/**
   * method for JSP to create valid TimeStampRequest
   *
   * @param file
   * @param tsr
   * @return
   */
  public TimeStampRequest createCorrespondingTSQ(byte[] file, TimeStampResponse tsr) {
    // get hash algorithm
    ASN1ObjectIdentifier algID =
        tsr.getTimeStampToken().getTimeStampInfo().getMessageImprintAlgOID();
    GeneralDigest digestAlgorithm = getDigestAlg(algID);

    logger.info(
        "The timestamp's algorithm was recognized as {}.", digestAlgorithm.getAlgorithmName());

    // create new hashed request
    byte[] digest = calculateMessageDigest(file, digestAlgorithm);
    TimeStampRequest tsq = getTSRequest(digest, algID);

    return tsq;
  }
 /**
  * prints details of received TimeStamp
  *
  * @param tsr {@link TimeStampResponse}
  */
 private void logResponse(final TimeStampResponse tsr) {
   logger.info("Timestamp: {}", tsr.getTimeStampToken().getTimeStampInfo().getGenTime());
   logger.info("TSA: {}", tsr.getTimeStampToken().getTimeStampInfo().getTsa());
   logger.info("Serial number: {}", tsr.getTimeStampToken().getTimeStampInfo().getSerialNumber());
   logger.info("Policy: {}", tsr.getTimeStampToken().getTimeStampInfo().getPolicy());
 }
  public byte[] getTimeStampToken(byte[] digest)
      throws NoSuchAlgorithmException, UnsupportedEncodingException, TSPException {

    TimeStampRequestGenerator tsqGenerator = new TimeStampRequestGenerator();
    tsqGenerator.setCertReq(true);
    if (tsaOid != null) tsqGenerator.setReqPolicy(tsaOid);
    TimeStampRequest tsReq =
        tsqGenerator.generate(TSPAlgorithms.SHA1, digest, BigInteger.valueOf(100));
    byte[] respBytes;
    try {
      byte[] requestBytes = tsReq.getEncoded();
      URL url = new URL(tsaURL);
      HttpsURLConnection tsaConnection = (HttpsURLConnection) url.openConnection();
      String user_pass = Base64.encodeToString((tsaUsername + ":" + tsaPassword).getBytes(), 0);
      tsaConnection.setRequestProperty("Authorization", "Basic " + user_pass);
      tsaConnection.setDoInput(true);
      tsaConnection.setDoOutput(true);
      tsaConnection.setUseCaches(false);
      tsaConnection.setRequestProperty("Content-Type", "application/timestamp-query");
      tsaConnection.setRequestProperty("Content-Transfer-Encoding", "binary");
      OutputStream out = tsaConnection.getOutputStream();
      out.write(requestBytes);
      out.close();
      InputStream inp = tsaConnection.getInputStream();
      ByteArrayOutputStream baos = new ByteArrayOutputStream();
      byte[] buffer = new byte[1024];
      int bytesRead = 0;
      while ((bytesRead = inp.read(buffer, 0, buffer.length)) >= 0) {
        baos.write(buffer, 0, bytesRead);
      }
      respBytes = baos.toByteArray();
      String encoding = tsaConnection.getContentEncoding();
      if (encoding != null && encoding.equalsIgnoreCase("base64")) {
        respBytes = Base64.decode(new String(respBytes), 0);
      }

      if (respBytes == null) {
        String error = "Error: Impossible to get TSA response";
        Log.e(TAG, error);
      }
      TimeStampResponse tsRes = new TimeStampResponse(respBytes);

      tsRes.validate(tsReq);
      PKIFailureInfo failure = tsRes.getFailInfo();
      int value = (failure == null) ? 0 : failure.intValue();
      if (value != 0) {
        String error = "Error: Invalid TSA response (" + tsRes.getStatusString() + ")";
        Log.e(TAG, error);
        return null;
      }
      TimeStampToken myTSToken = tsRes.getTimeStampToken();
      if (myTSToken == null) {
        String error = "Error: Invalid TSA response (NULL)";
        Log.e(TAG, error);
        return null;
      }
      return myTSToken.getEncoded();
    } catch (IOException | TSPException e) {
      Log.e(TAG, e.getMessage());
    }
    return null;
  }
  /**
   * Main method for validating files with stamps. It serves as an example of whole process in one
   * go.
   *
   * @param originalFile
   * @param timeStamp
   * @throws IOException
   * @throws TSPException
   * @throws CertificateException
   * @throws CertificateEncodingException
   * @throws OperatorCreationException
   */
  public void verify(InputStream originalFile, InputStream timeStamp)
      throws IOException, TSPException, CertificateException, CertificateEncodingException,
          OperatorCreationException {
    logger.entry();

