Certificate generated through CSR signing with Bou

I am struggling with the following issue:

I have a CSR which I am signing with this code:

@Override
public X509Certificate signCSR( Reader pemcsr, int validityDays ) throws APIException
{
try ( PEMParser reader = new PEMParser( pemcsr ) )
{

  KeyStore keystore = getKeyStore();

  Properties cryptoProps = getCryptoProperties();

  String caKeyAlias = cryptoProps.getProperty( PROPERTY_KEYSTORE_CA_CERT_ALIAS );
  String caKeyPassword = cryptoProps.getProperty( PROPERTY_KEYSTORE_CA_CERT_PASSWORD );

  PrivateKey cakey = (PrivateKey) keystore.getKey( caKeyAlias, caKeyPassword.toCharArray() );
  X509Certificate cacert = (X509Certificate) keystore.getCertificate( caKeyAlias );

  PKCS10CertificationRequest csr = (PKCS10CertificationRequest) reader.readObject();

  AlgorithmIdentifier sigAlgId = new DefaultSignatureAlgorithmIdentifierFinder().find( "SHA1withRSA" );
  AlgorithmIdentifier digAlgId = new DefaultDigestAlgorithmIdentifierFinder().find( sigAlgId );
  X500Name issuer = new X500Name( cacert.getSubjectX500Principal().getName() );
  BigInteger serial = new BigInteger( 32, new SecureRandom() );
  Date from = new Date();
  Date to = new Date( System.currentTimeMillis() + ( validityDays * 86400000L ) );

  DigestCalculator digCalc = new BcDigestCalculatorProvider().get( new AlgorithmIdentifier( OIWObjectIdentifiers.idSHA1 ) );
  X509ExtensionUtils x509ExtensionUtils = new X509ExtensionUtils( digCalc );

  X509v3CertificateBuilder certgen = new X509v3CertificateBuilder( issuer, serial, from, to, csr.getSubject(), csr.getSubjectPublicKeyInfo() );

  // Basic Constraints
  // certgen.addExtension( Extension.basicConstraints, true, new
  // BasicConstraints( 0 ) );

  // Subject Key Identifier
  // certgen.addExtension( Extension.subjectKeyIdentifier, false,
  // x509ExtensionUtils.createSubjectKeyIdentifier(
  // csr.getSubjectPublicKeyInfo() ) );

  // Authority Key Identifier
  // byte[] caKeyEncoded = cacert.getPublicKey().getEncoded();
  // SubjectPublicKeyInfo caSubjectPublicKeyInfo =
  // SubjectPublicKeyInfo.getInstance( caKeyEncoded );
  // certgen.addExtension( Extension.authorityKeyIdentifier, false,
  // x509ExtensionUtils.createAuthorityKeyIdentifier( caSubjectPublicKeyInfo
  // ) );

  // Key Usage
  // certgen.addExtension( Extension.keyUsage, false, new KeyUsage(
  // KeyUsage.digitalSignature | KeyUsage.keyCertSign | KeyUsage.cRLSign )
  // );

  ContentSigner signer = new BcRSAContentSignerBuilder( sigAlgId, digAlgId ).build( PrivateKeyFactory.createKey( cakey.getEncoded() ) );

  // ContentSigner signer = new JcaContentSignerBuilder(
  // "SHA1WithRSAEncryption" ).setProvider( "BC" ).build( cakey );

  X509CertificateHolder holder = certgen.build( signer );

  return new JcaX509CertificateConverter().setProvider( "BC" ).getCertificate( holder );
}
catch ( NoSuchAlgorithmException | KeyStoreException | CertificateException | OperatorCreationException | UnrecoverableKeyException | CertIOException e )
{
  throw new APIException( API_ERROR_CODE.CRYPTOGRAPHY_ERROR, e );
}
catch ( IOException e )
{
  throw new APIException( API_ERROR_CODE.IO_ERROR, e );
}

}

This runs through successfully. However, when I try to check the key using:

KeyStore ks = getKeyStore();

  TrustManagerFactory trustManagerFactory = TrustManagerFactory.getInstance( TrustManagerFactory.getDefaultAlgorithm() );
  trustManagerFactory.init( ks );

  for ( TrustManager trustManager : trustManagerFactory.getTrustManagers() )
  {
    if ( trustManager instanceof X509TrustManager )
    {
      X509TrustManager x509TrustManager = (X509TrustManager) trustManager;
      x509TrustManager.checkClientTrusted( new X509Certificate[] { certificate }, "RSA" );
    }
  }

...it fails with a CertificateException. Please note that I am using the VERY SAME keystore here, which means the CA key I am signing with is included therein. Why does this happen?

By the way, strangely enough, when I open the generated signed certificate using Windows's certificate viewer, it DOES show the issuing CA name but its entry does not show up in the certificate chain. It seems as if the CA root certificate were not present in the Windows trusted authirities list, but in fact it is also there.

Even stranger: if I sign the CSR using OpenSSL, the certificate chain looks OK. I also had the idea that the process of importing the CA key pair from OpenSSL to the Java keystore via PKCS12 as an intermediate format wasn't successful, but actually if I export the CA certificate from the Java keystore and open it with the Windows certificate viewer, it is shown as trusted...

UPDATE: For those familiar with ASN.1, here are two encoded certificates. One is made with BouncyCastle and is NOT trusted, the other one is signed by the same CA key with OpenSSL and that IS trusted. They can be decoded with a tool like this: ASN.1 decoder I would be very grateful is somebody could view this decoded data and tell me what could cause the difference between them.

This one is NOT trusted:

This one is TRUSTED, this has been generated using theoretically the same CA certificate but through OpenSSL:

UPDATE 2:

Thanks to Bruno's answer, the certificate chain now looks OK and the following certificate is generated:

However, the TrustManager code above rejects it. If I circumvent the TrustManager and do something like this:

 KeyStore ks = getKeyStore();

  Enumeration<String> aliases = ks.aliases();

  while ( aliases.hasMoreElements() )
  {
    String alias = aliases.nextElement();
    Certificate currentCert = ks.getCertificate( alias );
    try
    {
      certificate.verify( currentCert.getPublicKey() );
      return true;
    }
    catch ( Exception e )
    {
      // the certificate cannot be verified with this key.
    }
  }

  return false;

...it passes. Does anybody know why it fails on the TrustManager check?

P.s. the CA certificate looks like this:

If you look at the Issuer DN in your two certificates, they don't match (output from openssl x509 -text):

Issuer: C=AT, ST=Wien, L=Wien, O=Test CA, OU=Test CA, CN=Test CA/emailAddress=testca@testca.com

and

Issuer: emailAddress=testca@testca.com, CN=Test CA, OU=Test CA, O=Test CA, L=Wien, ST=Wien, C=AT

As a result, it's not going to be able to match the wrong issuer to the CA's Subject DN.

Unfortunately, X500Name issuer = new X500Name(cacert.getSubjectX500Principal().getName()) doesn't do what you'd expect. The order of the RDNs is reversed. Generally, re-building the DN from a string representation can fail, since there are different ways of serialising the ASN.1 representation into a string. Java's X500Principal has multiple formats available for getName(...) and it even provides a way to provide your own OID to string maps (for more obscure OIDs). The way emailAddress is separated can also cause problems (notice the way it's separated with a comma or with a slash).

Instead, build the X500Name from the encoded form, this should always work:

X500Name x500Name = X500Name.getInstance(cert
                        .getSubjectX500Principal().getEncoded());

Certificate generated through CSR signing with Bou

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Certificate generated through CSR signing with Bou

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