.getIssuerName()).getName());
return select(xcs);
    } else if (obj instanceof String) {
String sn = (String)obj;
X509CertSelector xcs = new X509CertSelector();
xcs.setSubjectPublicKeyAlgID(oid);
xcs.setSubject(new X500Principal(sn).getName());
return select(xcs);
    } else if (obj instanceof byte[]) {
byte[] ski = (byte[])obj;
X509CertSelector xcs = new X509CertSelector();
xcs.setSubjectPublicKeyAlgID(oid);
byte[] encodedSki = new byte[ski.length+2];
encodedSki[0] = 0x04; // OCTET STRING tag value
encodedSki[1] = (byte)ski.length;
System.arraycopy(ski, 0, encodedSki, 2, ski.length);
xcs.setSubjectKeyIdentifier(encodedSki);
return select(xcs);
    }
} catch (IOException e) {
    throw new KeySelectorException(e);
} catch (KeyStoreException e) {
    throw new KeySelectorException(e);
} catch (NoSuchElementException e) {
    throw new KeySelectorException(e);
}
    }
    return null;
}

/**
 * Return the certificate in the key store that matches the specified selector
 *
 * @throws NoSuchElementException if there is no match
 */
KeySelectorResult select(X509CertSelector cs) throws KeyStoreException, NoSuchElementException {
    for (Enumeration e = keyStore.aliases(); e.hasMoreElements(); ) {
Certificate cert = keyStore.getCertificate((String)e.nextElement());
if (cert != null && cs.match(cert)) {
    return new SimpleKeySelectorResult(cert.getPublicKey());
}
    }
    throw new NoSuchElementException(cs.getSubject().toString());
}

/**
 * Return the certificate in the key store that matches the specified X509 certificate (or null if there is no match).
 *
 * @throws NoSuchElementException if there is no match
 */
KeySelectorResult select(X509Certificate xc, SignatureMethod sm) throws KeyStoreException, NoSuchElementException {
    boolean[] keyUsage = xc.getKeyUsage();
    if (keyUsage[0]) {
String alias = keyStore.getCertificateAlias(xc);
if (alias != null) {
    PublicKey pk = keyStore.getCertificate(alias).getPublicKey();
    if (equals(sm.getAlgorithm(), pk.getAlgorithm())) {
return new SimpleKeySelectorResult(pk);
    }
}
    }
    throw new NoSuchElementException(xc.getSubjectX500Principal().toString());
}

/**
 * Return the OID corresponding to the Algorithm URI.
 */
String getOid(String uri) {
    if (uri.equalsIgnoreCase(SignatureMethod.DSA_SHA1)) {
return  " 1.2.840.10040.4.1 " ;
    } else if (uri.equalsIgnoreCase(SignatureMethod.RSA_SHA1)) {
return  " 1.2.840.113549.1.1 " ;
    } else {
return null;
    }
}

/**
 * Determine whether the algorithm URI matches the algorithm name.
 */
boolean equals(String uri, String name) {
    if (name.equalsIgnoreCase( " DSA " ) && uri.equalsIgnoreCase(SignatureMethod.DSA_SHA1)) {
return true;
    } else if (name.equalsIgnoreCase( " RSA " ) && uri.equalsIgnoreCase(SignatureMethod.RSA_SHA1)) {
return true;
    } else {
return false;
    }
}
    }

    /**
     * A simple KeySelectorResult implementation.
     */
    static class SimpleKeySelectorResult implements KeySelectorResult {
private Key key;

SimpleKeySelectorResult(Key key) {
    this.key = key;
}

// Implement KeySelectorResult

public Key getKey() {
    return key;
}
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
We will have to distribute our application with an earlier release of Java, such as 170_21.