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

Introduction

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

Prototype

public Base64() 

Source Link

Document

Creates a Base64 codec used for decoding (all modes) and encoding in URL-unsafe mode.

Usage

From source file:fi.aalto.seqpig.filter.CoordinateFilter.java

protected void decodeSAMFileHeader() {
    try {//from   w w  w. j a  va  2 s .  com
        Base64 codec = new Base64();
        Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
        String datastr;

        datastr = p.getProperty("samfileheader");
        byte[] buffer = codec.decodeBase64(datastr);
        ByteArrayInputStream bstream = new ByteArrayInputStream(buffer);
        ObjectInputStream ostream = new ObjectInputStream(bstream);

        this.samfileheader = (String) ostream.readObject();
    } catch (Exception e) {
    }

    this.samfileheader_decoded = getSAMFileHeader();
}

---

From source file:cross.io.misc.Base64Util.java

/**
 *
 * @param floatList//from   w  ww.  j av a  2 s.c  o  m
 * @param bigEndian
 * @return
 * @throws EncoderException
 */
public static String floatListToBase64String(final List<Float> floatList, final boolean bigEndian)
        throws EncoderException {
    final byte[] raw = Base64Util.floatListToByteArray(floatList, bigEndian);
    final Base64 base64 = new Base64();
    final byte[] encoded = base64.encode(raw);
    return new String(encoded);
}

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From source file:com.novartis.opensource.yada.adaptor.RESTAdaptor.java

/**
 * Gets the input stream from the {@link URLConnection} and stores it in 
 * the {@link YADAQueryResult} in {@code yq}
 * @see com.novartis.opensource.yada.adaptor.Adaptor#execute(com.novartis.opensource.yada.YADAQuery)
 *///from ww w  . j  a v a  2 s .  co  m
@Override
public void execute(YADAQuery yq) throws YADAAdaptorExecutionException {
    boolean isPostPutPatch = this.method.equals(YADARequest.METHOD_POST)
            || this.method.equals(YADARequest.METHOD_PUT) || this.method.equals(YADARequest.METHOD_PATCH);
    resetCountParameter(yq);
    int rows = yq.getData().size() > 0 ? yq.getData().size() : 1;
    /*
     * Remember:
     * A row is an set of YADA URL parameter values, e.g.,
     * 
     *  x,y,z in this:      
     *    ...yada/q/queryname/p/x,y,z
     *  so 1 row
     *    
     *  or each of {col1:x,col2:y,col3:z} and {col1:a,col2:b,col3:c} in this:
     *    ...j=[{qname:queryname,DATA:[{col1:x,col2:y,col3:z},{col1:a,col2:b,col3:c}]}]
     *  so 2 rows
     */
    for (int row = 0; row < rows; row++) {
        String result = "";

        // creates result array and assigns it
        yq.setResult();
        YADAQueryResult yqr = yq.getResult();

        String urlStr = yq.getUrl(row);

        for (int i = 0; i < yq.getParamCount(row); i++) {
            Matcher m = PARAM_URL_RX.matcher(urlStr);
            if (m.matches()) {
                String param = yq.getVals(row).get(i);
                urlStr = urlStr.replaceFirst(PARAM_SYMBOL_RX, m.group(1) + param);
            }
        }

        l.debug("REST url w/params: [" + urlStr + "]");
        try {
            URL url = new URL(urlStr);
            URLConnection conn = null;

            if (this.hasProxy()) {
                String[] proxyStr = this.proxy.split(":");
                Proxy proxySvr = new Proxy(Proxy.Type.HTTP,
                        new InetSocketAddress(proxyStr[0], Integer.parseInt(proxyStr[1])));
                conn = url.openConnection(proxySvr);
            } else {
                conn = url.openConnection();
            }

            // basic auth
            if (url.getUserInfo() != null) {
                //TODO issue with '@' sign in pw, must decode first
                String basicAuth = "Basic " + new String(new Base64().encode(url.getUserInfo().getBytes()));
                conn.setRequestProperty("Authorization", basicAuth);
            }

            // cookies
            if (yq.getCookies() != null && yq.getCookies().size() > 0) {
                String cookieStr = "";
                for (HttpCookie cookie : yq.getCookies()) {
                    cookieStr += cookie.getName() + "=" + cookie.getValue() + ";";
                }
                conn.setRequestProperty("Cookie", cookieStr);
            }

            if (yq.getHttpHeaders() != null && yq.getHttpHeaders().length() > 0) {
                l.debug("Processing custom headers...");
                @SuppressWarnings("unchecked")
                Iterator<String> keys = yq.getHttpHeaders().keys();
                while (keys.hasNext()) {
                    String name = keys.next();
                    String value = yq.getHttpHeaders().getString(name);
                    l.debug("Custom header: " + name + " : " + value);
                    conn.setRequestProperty(name, value);
                    if (name.equals(X_HTTP_METHOD_OVERRIDE) && value.equals(YADARequest.METHOD_PATCH)) {
                        l.debug("Resetting method to [" + YADARequest.METHOD_POST + "]");
                        this.method = YADARequest.METHOD_POST;
                    }
                }
            }

