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The Bouncy Castle Java API for handling the OpenPGP protocol. This jar contains the OpenPGP API for JDK 1.5 to JDK 1.7. The APIs can be used in conjunction with a JCE/JCA provider such as the one provided with the Bouncy Castle Cryptography APIs.
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package org.bouncycastle.openpgp.examples;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.OutputStream;
import java.security.Security;
import java.util.Iterator;

import org.bouncycastle.bcpg.ArmoredOutputStream;
import org.bouncycastle.bcpg.BCPGOutputStream;
import org.bouncycastle.bcpg.sig.NotationData;
import org.bouncycastle.jce.provider.BouncyCastleProvider;
import org.bouncycastle.openpgp.PGPPrivateKey;
import org.bouncycastle.openpgp.PGPPublicKey;
import org.bouncycastle.openpgp.PGPPublicKeyRing;
import org.bouncycastle.openpgp.PGPSecretKey;
import org.bouncycastle.openpgp.PGPSecretKeyRing;
import org.bouncycastle.openpgp.PGPSignature;
import org.bouncycastle.openpgp.PGPSignatureGenerator;
import org.bouncycastle.openpgp.PGPSignatureSubpacketGenerator;
import org.bouncycastle.openpgp.PGPSignatureSubpacketVector;
import org.bouncycastle.openpgp.PGPUtil;
import org.bouncycastle.openpgp.operator.jcajce.JcaKeyFingerprintCalculator;
import org.bouncycastle.openpgp.operator.jcajce.JcaPGPContentSignerBuilder;
import org.bouncycastle.openpgp.operator.jcajce.JcePBESecretKeyDecryptorBuilder;

/**
 * A simple utility class that directly signs a public key and writes the signed key to "SignedKey.asc" in 
 * the current working directory.
 * 
 * To sign a key: DirectKeySignature secretKeyFile secretKeyPass publicKeyFile(key to be signed) NotationName NotationValue.

 * 

 * To display a NotationData packet from a publicKey previously signed: DirectKeySignature signedPublicKeyFile.

 * 

 * Note: this example will silently overwrite files, nor does it pay any attention to
 * the specification of "_CONSOLE" in the filename. It also expects that a single pass phrase
 * will have been used.
 * 
 */
public class DirectKeySignature
{
    public static void main(
        String[] args)
    throws Exception
    {
        Security.addProvider(new BouncyCastleProvider());

        if (args.length == 1)
        {
            PGPPublicKeyRing ring = new PGPPublicKeyRing(PGPUtil.getDecoderStream(new FileInputStream(args[0])), new JcaKeyFingerprintCalculator());
            PGPPublicKey key = ring.getPublicKey();
            
            // iterate through all direct key signautures and look for NotationData subpackets
            Iterator iter = key.getSignaturesOfType(PGPSignature.DIRECT_KEY);
            while(iter.hasNext())
            {
                PGPSignature    sig = (PGPSignature)iter.next();
                
                System.out.println("Signature date is: " + sig.getHashedSubPackets().getSignatureCreationTime());

                NotationData[] data = sig.getHashedSubPackets().getNotationDataOccurences();//.getSubpacket(SignatureSubpacketTags.NOTATION_DATA);
                
                for (int i = 0; i < data.length; i++)
                {
                    System.out.println("Found Notaion named '"+data[i].getNotationName()+"' with content '"+data[i].getNotationValue()+"'.");
                }
            }
        }
        else if (args.length == 5)
        {
            // gather command line arguments
            PGPSecretKeyRing secRing = new PGPSecretKeyRing(PGPUtil.getDecoderStream(new FileInputStream(args[0])), new JcaKeyFingerprintCalculator());
            String secretKeyPass = args[1];
            PGPPublicKeyRing ring = new PGPPublicKeyRing(PGPUtil.getDecoderStream(new FileInputStream(args[2])), new JcaKeyFingerprintCalculator());
            String notationName = args[3];
            String notationValue = args[4];

            // create the signed keyRing
            PGPPublicKeyRing sRing = new PGPPublicKeyRing(new ByteArrayInputStream(signPublicKey(secRing.getSecretKey(), secretKeyPass, ring.getPublicKey(), notationName, notationValue, true)), new JcaKeyFingerprintCalculator());
            ring = sRing;

            // write the created keyRing to file
            ArmoredOutputStream out = new ArmoredOutputStream(new FileOutputStream("SignedKey.asc"));
            sRing.encode(out);
            out.flush();
            out.close();
        }
        else
        {
            System.err.println("usage: DirectKeySignature secretKeyFile secretKeyPass publicKeyFile(key to be signed) NotationName NotationValue");
            System.err.println("or: DirectKeySignature signedPublicKeyFile");

        }
    }

    private static byte[] signPublicKey(PGPSecretKey secretKey, String secretKeyPass, PGPPublicKey keyToBeSigned, String notationName, String notationValue, boolean armor) throws Exception
    {
        OutputStream out = new ByteArrayOutputStream();

        if (armor)
        {
            out = new ArmoredOutputStream(out);
        }

        PGPPrivateKey pgpPrivKey = secretKey.extractPrivateKey(new JcePBESecretKeyDecryptorBuilder().setProvider("BC").build(secretKeyPass.toCharArray()));

        PGPSignatureGenerator       sGen = new PGPSignatureGenerator(new JcaPGPContentSignerBuilder(secretKey.getPublicKey().getAlgorithm(), PGPUtil.SHA1).setProvider("BC"));

        sGen.init(PGPSignature.DIRECT_KEY, pgpPrivKey);

        BCPGOutputStream            bOut = new BCPGOutputStream(out);

        sGen.generateOnePassVersion(false).encode(bOut);

        PGPSignatureSubpacketGenerator spGen = new PGPSignatureSubpacketGenerator();

        boolean isHumanReadable = true;

        spGen.setNotationData(true, isHumanReadable, notationName, notationValue);

        PGPSignatureSubpacketVector packetVector = spGen.generate();
        sGen.setHashedSubpackets(packetVector);

        bOut.flush();

        if (armor)
        {
            out.close();
        }

        return PGPPublicKey.addCertification(keyToBeSigned, sGen.generate()).getEncoded();
    }
}