    // open files
    byte[] file = getBytesFromInputStream(originalFile);
    TimeStampResponse tsr = parseTSR(timeStamp);

    logger.info("The timestamp was sucessfully opened.");
    logResponse(tsr);

    // get hash algorithm
    ASN1ObjectIdentifier algID =
        tsr.getTimeStampToken().getTimeStampInfo().getMessageImprintAlgOID();
    GeneralDigest digestAlgorithm = getDigestAlg(algID);

    logger.info(
        "The timestamp's algorithm was recognized as {}.", digestAlgorithm.getAlgorithmName());

    // create new hashed request
    byte[] digest = calculateMessageDigest(file, digestAlgorithm);
    TimeStampRequest tsq = getTSRequest(digest, algID);

    logger.info(
        "The timestamp fits the file (the file was not changed), now verifying certificates..");

    InputStream is = null;

    if (is == null) {
      throw new UnsupportedOperationException(
          "Timestamp fits the file (the file was not changed), certificate not implemented yet.");
    }

    // <editor-fold defaultstate="collapsed" desc="varianta 1 - ze souboru">
    CertificateFactory factory;
    X509Certificate cert;
    try {
      factory = CertificateFactory.getInstance("X.509");
      cert = (X509Certificate) factory.generateCertificate(null); // TODO: get inputstream
    } catch (CertificateException e) {
      logger.catching(e);
      throw e;
    }

    // RSA Signature processing with BC
    X509CertificateHolder holder;
    SignerInformationVerifier siv;
    try {
      holder = new X509CertificateHolder(cert.getEncoded());
      siv =
          new BcRSASignerInfoVerifierBuilder(
                  new DefaultCMSSignatureAlgorithmNameGenerator(),
                      new DefaultSignatureAlgorithmIdentifierFinder(),
                  new DefaultDigestAlgorithmIdentifierFinder(), new BcDigestCalculatorProvider())
              .build(holder);
    } catch (CertificateEncodingException | OperatorCreationException e) {
      logger.catching(e);
      throw e;
    }

    // Signature processing with JCA and other provider
    // X509CertificateHolder holderJca = new JcaX509CertificateHolder(cert);
    // SignerInformationVerifier sivJca = new
    // JcaSimpleSignerInfoVerifierBuilder().setProvider("anotherprovider").build(holderJca);

    try {
      tsr.getTimeStampToken().validate(siv);
    } catch (TSPException e) {
      logger.catching(e);
      throw e;
    }
    /* konec varianty 1 */
    // </editor-fold>

    // <editor-fold defaultstate="collapsed" desc="varianta 2 - z razitka">
    /*/ get certificates
            CollectionStore certs = (CollectionStore) tst.getCertificates();
            SignerInformationStore signers = tst.toCMSSignedData().getSignerInfos();

            int certsCount = 0;
            for (Iterator it = certs.iterator(); it.hasNext();) {
                certsCount++; // stupid hack to get actual number of certificates
            }
            if (certsCount < 1) {
                logger.error("No certificate found.");
                return;
            }

            for (SignerInformation signer : signers) {
                Collection<X509Certificate> col = certs.getMatches(signer.getSID());
                X509Certificate[] signerCerts = new X509Certificate[0];
                col.toArray(signerCerts);

                if (signerCerts.length != 1) {
                    logger.error("Expected only one certificate per signer.");
                    return;
                }

                try {
                    signerCerts[0].checkValidity();
                } catch (CertificateExpiredException | CertificateNotYetValidException ex) {
                    java.util.logging.Logger.getLogger(TSAConnector.class.getName()).log(Level.SEVERE, null, ex);
                }

    //            signer.verify(signerCerts[0]); // should verify that the timestamp is signed correctly
            }
            /* konec varianty 2 */
    // </editor-fold>

    logger.info("All certificates successfully verified, the timestamp is trusted.");
    logger.exit();
  }
  public byte[] timeStamp(byte[] data, RevocationData revocationData) throws Exception {
    // digest the message
    MessageDigest messageDigest = MessageDigest.getInstance(this.digestAlgo);
    byte[] digest = messageDigest.digest(data);

    // generate the TSP request
    BigInteger nonce = new BigInteger(128, new SecureRandom());
    TimeStampRequestGenerator requestGenerator = new TimeStampRequestGenerator();
    requestGenerator.setCertReq(true);
    if (null != this.requestPolicy) {
      requestGenerator.setReqPolicy(this.requestPolicy);
    }
    TimeStampRequest request = requestGenerator.generate(this.digestAlgoOid, digest, nonce);
    byte[] encodedRequest = request.getEncoded();

    // create the HTTP client
    HttpClient httpClient = new HttpClient();
    if (null != this.username) {
      Credentials credentials = new UsernamePasswordCredentials(this.username, this.password);
      httpClient.getState().setCredentials(AuthScope.ANY, credentials);
    }
    if (null != this.proxyHost) {
      httpClient.getHostConfiguration().setProxy(this.proxyHost, this.proxyPort);
    }

