Example usage for org.apache.commons.codec.binary Base64 encodeBase64String

List of usage examples for org.apache.commons.codec.binary Base64 encodeBase64String

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Introduction

In this page you can find the example usage for org.apache.commons.codec.binary Base64 encodeBase64String.

Prototype

public static String encodeBase64String(final byte[] binaryData)

Source Link

Document

Encodes binary data using the base64 algorithm but does not chunk the output.

Usage

From source file:fi.aalto.seqpig.io.BamStorer.java

public BamStorer(String samfileheaderfilename) {

    String str = "";
    this.samfileheader = "";

    try {/*from  www  .  j a  v a2 s .c  o m*/
        Configuration conf = UDFContext.getUDFContext().getJobConf();

        // see https://issues.apache.org/jira/browse/PIG-2576
        if (conf == null || conf.get("mapred.task.id") == null) {
            // we are running on the frontend
            decodeSAMFileHeader();
            return;
        }

        URI uri = new URI(samfileheaderfilename);
        FileSystem fs = FileSystem.get(uri, conf);

        BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(samfileheaderfilename))));

        while (true) {
            str = in.readLine();

            if (str == null)
                break;
            else
                this.samfileheader += str + "\n";
        }

        in.close();
    } catch (Exception e) {
        System.out.println("ERROR: could not read BAM header from file " + samfileheaderfilename);
        System.out.println("exception was: " + e.toString());
    }

    try {
        Base64 codec = new Base64();
        Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());

        ByteArrayOutputStream bstream = new ByteArrayOutputStream();
        ObjectOutputStream ostream = new ObjectOutputStream(bstream);
        ostream.writeObject(this.samfileheader);
        ostream.close();
        String datastr = codec.encodeBase64String(bstream.toByteArray());
        p.setProperty("samfileheader", datastr);
    } catch (Exception e) {
        System.out.println("ERROR: Unable to store SAMFileHeader in BamStorer!");
    }

    this.samfileheader_decoded = getSAMFileHeader();
}

From source file:fi.aalto.seqpig.io.BamStorer.java

@Override
public void checkSchema(ResourceSchema s) throws IOException {

    selectedBAMAttributes = new HashMap<String, Integer>();
    allBAMFieldNames = new HashMap<String, Integer>();
    String[] fieldNames = s.fieldNames();

    for (int i = 0; i < fieldNames.length; i++) {
        System.out.println("field: " + fieldNames[i]);
        allBAMFieldNames.put(fieldNames[i], new Integer(i));

        if (fieldNames[i].equalsIgnoreCase("RG") || fieldNames[i].equalsIgnoreCase("LB")
                || fieldNames[i].equalsIgnoreCase("PU") || fieldNames[i].equalsIgnoreCase("PG")
                || fieldNames[i].equalsIgnoreCase("AS") || fieldNames[i].equalsIgnoreCase("SQ")
                || fieldNames[i].equalsIgnoreCase("MQ") || fieldNames[i].equalsIgnoreCase("NM")
                || fieldNames[i].equalsIgnoreCase("H0") || fieldNames[i].equalsIgnoreCase("H1")
                || fieldNames[i].equalsIgnoreCase("H2") || fieldNames[i].equalsIgnoreCase("UQ")
                || fieldNames[i].equalsIgnoreCase("PQ") || fieldNames[i].equalsIgnoreCase("NH")
                || fieldNames[i].equalsIgnoreCase("IH") || fieldNames[i].equalsIgnoreCase("HI")
                || fieldNames[i].equalsIgnoreCase("MD") || fieldNames[i].equalsIgnoreCase("CS")
                || fieldNames[i].equalsIgnoreCase("CQ") || fieldNames[i].equalsIgnoreCase("CM")
                || fieldNames[i].equalsIgnoreCase("R2") || fieldNames[i].equalsIgnoreCase("Q2")
                || fieldNames[i].equalsIgnoreCase("S2") || fieldNames[i].equalsIgnoreCase("CC")
                || fieldNames[i].equalsIgnoreCase("CP") || fieldNames[i].equalsIgnoreCase("SM")
                || fieldNames[i].equalsIgnoreCase("AM") || fieldNames[i].equalsIgnoreCase("MF")
                || fieldNames[i].equalsIgnoreCase("E2") || fieldNames[i].equalsIgnoreCase("U2")
                || fieldNames[i].equalsIgnoreCase("OQ")) {

            System.out.println("selected attribute: " + fieldNames[i] + " i: " + i);
            selectedBAMAttributes.put(fieldNames[i], new Integer(i));
        }//  w  w w  .  jav a  2 s . c om
    }

    if (!(allBAMFieldNames.containsKey("name") && allBAMFieldNames.containsKey("start")
            && allBAMFieldNames.containsKey("end") && allBAMFieldNames.containsKey("read")
            && allBAMFieldNames.containsKey("cigar") && allBAMFieldNames.containsKey("basequal")
            && allBAMFieldNames.containsKey("flags") && allBAMFieldNames.containsKey("insertsize")
            && allBAMFieldNames.containsKey("mapqual") && allBAMFieldNames.containsKey("matestart")
            && allBAMFieldNames.containsKey("materefindex") && allBAMFieldNames.containsKey("refindex")))
        throw new IOException("Error: Incorrect BAM tuple-field name or compulsory field missing");

