List of usage examples for java.nio ByteBuffer flip
public final Buffer flip()
From source file:com.castis.sysComp.PoisConverterSysComp.java
public void parseRegionFile(File file) throws Exception { String line = ""; FileInputStream in = null;// www . j a v a2 s .com Reader isReader = null; LineNumberReader bufReader = null; FileOutputStream fos = null; String fileName = file.getName(); int index = fileName.indexOf("-"); if (index != -1) { fileName = fileName.substring(index + 1, fileName.length()); } String dir = filePolling.getValidFileDirectory(resultDir); String tempDir = dir + "/temp/"; File targetDirectory = new File(CiFileUtil.getReplaceFullPath(tempDir)); if (!targetDirectory.isDirectory()) { CiFileUtil.createDirectory(tempDir); } fos = new FileOutputStream(tempDir + fileName); int byteSize = 2048; ByteBuffer byteBuffer = ByteBuffer.allocateDirect(byteSize); GatheringByteChannel outByteCh = fos.getChannel(); try { in = new FileInputStream(file); isReader = new InputStreamReader(in, "UTF-16LE"); bufReader = new LineNumberReader(isReader); boolean first = true; while ((line = bufReader.readLine()) != null) { byte[] utf8 = line.getBytes("UTF-8"); String string = new String(utf8, "UTF-8"); String data[] = string.split("\t"); if (first == true) { first = false; if (data[0] == null || data[0].contains("region") == false) { throw new DataParsingException("data parsing error(not formatted)"); } continue; } if (data[0] == null || data[0].equals("")) { throw new DataParsingException("data parsing error(region id)"); } if (data[1] == null || data[1].equals("")) { throw new DataParsingException("data parsing error(region name)"); } if (data[2] == null || data[2].equals("")) { throw new DataParsingException("data parsing error(parent id)"); } StringBuffer strBuffer = new StringBuffer(); strBuffer.append(data[0]); strBuffer.append("\t"); strBuffer.append(data[1]); strBuffer.append("\t"); strBuffer.append(data[2]); strBuffer.append("\r\n"); byte[] outByte = null; try { outByte = strBuffer.toString().getBytes("UTF-8"); } catch (UnsupportedEncodingException e2) { e2.printStackTrace(); } byteBuffer.put(outByte); byteBuffer.flip(); try { outByteCh.write(byteBuffer); } catch (IOException e) { } byteBuffer.clear(); } fos.close(); index = fileName.indexOf("_"); String targetDir = resultDir; File sourceFile = new File(tempDir + fileName); if (index != -1) { String directory = fileName.substring(0, index); targetDir += "/" + directory; } try { File resultTargetDir = new File(CiFileUtil.getReplaceFullPath(targetDir)); if (!resultTargetDir.isDirectory()) { CiFileUtil.createDirectory(targetDir); } CiFileUtil.renameFile(sourceFile, targetDir, fileName); } catch (Exception e) { log.error(e.getMessage()); } } catch (Exception e) { String errorMsg = "Fail to parsing Line.[current line(" + bufReader.getLineNumber() + ") :" + line + "] : "; log.error(errorMsg, e); throw new DataParsingException(errorMsg, e); //throw(e); } finally { if (in != null) in.close(); if (isReader != null) isReader.close(); if (bufReader != null) bufReader.close(); } }
From source file:edu.hawaii.soest.hioos.storx.StorXParser.java
/** * Parses the binary STOR-X file. The binary file format is a sequence of * 'frames' that all begin with 'SAT'. The parser creates a list with the * individual frames. Some frames are StorX frames (SATSTX), some are from * external sensors (ISUS: 'SATNLB', 'SATNDB'; SBE CTD: 'SATSBE') * * @param fileBuffer - the binary data file as a ByteBuffer *///www. jav a 2s .c o m public void parse(ByteBuffer fileBuffer) throws Exception { logger.debug("StorXParser.parse() called."); this.fileBuffer = fileBuffer; //logger.debug(this.fileBuffer.toString()); try { // Create a buffer that will store a single frame of the file ByteBuffer frameBuffer = ByteBuffer.allocate(1024); // create four byte placeholders used to evaluate up to a four-byte // window. The FIFO layout looks like: // --------------------------- // in ---> | Four | Three | Two | One | ---> out // --------------------------- byte byteOne = 0x00, // set initial placeholder values byteTwo = 0x00, byteThree = 0x00, byteFour = 0x00; int