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Sign CSR with BouncyCastle

I have been looking for the past few days for a solution on my Problem and couldn't find anything. I am missing something in my Code but i cant figure out what :( Somehow when I sign my PKCS#10 the chain is broken.

Basically i have a server and a client. I want to have the client send a CSR to the server and the server signs it so they can communicate. Now i did set up a PKCS#12 with BouncyCastle for the Client and i did set up a RootCertificate for the Server (again with BouncyCastle, which is in my understanding just a PKCS#12 with the extension to be able to sign Certificates) In Code it looks like this:

Provider BC = new BouncyCastleProvider();
Security.addProvider(BC);
//create KeyPair
KeyPairGenerator kpGen = KeyPairGenerator.getInstance("RSA", "BC");
kpGen.initialize(2048, new SecureRandom());
pair = kpGen.generateKeyPair();
//building groundbase for certificate
X500NameBuilder builder = new X500NameBuilder(BCStyle.INSTANCE);
builder.addRDN(BCStyle.CN, commonName);
builder.addRDN(BCStyle.OU, organizationalUnit);
builder.addRDN(BCStyle.O, organization);
builder.addRDN(BCStyle.L, city);
builder.addRDN(BCStyle.ST, state);
builder.addRDN(BCStyle.C, country);
Date notBefore = new Date(System.currentTimeMillis() - 1000L * 60 * 60 * 24); //Yesterday
Date notAfter = new Date(System.currentTimeMillis() +  1000L * 365L * 24L * 60L * 60L); //in a year
BigInteger serial = BigInteger.valueOf(new SecureRandom().nextLong());
//creating a self-signed certificate from information in builder
X509v3CertificateBuilder certGen = new JcaX509v3CertificateBuilder(builder.build(),
serial, notBefore, notAfter, builder.build(), pair.getPublic());

//The next line will make the difference between a Certificate and a Ca Certificate
certGen.addExtension(Extension.basicConstraints, true, new BasicConstraints(true));

ContentSigner sigGen = new JcaContentSignerBuilder(").setProvider(BC).build(pair.getPrivate());
X509Certificate cert = new JcaX509CertificateConverter().setProvider(BC).getCertificate(certGen.build(sigGen));

Now i create a CSR for the Client (Client keystore has the just created PKCS#12 at first position):

String alias = keystore.aliases().nextElement();
X509Certificate cert = (X509Certificate) keystore.getCertificate(alias);
X500Name x500name = new JcaX509CertificateHolder(cert).getSubject();
//builder for the PKCS10
PKCS10CertificationRequestBuilder requestBuilder = new JcaPKCS10CertificationRequestBuilder(x500name, cert.getPublicKey());
//algorithm identifier
DefaultSignatureAlgorithmIdentifierFinder sigAlgFinder = new DefaultSignatureAlgorithmIdentifierFinder();
DefaultDigestAlgorithmIdentifierFinder digAlgFinder = new DefaultDigestAlgorithmIdentifierFinder();
AlgorithmIdentifier sigAlgId = sigAlgFinder.find("SHA512WithRSA");
digAlgFinder.find(sigAlgId);
//content Signer
JcaContentSignerBuilder contentSignerBuilder = new JcaContentSignerBuilder("SHA512WithRSA");
//and build the Cert
ContentSigner signer = contentSignerBuilder.build((PrivateKey) keystore.getKey(alias, password));
PKCS10CertificationRequest req = requestBuilder.build(signer);
JcaPKCS10CertificationRequest req2 = new JcaPKCS10CertificationRequest(req.getEncoded()).setProvider("BC");

I send this JcaPKCS10CertificationRequest encoded over the network. The Server gets it and creates his CA Certificate and now has to sign the PKCS#10 but i am missing something here because he is not including the chain. The Certificate he is creating has the information about the issuer and BasicConstraints but the certification path is only including the Clients Certificate and NOT the Certificate of the Server so it is not trustworthy since the chain is broken.