    Base64 codec = new Base64();
    Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
    String datastr;

    ByteArrayOutputStream bstream = new ByteArrayOutputStream();
    ObjectOutputStream ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(selectedBAMAttributes);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("selectedBAMAttributes", datastr);

    bstream = new ByteArrayOutputStream();
    ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(allBAMFieldNames);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("allBAMFieldNames", datastr);
}

From source file:fi.aalto.seqpig.io.SamStorer.java

public SamStorer(String samfileheaderfilename) {

    String str = "";
    this.samfileheader = "";

    try {/*from w w  w. j  a  va2 s  .c om*/
        Configuration conf = UDFContext.getUDFContext().getJobConf();

        // see https://issues.apache.org/jira/browse/PIG-2576
        if (conf == null || conf.get("mapred.task.id") == null) {
            // we are running on the frontend
            decodeSAMFileHeader();
            return;
        }

        URI uri = new URI(samfileheaderfilename);
        FileSystem fs = FileSystem.get(uri, conf);

        BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(samfileheaderfilename))));

        while (true) {
            str = in.readLine();

            if (str == null)
                break;
            else
                this.samfileheader += str + "\n";
        }

        in.close();
    } catch (Exception e) {
        System.out.println("ERROR: could not read SAM header from file " + samfileheaderfilename);
        System.out.println("exception was: " + e.toString());
    }

    try {
        Base64 codec = new Base64();
        Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());

        ByteArrayOutputStream bstream = new ByteArrayOutputStream();
        ObjectOutputStream ostream = new ObjectOutputStream(bstream);
        ostream.writeObject(this.samfileheader);
        ostream.close();

        String datastr = codec.encodeBase64String(bstream.toByteArray());
        p.setProperty("samfileheader", datastr);
    } catch (Exception e) {
        System.out.println("ERROR: Unable to store SAMFileHeader in BamStorer!");
    }

    this.samfileheader_decoded = getSAMFileHeader();
}

From source file:fi.aalto.seqpig.io.SamStorer.java

@Override
public void checkSchema(ResourceSchema s) throws IOException {

    selectedSAMAttributes = new HashMap<String, Integer>();
    allSAMFieldNames = new HashMap<String, Integer>();
    String[] fieldNames = s.fieldNames();

    for (int i = 0; i < fieldNames.length; i++) {
        System.out.println("field: " + fieldNames[i]);
        allSAMFieldNames.put(fieldNames[i], new Integer(i));

        if (fieldNames[i].equalsIgnoreCase("RG") || fieldNames[i].equalsIgnoreCase("LB")
                || fieldNames[i].equalsIgnoreCase("PU") || fieldNames[i].equalsIgnoreCase("PG")
                || fieldNames[i].equalsIgnoreCase("AS") || fieldNames[i].equalsIgnoreCase("SQ")
                || fieldNames[i].equalsIgnoreCase("MQ") || fieldNames[i].equalsIgnoreCase("NM")
                || fieldNames[i].equalsIgnoreCase("H0") || fieldNames[i].equalsIgnoreCase("H1")
                || fieldNames[i].equalsIgnoreCase("H2") || fieldNames[i].equalsIgnoreCase("UQ")
                || fieldNames[i].equalsIgnoreCase("PQ") || fieldNames[i].equalsIgnoreCase("NH")
                || fieldNames[i].equalsIgnoreCase("IH") || fieldNames[i].equalsIgnoreCase("HI")
                || fieldNames[i].equalsIgnoreCase("MD") || fieldNames[i].equalsIgnoreCase("CS")
                || fieldNames[i].equalsIgnoreCase("CQ") || fieldNames[i].equalsIgnoreCase("CM")
                || fieldNames[i].equalsIgnoreCase("R2") || fieldNames[i].equalsIgnoreCase("Q2")
                || fieldNames[i].equalsIgnoreCase("S2") || fieldNames[i].equalsIgnoreCase("CC")
                || fieldNames[i].equalsIgnoreCase("CP") || fieldNames[i].equalsIgnoreCase("SM")
                || fieldNames[i].equalsIgnoreCase("AM") || fieldNames[i].equalsIgnoreCase("MF")
                || fieldNames[i].equalsIgnoreCase("E2") || fieldNames[i].equalsIgnoreCase("U2")
                || fieldNames[i].equalsIgnoreCase("OQ")) {