    // create the HTTP POST request
    PostMethod postMethod = new PostMethod(this.tspServiceUrl);
    RequestEntity requestEntity =
        new ByteArrayRequestEntity(encodedRequest, "application/timestamp-query");
    postMethod.addRequestHeader("User-Agent", this.userAgent);
    postMethod.setRequestEntity(requestEntity);

    // invoke TSP service
    int statusCode = httpClient.executeMethod(postMethod);
    if (HttpStatus.SC_OK != statusCode) {
      LOG.error("Error contacting TSP server " + this.tspServiceUrl);
      throw new Exception("Error contacting TSP server " + this.tspServiceUrl);
    }

    // HTTP input validation
    Header responseContentTypeHeader = postMethod.getResponseHeader("Content-Type");
    if (null == responseContentTypeHeader) {
      throw new RuntimeException("missing Content-Type header");
    }
    String contentType = responseContentTypeHeader.getValue();
    if (!contentType.startsWith("application/timestamp-reply")) {
      LOG.debug("response content: " + postMethod.getResponseBodyAsString());
      throw new RuntimeException("invalid Content-Type: " + contentType);
    }
    if (0 == postMethod.getResponseContentLength()) {
      throw new RuntimeException("Content-Length is zero");
    }

    // TSP response parsing and validation
    InputStream inputStream = postMethod.getResponseBodyAsStream();
    TimeStampResponse timeStampResponse = new TimeStampResponse(inputStream);
    timeStampResponse.validate(request);

    if (0 != timeStampResponse.getStatus()) {
      LOG.debug("status: " + timeStampResponse.getStatus());
      LOG.debug("status string: " + timeStampResponse.getStatusString());
      PKIFailureInfo failInfo = timeStampResponse.getFailInfo();
      if (null != failInfo) {
        LOG.debug("fail info int value: " + failInfo.intValue());
        if (PKIFailureInfo.unacceptedPolicy == failInfo.intValue()) {
          LOG.debug("unaccepted policy");
        }
      }
      throw new RuntimeException(
          "timestamp response status != 0: " + timeStampResponse.getStatus());
    }
    TimeStampToken timeStampToken = timeStampResponse.getTimeStampToken();
    SignerId signerId = timeStampToken.getSID();
    BigInteger signerCertSerialNumber = signerId.getSerialNumber();
    X500Principal signerCertIssuer = signerId.getIssuer();
    LOG.debug("signer cert serial number: " + signerCertSerialNumber);
    LOG.debug("signer cert issuer: " + signerCertIssuer);

    // TSP signer certificates retrieval
    CertStore certStore =
        timeStampToken.getCertificatesAndCRLs("Collection", BouncyCastleProvider.PROVIDER_NAME);
    Collection<? extends Certificate> certificates = certStore.getCertificates(null);
    X509Certificate signerCert = null;
    Map<String, X509Certificate> certificateMap = new HashMap<String, X509Certificate>();
    for (Certificate certificate : certificates) {
      X509Certificate x509Certificate = (X509Certificate) certificate;
      if (signerCertIssuer.equals(x509Certificate.getIssuerX500Principal())
          && signerCertSerialNumber.equals(x509Certificate.getSerialNumber())) {
        signerCert = x509Certificate;
      }
      String ski = Hex.encodeHexString(getSubjectKeyId(x509Certificate));
      certificateMap.put(ski, x509Certificate);
      LOG.debug(
          "embedded certificate: " + x509Certificate.getSubjectX500Principal() + "; SKI=" + ski);
    }

    // TSP signer cert path building
    if (null == signerCert) {
      throw new RuntimeException("TSP response token has no signer certificate");
    }
    List<X509Certificate> tspCertificateChain = new LinkedList<X509Certificate>();
    X509Certificate certificate = signerCert;
    do {
      LOG.debug("adding to certificate chain: " + certificate.getSubjectX500Principal());
      tspCertificateChain.add(certificate);
      if (certificate.getSubjectX500Principal().equals(certificate.getIssuerX500Principal())) {
        break;
      }
      String aki = Hex.encodeHexString(getAuthorityKeyId(certificate));
      certificate = certificateMap.get(aki);
    } while (null != certificate);

    // verify TSP signer signature
    timeStampToken.validate(tspCertificateChain.get(0), BouncyCastleProvider.PROVIDER_NAME);

    // verify TSP signer certificate
    this.validator.validate(tspCertificateChain, revocationData);

    LOG.debug("time-stamp token time: " + timeStampToken.getTimeStampInfo().getGenTime());

    byte[] timestamp = timeStampToken.getEncoded();
    return timestamp;
  }