This is what i do (Server Keystore has the CA Certificate at position 0, CSR is the JcaPKCS10CertificationRequest):

String alias = keystore.aliases().nextElement();
// PKCS#12 Root Certificate
X509Certificate cert = (X509Certificate) keystore.getCertificate(alias);
// generated Serial
BigInteger serial = BigInteger.valueOf(new SecureRandom().nextLong());
//identify algorithm
AlgorithmIdentifier sigAlgId = new DefaultSignatureAlgorithmIdentifierFinder().find("SHA512WithRSA");
AlgorithmIdentifier digAlgId = new DefaultDigestAlgorithmIdentifierFinder().find( sigAlgId );

JcaX509ExtensionUtils extUtils = new JcaX509ExtensionUtils();
JcaX509v3CertificateBuilder certGen = new JcaX509v3CertificateBuilder(cert, serial, cert.getNotBefore(), cert.getNotAfter(),
            CSR.getSubject(), CSR.getPublicKey());
certGen.addExtension(Extension.authorityKeyIdentifier, false, extUtils.createAuthorityKeyIdentifier(cert));

certGen.addExtension(Extension.basicConstraints, true, new BasicConstraints(false));
certGen.addExtension(Extension.subjectKeyIdentifier, true, extUtils.createSubjectKeyIdentifier(inputCSR.getPublicKey()));
certGen.addExtension(Extension.keyUsage, true, new KeyUsage(KeyUsage.digitalSignature | KeyUsage.keyEncipherment | KeyUsage.dataEncipherment | KeyUsage.nonRepudiation));
ContentSigner signer = new JcaContentSignerBuilder(sigAlgName).setProvider("BC").build((PrivateKey)keystore.getKey(alias, password));
X509CertificateHolder holder = certGen.build(signer);
X509Certificate signedCert = new JcaX509CertificateConverter().setProvider("BC").getCertificate(holder);
signedCert.verify(cert.getPublicKey());
JcaPEMWriter pemWriter = new JcaPEMWriter(new FileWriter(new File("cer.cer")));
pemWriter.writeObject(signedCert);
pemWriter.writeObject(cert);
pemWriter.close();

Now as i said the generated File "cer.cer" has not the Chain in it. How can i add the chain? Can i then send that signedCert back to the client and it can be used in a ssl handshake?

To add the chain, this worked for me

After X509CertificateHolder holder = certGen.build(signer);

  byte[] certencoded = holder.toASN1Structure().getEncoded();
  ContentSigner signer = new JcaContentSignerBuilder("SHA1withRSA").build(caPrivateKkey);
  CMSSignedDataGenerator generator = new CMSSignedDataGenerator();
  generator.addSignerInfoGenerator(new JcaSignerInfoGeneratorBuilder(new JcaDigestCalculatorProviderBuilder().build()).build(signer, cacert));
  generator.addCertificate(new X509CertificateHolder(certencoded));
  generator.addCertificate(new X509CertificateHolder(cacert.getEncoded()));
  CMSTypedData content = new CMSProcessableByteArray(certencoded);
  CMSSignedData signeddata = generator.generate(content, true);

  byte certificateP7b[] = signedData.getEncoded();

With this code you get a Certificate with the full chain in PCKS#7 format. If you prefer to work with X509 format

public static List<X509Certificate> p7BToX509(byte signedCert[]) throws CertificateException{
    ByteArrayInputStream is = new ByteArrayInputStream( signedCert);
    CertificateFactory cf = CertificateFactory.getInstance( "X.509" );

    ArrayList<X509Certificate> certificates = new ArrayList<X509Certificate>();
    Iterator i = cf.generateCertificates( is ).iterator();
    while ( i.hasNext() ){
       X509Certificate c = (X509Certificate)i.next();
       certificates.add(c);

    }
    return certificates;

}

This is the public certificate. In your client you should have the private key. These are all elements you need to perform and ssl handshake

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