            HttpURLConnection hConn = (HttpURLConnection) conn;
            if (!this.method.equals(YADARequest.METHOD_GET)) {
                hConn.setRequestMethod(this.method);
                if (isPostPutPatch) {
                    //TODO make YADA_PAYLOAD case-insensitive and create an alias for it, e.g., ypl
                    // NOTE: YADA_PAYLOAD is a COLUMN NAME found in a JSONParams DATA object.  It 
                    //       is not a YADA param
                    String payload = yq.getDataRow(row).get(YADA_PAYLOAD)[0];
                    hConn.setDoOutput(true);
                    OutputStreamWriter writer;
                    writer = new OutputStreamWriter(conn.getOutputStream());
                    writer.write(payload.toString());
                    writer.flush();
                }
            }

            // debug
            Map<String, List<String>> map = conn.getHeaderFields();
            for (Map.Entry<String, List<String>> entry : map.entrySet()) {
                l.debug("Key : " + entry.getKey() + " ,Value : " + entry.getValue());
            }

            try (BufferedReader in = new BufferedReader(new InputStreamReader(hConn.getInputStream()))) {
                String inputLine;
                while ((inputLine = in.readLine()) != null) {
                    result += String.format("%1s%n", inputLine);
                }
            }
            yqr.addResult(row, result);
        } catch (MalformedURLException e) {
            String msg = "Unable to access REST source due to a URL issue.";
            throw new YADAAdaptorExecutionException(msg, e);
        } catch (IOException e) {
            String msg = "Unable to read REST response.";
            throw new YADAAdaptorExecutionException(msg, e);
        }
    }
}

---

From source file:com.hazelcast.qasonar.utils.Utils.java

public static String getBasicAuthString(String username, String password) {
    String authString = username + ":" + password;
    return "Basic " + new String(new Base64().encode(authString.getBytes()));
}

---

From source file:com.ligadata.EncryptUtils.EncryptionUtil.java

/**
 * Decode(Base64 decoding) given string to a byte array
 * /*from  ww  w  .  j a  v  a  2  s.  com*/
 * @param s
 *          : an encoded string 
 * @return byte array
 * @throws java.lang.Exception and exception is thrown
 */

public static byte[] decode(String s) throws Exception {
    try {
        Base64 base64 = new Base64();
        byte[] decoded = base64.decode(s.getBytes());
        return decoded;
    } catch (Exception e) {
        logger.error("Failed to decode a byte array", e);
        throw e;
    }
}

---

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

@Override
public void putNext(Tuple f) throws IOException {

    if (selectedBAMAttributes == null || allBAMFieldNames == null) {
        try {//from w w w  .j av a  2s.  co m
            Base64 codec = new Base64();
            Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
            String datastr;

            datastr = p.getProperty("selectedBAMAttributes");
            byte[] buffer = codec.decodeBase64(datastr);
            ByteArrayInputStream bstream = new ByteArrayInputStream(buffer);
            ObjectInputStream ostream = new ObjectInputStream(bstream);

            selectedBAMAttributes = (HashMap<String, Integer>) ostream.readObject();

            datastr = p.getProperty("allBAMFieldNames");
            buffer = codec.decodeBase64(datastr);
            bstream = new ByteArrayInputStream(buffer);
            ostream = new ObjectInputStream(bstream);

            allBAMFieldNames = (HashMap<String, Integer>) ostream.readObject();
        } catch (ClassNotFoundException e) {
            throw new IOException(e);
        }
    }

    SAMRecordWritable samrecwrite = new SAMRecordWritable();
    SAMRecord samrec = new SAMRecord(samfileheader_decoded);

    int index = getFieldIndex("name", allBAMFieldNames);

    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setReadName((String) f.get(index));
    }

    index = getFieldIndex("start", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setAlignmentStart(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("read", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setReadString((String) f.get(index));
    }

    index = getFieldIndex("cigar", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setCigarString((String) f.get(index));
    }

    index = getFieldIndex("basequal", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setBaseQualityString((String) f.get(index));
    }

    index = getFieldIndex("flags", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setFlags(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("insertsize", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setInferredInsertSize(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("mapqual", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setMappingQuality(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("matestart", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setMateAlignmentStart(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("materefindex", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setMateReferenceIndex(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("refindex", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setReferenceIndex(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("attributes", allBAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.MAP) {
        Set<Map.Entry<String, Object>> set = ((HashMap<String, Object>) f.get(index)).entrySet();

        for (Map.Entry<String, Object> pairs : set) {
            String attributeName = pairs.getKey();

            samrec.setAttribute(attributeName.toUpperCase(), pairs.getValue());
        }
    }

    samrec.hashCode(); // causes eagerDecode()
    samrecwrite.set(samrec);

    try {
        writer.write(null, samrecwrite);
    } catch (InterruptedException e) {
        throw new IOException(e);
    }
}