frameByteCount = 0; // keep track of bytes per frame int frameCount = 0; // keep track of frames this.fileBuffer.position(0); this.fileBuffer.limit(this.fileBuffer.capacity()); while (this.fileBuffer.hasRemaining()) { // load the next byte into the FIFO window byteOne = fileBuffer.get(); // show the byte stream coming in //logger.debug("b1: " + new String(Hex.encodeHex(new byte[]{byteOne})) + "\t" + // "b2: " + new String(Hex.encodeHex(new byte[]{byteTwo})) + "\t" + // "b3: " + new String(Hex.encodeHex(new byte[]{byteThree})) + "\t" + // "b4: " + new String(Hex.encodeHex(new byte[]{byteFour})) + "\t" + // "st: " + Integer.toString(this.state) + "\t" + // "po: " + this.fileBuffer.position() + "\t" + // "cp: " + this.fileBuffer.capacity() // ); // evaluate the bytes, separate the file frame by frame (SAT ...) switch (this.state) { case 0: // find a frame beginning (SAT) 53 41 54 if (byteOne == 0x54 && byteTwo == 0x41 && byteThree == 0x53) { // found a line, add the beginning to the line buffer frameBuffer.put(byteThree); frameBuffer.put(byteTwo); frameBuffer.put(byteOne); frameByteCount = frameByteCount + 3; this.state = 1; break; } else { break; } case 1: // find the next frame beginning (SAT) 53 41 54 if ((byteOne == 0x54 && byteTwo == 0x41 && byteThree == 0x53) || fileBuffer.position() == fileBuffer.capacity()) { // we have a line ending. store the line in the arrayList frameBuffer.put(byteOne); frameByteCount++; frameBuffer.flip(); byte[] frameArray = frameBuffer.array(); ByteBuffer currentFrameBuffer; if (fileBuffer.position() == fileBuffer.capacity()) { // create a true copy of the byte array subset (no trailing 'SAT') byte[] frameCopy = new byte[frameByteCount]; System.arraycopy(frameArray, 0, frameCopy, 0, frameByteCount); currentFrameBuffer = ByteBuffer.wrap(frameCopy); } else { // create a true copy of the byte array subset (less the 'SAT') byte[] frameCopy = new byte[frameByteCount - 3]; System.arraycopy(frameArray, 0, frameCopy, 0, frameByteCount - 3); currentFrameBuffer = ByteBuffer.wrap(frameCopy); } // parse the current frame and add it to the frameMap frameCount++; // create a map to store frames as they are encountered BasicHierarchicalMap frameMap = new BasicHierarchicalMap(); // peek at the first six header bytes as a string byte[] sixBytes = new byte[6]; currentFrameBuffer.get(sixBytes); currentFrameBuffer.position(0); String frameHeader = new String(sixBytes, "US-ASCII"); // determine the frame type based on the header if (frameHeader.matches(this.STOR_X_HEADER_ID)) { frameMap.put("rawFrame", currentFrameBuffer); frameMap.put("id", frameHeader); frameMap.put("type", frameHeader.substring(3, 6)); frameMap.put("serialNumber", null); frameMap.put("date", null); String headerString = new String(currentFrameBuffer.array()); // trim trailing null characters and line endings int nullIndex = headerString.indexOf(0); headerString = headerString.substring(0, nullIndex).trim(); frameMap.put("parsedFrameObject", headerString); // Add the frame to the frames map this.framesMap.add("/frames/frame", (BasicHierarchicalMap) frameMap.clone()); frameMap.removeAll("frame"); currentFrameBuffer.clear(); } else if (frameHeader.matches(this.STOR_X_FRAME_ID)) { // test if the frame is complete if (currentFrameBuffer.capacity() == this.STOR_X_FRAME_SIZE) { // convert the frame buffer to a StorXFrame StorXFrame storXFrame = new StorXFrame(currentFrameBuffer); frameMap.put("rawFrame", currentFrameBuffer); frameMap.put("id", frameHeader); frameMap.put("type", frameHeader.substring(3, 6)); frameMap.put("serialNumber", storXFrame.getSerialNumber()); frameMap.put("date", parseTimestamp(storXFrame.getTimestamp())); frameMap.put("parsedFrameObject", storXFrame); // Add the frame to the frames map this.framesMap.add("/frames/frame", (BasicHierarchicalMap) frameMap.clone()); frameMap.removeAll("frame"); currentFrameBuffer.clear(); } else { logger.debug(frameHeader + " frame " + frameCount + " length is " + currentFrameBuffer.capacity() + " not " + this.STOR_X_FRAME_SIZE); } } else if (frameHeader.matches(this.SBE_CTD_FRAME_ID)) { // convert the frame buffer to a CTDFrame CTDFrame ctdFrame = new CTDFrame(currentFrameBuffer); // add in a sample if it matches a general data sample pattern if (ctdFrame.getSample().matches(" [0-9].