            System.out.println("selected attribute: " + fieldNames[i] + " i: " + i);
            selectedSAMAttributes.put(fieldNames[i], new Integer(i));
        }//w  ww  .  ja  v a  2  s .  c  o  m
    }

    if (!(allSAMFieldNames.containsKey("name") && allSAMFieldNames.containsKey("start")
            && allSAMFieldNames.containsKey("end") && allSAMFieldNames.containsKey("read")
            && allSAMFieldNames.containsKey("cigar") && allSAMFieldNames.containsKey("basequal")
            && allSAMFieldNames.containsKey("flags") && allSAMFieldNames.containsKey("insertsize")
            && allSAMFieldNames.containsKey("mapqual") && allSAMFieldNames.containsKey("matestart")
            && allSAMFieldNames.containsKey("materefindex") && allSAMFieldNames.containsKey("refindex")))
        throw new IOException("Error: Incorrect SAM tuple-field name or compulsory field missing");

    Base64 codec = new Base64();
    Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
    String datastr;

    ByteArrayOutputStream bstream = new ByteArrayOutputStream();
    ObjectOutputStream ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(selectedSAMAttributes);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("selectedSAMAttributes", datastr);

    bstream = new ByteArrayOutputStream();
    ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(allSAMFieldNames);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("allSAMFieldNames", datastr);
}

From source file:com.sshutils.utils.CryptHelper.java

public static String encrypt(String strToEncrypt) {
    try {//from w  ww.  j  av a 2s  . c om

        Cipher cipher = Cipher.getInstance(ENCRYPT_TYPE, "BC");
        final SecretKeySpec secretKey = new SecretKeySpec(key, "AES");
        cipher.init(Cipher.ENCRYPT_MODE, secretKey);
        final String encryptedString = Base64.encodeBase64String(cipher.doFinal(strToEncrypt.getBytes()));
        return encryptedString;
    } catch (Exception e) {
        log.error("Error while encrypting", e);
    }
    return null;

}

From source file:br.com.topsys.cd.applet.AutenticacaoApplet.java

@Override
public void complemento(CertificadoDigital certificadoDigital) {
    try {// w  w w .j av  a2  s.  c om

        JSObject window = JSObject.getWindow(this);
        window.call("setCertificado", new Object[] {
                Base64.encodeBase64String(certificadoDigital.getX509Certificado().getEncoded()) });
        this.closeSuccess();

    } catch (ExcecaoCertificado ex) {
        JOptionPane.showMessageDialog(null, ex.getMessage(), "Aviso", JOptionPane.ERROR_MESSAGE);
        this.closeError();
    }

}

From source file:com.connorbrezinsky.msg.security.Hash.java

/**
 * Computes a salted PBKDF2 hash of given plaintext password suitable for
 * storing in a database. Empty passwords are not supported.
 *///from w  w  w.  j ava 2s  .  com
public static String getSaltedHash(String password) throws Exception {
    byte[] salt = SecureRandom.getInstance("SHA1PRNG").generateSeed(saltLen);
    // store the salt with the password
    return Base64.encodeBase64String(salt) + "$" + hash(password, salt);
}

From source file:com.bloatit.framework.utils.Hash.java

/**
 * From a password and a salt, returns the corresponding digest
 * //from www . ja v a  2s.  co  m
 * @param password The password to encrypt
 * @param salt The salt
 * @return String The digested password in base64
 */
public static String calculateHash(final String password, final String salt) {
    byte[] value = (password + salt).getBytes();
    for (int i = 0; i < ITERATION_NUMBER; i++) {
        value = DigestUtils.sha512(value);
    }
    return Base64.encodeBase64String(value);
}

From source file:com.netsteadfast.greenstep.util.EncryptorUtils.java

public static String encrypt(String key1, String iv1, String value) {
    try {// w  w  w  .  jav  a  2s .  c  o m
        IvParameterSpec iv = new IvParameterSpec(iv1.getBytes(Constants.BASE_ENCODING));
        SecretKeySpec skeySpec = new SecretKeySpec(key1.getBytes(Constants.BASE_ENCODING), "AES");
        Cipher cipher = Cipher.getInstance("AES/CBC/PKCS5PADDING");
        cipher.init(Cipher.ENCRYPT_MODE, skeySpec, iv);
        byte[] encrypted = cipher.doFinal(value.getBytes());
        //System.out.println("encrypted string:" + Base64.encodeBase64String(encrypted));
        return Base64.encodeBase64String(encrypted);
    } catch (Exception ex) {
        ex.printStackTrace();
    }
    return null;
}

From source file:com.liferay.sync.engine.lan.util.LanTokenUtil.java

public static String createEncryptedToken(String lanTokenKey) throws Exception {

    String lanToken = RandomStringUtils.random(32, 0, 0, true, true, null, _secureRandom);

    byte[] bytes = DigestUtils.sha1(lanTokenKey);

    bytes = Arrays.copyOf(bytes, 16);

    Cipher cipher = Cipher.getInstance("AES");

    cipher.init(Cipher.ENCRYPT_MODE, new SecretKeySpec(bytes, "AES"));

    String encryptedToken = Base64
            .encodeBase64String(cipher.doFinal(lanToken.getBytes(Charset.forName("UTF-8"))));

    _lanTokens.add(lanToken);/*ww  w.j  a va2  s. c  o  m*/

    return encryptedToken;
}