---

From source file:com.titilink.camel.rest.util.OtherUtil.java

/**
 * BASE64?/*from   w w  w.  j  a va 2 s.c om*/
 *
 * @param str --?
 * @return --??
 */
public static String strBase64Encode(String str) {
    Base64 b64 = new Base64();
    byte[] b = b64.encode(str.getBytes());
    return new String(b);
}

---

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

@Override
public void putNext(Tuple f) throws IOException {

    if (selectedSAMAttributes == null || allSAMFieldNames == null) {
        try {/*from w  w w .  j a  v a2  s .c  o  m*/
            Base64 codec = new Base64();
            Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
            String datastr;

            datastr = p.getProperty("selectedSAMAttributes");
            byte[] buffer = codec.decodeBase64(datastr);
            ByteArrayInputStream bstream = new ByteArrayInputStream(buffer);
            ObjectInputStream ostream = new ObjectInputStream(bstream);

            selectedSAMAttributes = (HashMap<String, Integer>) ostream.readObject();

            datastr = p.getProperty("allSAMFieldNames");
            buffer = codec.decodeBase64(datastr);
            bstream = new ByteArrayInputStream(buffer);
            ostream = new ObjectInputStream(bstream);

            allSAMFieldNames = (HashMap<String, Integer>) ostream.readObject();
        } catch (ClassNotFoundException e) {
            throw new IOException(e);
        }
    }

    SAMRecordWritable samrecwrite = new SAMRecordWritable();
    SAMRecord samrec = new SAMRecord(samfileheader_decoded);

    int index = getFieldIndex("name", allSAMFieldNames);

    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setReadName((String) f.get(index));
    }

    index = getFieldIndex("start", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setAlignmentStart(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("read", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setReadString((String) f.get(index));
    }

    index = getFieldIndex("cigar", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setCigarString((String) f.get(index));
    }

    index = getFieldIndex("basequal", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.CHARARRAY) {
        samrec.setBaseQualityString((String) f.get(index));
    }

    index = getFieldIndex("flags", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setFlags(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("insertsize", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setInferredInsertSize(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("mapqual", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setMappingQuality(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("matestart", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setMateAlignmentStart(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("materefindex", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setMateReferenceIndex(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("refindex", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.INTEGER) {
        samrec.setReferenceIndex(((Integer) f.get(index)).intValue());
    }

    index = getFieldIndex("attributes", allSAMFieldNames);
    if (index > -1 && DataType.findType(f.get(index)) == DataType.MAP) {
        Set<Map.Entry<String, Object>> set = ((HashMap<String, Object>) f.get(index)).entrySet();

        for (Map.Entry<String, Object> pairs : set) {
            String attributeName = pairs.getKey();

            samrec.setAttribute(attributeName.toUpperCase(), pairs.getValue());
        }
    }

    samrec.hashCode(); // causes eagerDecode()
    samrecwrite.set(samrec);

    try {
        writer.write(null, samrecwrite);
    } catch (InterruptedException e) {
        throw new IOException(e);
    }
}

---

From source file:com.amazonbird.amazonproxy.SignedRequestsHelper.java

/**
 * Compute the HMAC.//from w  ww  .  j  a v a 2 s.c om
 *  
 * @param stringToSign  String to compute the HMAC over.
 * @return              base64-encoded hmac value.
 */
private String hmac(String stringToSign) {
    String signature = null;
    byte[] data;
    byte[] rawHmac;
    try {
        data = stringToSign.getBytes(UTF8_CHARSET);
        rawHmac = mac.doFinal(data);
        Base64 encoder = new Base64();
        signature = new String(encoder.encode(rawHmac));
    } catch (UnsupportedEncodingException e) {
        throw new RuntimeException(UTF8_CHARSET + " is unsupported!", e);
    }
    return signature.trim();
}

---

From source file:com.cs194.windowshopping.SignedRequestsHelper.java

/**
 * Compute the HMAC.//from  w  w w .j  ava  2 s  .c om
 *  
 * @param stringToSign  String to compute the HMAC over.
 * @return              base64-encoded hmac value.
 */
private String hmac(String stringToSign) {
    String signature = null;
    byte[] data;
    byte[] rawHmac;
    try {
        data = stringToSign.getBytes(UTF8_CHARSET);
        rawHmac = mac.doFinal(data);
        Base64 encoder = new Base64();
        //            Base64 encoder = new Base64(76, new byte[0]);
        signature = new String(encoder.encode(rawHmac));
    } catch (UnsupportedEncodingException e) {
        throw new RuntimeException(UTF8_CHARSET + " is unsupported!", e);
    }
    return signature;
}

---

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