*[0-9]\r\n")) { // extract the sample bytes from the frame frameMap.put("rawFrame", currentFrameBuffer); frameMap.put("id", frameHeader); frameMap.put("type", frameHeader.substring(3, 6)); frameMap.put("serialNumber", ctdFrame.getSerialNumber()); frameMap.put("date", parseTimestamp(ctdFrame.getTimestamp())); frameMap.put("parsedFrameObject", ctdFrame); // Add the frame to the frames map this.framesMap.add("/frames/frame", (BasicHierarchicalMap) frameMap.clone()); } else { logger.debug("This CTD frame is not a data sample." + " Skipping it. The string is: " + ctdFrame.getSample()); } frameMap.removeAll("frame"); currentFrameBuffer.clear(); } else if (frameHeader.matches(this.ISUS_DARK_FRAME_ID)) { // test if the frame is complete if (currentFrameBuffer.capacity() == this.ISUS_FRAME_SIZE) { // convert the frame buffer to a ISUSFrame ISUSFrame isusFrame = new ISUSFrame(currentFrameBuffer); frameMap.put("rawFrame", currentFrameBuffer); frameMap.put("id", frameHeader); frameMap.put("type", frameHeader.substring(3, 6)); frameMap.put("serialNumber", isusFrame.getSerialNumber()); frameMap.put("date", parseTimestamp(isusFrame.getTimestamp())); frameMap.put("parsedFrameObject", isusFrame); // Add the frame to the frames map this.framesMap.add("/frames/frame", (BasicHierarchicalMap) frameMap.clone()); frameMap.removeAll("frame"); currentFrameBuffer.clear(); } else { logger.debug(frameHeader + " frame " + frameCount + " length is " + currentFrameBuffer.capacity() + " not " + this.ISUS_FRAME_SIZE); } currentFrameBuffer.clear(); } else if (frameHeader.matches(this.ISUS_LIGHT_FRAME_ID)) { // test if the frame is complete if (currentFrameBuffer.capacity() == this.ISUS_FRAME_SIZE) { // convert the frame buffer to a ISUSFrame ISUSFrame isusFrame = new ISUSFrame(currentFrameBuffer); frameMap.put("rawFrame", currentFrameBuffer); frameMap.put("id", frameHeader); frameMap.put("type", frameHeader.substring(3, 6)); frameMap.put("serialNumber", isusFrame.getSerialNumber()); frameMap.put("date", parseTimestamp(isusFrame.getTimestamp())); frameMap.put("parsedFrameObject", isusFrame); // Add the frame to the frames map this.framesMap.add("/frames/frame", (BasicHierarchicalMap) frameMap.clone()); frameMap.removeAll("frame"); currentFrameBuffer.clear(); } else { logger.debug(frameHeader + " frame " + frameCount + " length is " + currentFrameBuffer.capacity() + " not " + this.ISUS_FRAME_SIZE); } currentFrameBuffer.clear(); } else { logger.info("The current frame type is not recognized. " + "Discarding it. The header was: " + frameHeader); currentFrameBuffer.clear(); } // reset the frame buffer for the next frame, but add the 'SAT' // bytes already encountered frameBuffer.clear(); frameByteCount = 0; this.fileBuffer.position(this.fileBuffer.position() - 3); this.state = 0; break; } else { // no full line yet, keep adding bytes frameBuffer.put(byteOne); frameByteCount++; break; } } // end switch() // shift the bytes in the FIFO window byteFour = byteThree; byteThree = byteTwo; byteTwo = byteOne; } // end while() logger.debug(this.framesMap.toXMLString(1000)); } catch (Exception e) { logger.debug("Failed to parse the data file. The error message was:" + e.getMessage()); e.printStackTrace(); } }
From source file:com.castis.sysComp.PoisConverterSysComp.java
private void writeClientUIFile(List<sceneDTO> list, String platform, File file) throws FileNotFoundException { FileOutputStream fos = null;//from ww w . j av a 2 s.c o m String dir = filePolling.getValidFileDirectory(resultDir); String fileName = file.getName(); String tempDir = dir + "/temp/"; File targetDirectory = new File(CiFileUtil.getReplaceFullPath(tempDir)); if (!targetDirectory.isDirectory()) { CiFileUtil.createDirectory(tempDir); } fos = new FileOutputStream(tempDir + fileName); int byteSize = 2048; ByteBuffer byteBuffer = ByteBuffer.allocateDirect(byteSize); GatheringByteChannel outByteCh = fos.getChannel(); try { for (int i = 0; i < list.size(); i++) { sceneDTO scene = list.get(i); StringBuffer strBuffer = new StringBuffer(); if (i == 0) { strBuffer.append("policy"); strBuffer.append("|"); strBuffer.append(platform); strBuffer.append("|"); strBuffer.append("ClientUI"); strBuffer.append("\r\n"); } strBuffer.append("info"); strBuffer.append("|"); strBuffer.append(platform); strBuffer.append("|"); strBuffer.append(scene.getId()); strBuffer.append("|"); strBuffer.append(scene.getName()); strBuffer.append("|"); strBuffer.append(scene.getTemplateFileName()); strBuffer.append("|"); strBuffer.append(scene.getMenuId()); strBuffer.append("|"); strBuffer.append(scene.getMenuName()); strBuffer.append("|"); strBuffer.append(scene.getSpaceId()); strBuffer.append("|"); strBuffer.append(scene.getSpaceName()); strBuffer.append("|"); strBuffer.append(scene.getResolution()); strBuffer.append("|"); strBuffer.append(scene.getResolutionOnFocus()); strBuffer.append("|"); strBuffer.append(scene.getSizeLimit()); strBuffer.append("|"); strBuffer.append(scene.getClickable()); strBuffer.append("\r\n"); byte[] outByte = null; try { outByte = strBuffer.toString().getBytes("UTF-8"); } catch (UnsupportedEncodingException e2) { e2.printStackTrace(); } byteBuffer.put(outByte); byteBuffer.flip(); try { outByteCh.write(byteBuffer); } catch (IOException e) { } byteBuffer.clear(); } fos.close(); String targetDir = resultDir; File sourceFile = new File(tempDir + fileName); int index = fileName.indexOf("-"); if (index != -1) { fileName = fileName.substring(index + 1, fileName.length()); } index = fileName.indexOf("_"); if (index != -1) { String directory = fileName.substring(0, index); targetDir += "/" + directory; } index = fileName.indexOf("."); if (index != -1) { fileName = fileName.substring(0, index) + ".csv"; } try { File resultTargetDir = new File(CiFileUtil.getReplaceFullPath(targetDir)); if (!resultTargetDir.isDirectory()) { CiFileUtil.createDirectory(targetDir); } CiFileUtil.renameFile(sourceFile, targetDir, fileName); } catch (Exception e) { log.error(e.getMessage()); } } catch (Exception e) { String errorMsg = e.getMessage(); log.error(errorMsg, e); throw new DataParsingException(errorMsg, e); //throw(e); } }
From source file:edu.harvard.iq.dvn.core.web.ExploreDataPage.java
private void writeFile(File fileIn, char[] charArrayIn, int bufSize) { try {/*ww w . j a v a 2 s . c o m*/ FileOutputStream outputFile = null; outputFile = new FileOutputStream(fileIn, true); FileChannel outChannel = outputFile.getChannel(); ByteBuffer buf = ByteBuffer.allocate((bufSize * 2) + 1000); for (char ch : charArrayIn) { buf.putChar(ch); } buf.flip(); try { outChannel.write(buf); outputFile.close(); } catch (IOException e) { e.printStackTrace(System.err); } } catch (IOException e) { throw new EJBException(e); } }
From source file:org.apache.hadoop.hdfs.hoss.db.FileStreamStore.java
/** * Read block from file/*from w w w.jav a2s .c o m*/ * * @param offset * of block * @param ByteBuffer * @return new offset (offset+headerlen+datalen+footer) */ public synchronized long read(long offset, final ByteBuffer buf) { if (!validState) throw new InvalidStateException(); try { int readed; while (true) { if (offset >= offsetOutputCommited) { if (bufOutput.position() > 0) { LOG.warn("WARN: autoflush forced"); flushBuffer(); } } bufInput.clear(); readed = fcInput.position(offset).read(bufInput); // Read 1 // sector if (readed < HEADER_LEN) { // short+int (6 bytes) return -1; } bufInput.flip(); final int magicB1 = (bufInput.get() & 0xFF); // Header - Magic // (short, 2 bytes, msb-first) final int magicB2 = (bufInput.get() & 0xFF); // Header - Magic // (short, 2 bytes, lsb-last) if (alignBlocks && (magicB1 == MAGIC_PADDING)) { final int diffOffset = nextBlockBoundary(offset); if (diffOffset > 0) { offset += diffOffset; continue; } } final int magic = ((magicB1 << 8) | magicB2); if (magic != MAGIC) { LOG.error("MAGIC HEADER fake=" + Integer.toHexString(magic) + " expected=" + Integer.toHexString(MAGIC)); return -1; } break; } // Header - Data Size (int, 4 bytes) final int datalen = bufInput.getInt(); final int dataUnderFlow = (datalen - (readed - HEADER_LEN)); int footer = -12345678; if (dataUnderFlow < 0) { footer = bufInput.get(datalen + HEADER_LEN); // Footer (byte) } bufInput.limit(Math.min(readed, datalen + HEADER_LEN)); buf.put(bufInput); if (dataUnderFlow > 0) { buf.limit(datalen); int len = fcInput.read(buf); if (len < dataUnderFlow) { LOG.error("Unable to read payload readed=" + len + " expected=" + dataUnderFlow); return -1; } } if (dataUnderFlow >= 0) { // Read Footer (byte) bufInput.clear(); bufInput.limit(FOOTER_LEN); if (fcInput.read(bufInput) < FOOTER_LEN) return -1; bufInput.flip(); footer = bufInput.get(); } if (footer != MAGIC_FOOT) { LOG.error("MAGIC FOOT fake=" + Integer.toHexString(footer) + " expected=" + Integer.toHexString(MAGIC_FOOT)); return -1; } buf.flip(); return (offset + HEADER_LEN + datalen + FOOTER_LEN); } catch (Exception e) { LOG.error("Exception in read(" + offset + ")", e); } return -1; }
From source file:edu.hawaii.soest.kilonalu.ctd.CTDSource.java
/** * A method that executes the streaming of data from the source to the RBNB * server after all configuration of settings, connections to hosts, and * thread initiatizing occurs. This method contains the detailed code for * streaming the data and interpreting the stream. *//*from www. j a va 2 s .c om*/ protected boolean execute() { logger.debug("CTDSource.execute() called."); // do not execute the stream if there is no connection if (!isConnected()) return false; boolean failed = false; // test the connection type if (this.connectionType.equals("serial")) { // create a serial connection to the local serial port this.channel = getSerialConnection(); } else if (this.connectionType.equals("socket")) { // otherwise create a TCP or UDP socket connection to the remote host this.channel = getSocketConnection(); } else { logger.info("There was an error establishing either a serial or " + "socket connection to the instrument. Please be sure " + "the connection type is set to either 'serial' or 'socket'."); return false; } // while data are being sent, read them into the buffer try { // create four byte placeholders used to evaluate up to a four-byte // window. The FIFO layout looks like: // ------------------------- // in ---> | One | Two |Three|Four | ---> out // ------------------------- byte byteOne = 0x00, // set initial placeholder values byteTwo = 0x00, byteThree = 0x00, byteFour = 0x00; // Create a buffer that will store the sample bytes as they are read ByteBuffer sampleBuffer = ByteBuffer.allocate(getBufferSize()); // Declare sample variables to be used in the response parsing byte[] sampleArray; // create a byte buffer to store bytes from the TCP stream ByteBuffer buffer = ByteBuffer.allocateDirect(getBufferSize()); // add a channel of data that will be pushed to the server. // Each sample will be sent to the Data Turbine as an rbnb frame. ChannelMap rbnbChannelMap = new ChannelMap(); // while there are bytes to read from the channel ... while (this.channel.read(buffer) != -1 || buffer.position() > 0) { // prepare the buffer for reading buffer.flip(); // while there are unread bytes in the ByteBuffer while (buffer.hasRemaining()) { byteOne = buffer.get(); logger.debug("b1: " + new String(Hex.encodeHex((new byte[] { byteOne }))) + "\t" + "b2: " + new String(Hex.encodeHex((new byte[] { byteTwo }))) + "\t" + "b3: " + new String(Hex.encodeHex((new byte[] { byteThree }))) + "\t" + "b4: " + new String(Hex.encodeHex((new byte[] { byteFour }))) + "\t" + "sample pos: " + sampleBuffer.position() + "\t" + "sample rem: " + sampleBuffer.remaining() + "\t" + "sample cnt: " + sampleByteCount + "\t" + "buffer pos: " + buffer.position() + "\t" + "buffer rem: " + buffer.remaining() + "\t" + "state: " + this.state); // Use a State Machine to process the byte stream. // Start building an rbnb frame for the entire sample, first by // inserting a timestamp into the channelMap. This time is merely // the time of insert into the data turbine, not the time of // observations of the measurements. That time should be parsed out // of the sample in the Sink client code switch (this.state) { case 0: // wake up the instrument // check for instrument metadata fields if (this.enableSendCommands && !this.hasMetadata) { // wake the instrument with an initial '\r\n' command this.command = this.commandSuffix; this.sentCommand = queryInstrument(this.command); this.sentCommand = queryInstrument(this.command); streamingThread.sleep(2000); this.state = 1; break; } else { this.state = 11; break; } case 1: // stop the sampling // be sure the instrument woke (look for S> prompt) //if (byteOne == 0x3E && byteTwo == 0x53 ) { // // sampleByteCount = 0; // sampleBuffer.clear(); // // // send the stop sampling command this.command = this.commandPrefix + this.stopSamplingCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); sampleBuffer.clear(); sampleByteCount = 0; this.state = 2; break; //} else { // // handle instrument hardware response // sampleByteCount++; // add the last byte found to the count // // // add the last byte found to the sample buffer // if ( sampleBuffer.remaining() > 0 ) { // sampleBuffer.put(byteOne); // // } else { // sampleBuffer.compact(); // sampleBuffer.put(byteOne); // // } // // break; // continue reading bytes // //} case 2: // based on outputType, get metadata from the instrument // the response should end in <Executed/> if (byteOne == 0x3E && byteTwo == 0x2F && byteThree == 0x64 && byteFour == 0x65) { sampleBuffer.clear(); sampleByteCount = 0; this.samplingIsStopped = true; // for newer firmware CTDs, use xml-based query commands if (getOutputType().equals("xml")) { // create the CTD parser instance used to parse CTD output this.ctdParser = new CTDParser(); this.state = 3; break; // otherwise, use text-based query commands } else if (getOutputType().equals("text")) { this.state = 12; // process DS and DCal commands break; } else { logger.info("The CTD output type is not recognized. " + "Please set the output type to either " + "'xml' or 'text'."); failed = true; this.state = 0; // close the serial or socket channel if (this.channel != null && this.channel.isOpen()) { try { this.channel.close(); } catch (IOException cioe) { logger.debug("An error occurred trying to close the byte channel. " + " The error message was: " + cioe.getMessage()); return !failed; } } // disconnect from the RBNB if (isConnected()) { disconnect(); } return !failed; } } else { // handle instrument hardware response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } break; // continue reading bytes } case 3: // get the instrument status metadata if (!this.ctdParser.getHasStatusMetadata()) { this.command = this.commandPrefix + this.getStatusCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 4; break; } else { // get the configuration metadata this.command = this.commandPrefix + this.getConfigurationCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 5; break; } case 4: // handle instrument status response // command response ends with <Executed/> (so find: ed/>) if (byteOne == 0x3E && byteTwo == 0x2F && byteThree == 0x64 && byteFour == 0x65) { // handle instrument status response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // set the CTD metadata int executedIndex = this.responseString.indexOf("<Executed/>"); this.responseString = this.responseString.substring(0, executedIndex - 1); this.ctdParser.setMetadata(this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; // then get the instrument configuration metadata if (!this.ctdParser.getHasConfigurationMetadata()) { this.command = this.commandPrefix + this.getConfigurationCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 5; break; } else { // get the calibration metadata this.command = this.commandPrefix + this.getCalibrationCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 6; break; } } else { break; // continue reading bytes } case 5: // handle the instrument configuration metadata // command response ends with <Executed/> (so find: ed/>) if (byteOne == 0x3E && byteTwo == 0x2F && byteThree == 0x64 && byteFour == 0x65) { // handle instrument configration response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // set the CTD metadata int executedIndex = this.responseString.indexOf("<Executed/>"); this.responseString = this.responseString.substring(0, executedIndex - 1); this.ctdParser.setMetadata(this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; // then get the instrument calibration metadata if (!this.ctdParser.getHasCalibrationMetadata()) { this.command = this.commandPrefix + this.getCalibrationCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 6; break; } else { this.command = this.commandPrefix + this.getEventsCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 7; break; } } else { break; // continue reading bytes } case 6: // handle the instrument calibration metadata // command response ends with <Executed/> (so find: ed/>) if (byteOne == 0x3E && byteTwo == 0x2F && byteThree == 0x64 && byteFour == 0x65) { // handle instrument calibration response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // set the CTD metadata int executedIndex = this.responseString.indexOf("<Executed/>"); this.responseString = this.responseString.substring(0, executedIndex - 1); this.ctdParser.setMetadata(this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; // then get the instrument event metadata if (!this.ctdParser.getHasEventMetadata()) { this.command = this.commandPrefix + this.getEventsCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 7; break; } else { this.command = this.commandPrefix + this.getHardwareCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 8; break; } } else { break; // continue reading bytes } case 7: // handle instrument event metadata // command response ends with <Executed/> (so find: ed/>) if (byteOne == 0x3E && byteTwo == 0x2F && byteThree == 0x64 && byteFour == 0x65) { // handle instrument events response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // set the CTD metadata int executedIndex = this.responseString.indexOf("<Executed/>"); this.responseString = this.responseString.substring(0, executedIndex - 1); this.ctdParser.setMetadata(this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; // then get the instrument hardware metadata if (!this.ctdParser.getHasHardwareMetadata()) { this.command = this.commandPrefix + this.getHardwareCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 8; break; } else { this.state = 9; break; } } else { break; // continue reading bytes } case 8: // handle the instrument hardware response // command response ends with <Executed/> (so find: ed/>) if (byteOne == 0x3E && byteTwo == 0x2F && byteThree == 0x64 && byteFour == 0x65) { // handle instrument hardware response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // set the CTD metadata int executedIndex = this.responseString.indexOf("<Executed/>"); this.responseString = this.responseString.substring(0, executedIndex - 1); this.ctdParser.setMetadata(this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; // sync the clock if it is not synced if (!this.clockIsSynced) { this.state = 9; break; } else { this.state = 10; break; } } else { break; // continue reading bytes } case 9: // set the instrument clock // is sampling stopped? if (!this.samplingIsStopped) { // wake the instrument with an initial '\r\n' command this.command = this.commandSuffix; this.sentCommand = queryInstrument(this.command); streamingThread.sleep(2000); // then stop the sampling this.command = this.commandPrefix + this.stopSamplingCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); this.samplingIsStopped = true; } // now set the clock if (this.sentCommand) { this.clockSyncDate = new Date(); DATE_FORMAT.setTimeZone(TZ); String dateAsString = DATE_FORMAT.format(this.clockSyncDate); this.command = this.commandPrefix + this.setDateTimeCommand + dateAsString + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.clockIsSynced = true; logger.info("The instrument clock has bee synced at " + this.clockSyncDate.toString()); this.state = 10; break; } else { break; // try the clock sync again due to failure } case 10: // restart the instrument sampling if (this.samplingIsStopped) { this.hasMetadata = true; this.command = this.commandPrefix + this.startSamplingCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); if (this.sentCommand) { this.state = 11; break; } else { break; // try starting the sampling again due to failure } } else { break; } case 11: // read bytes to the next EOL characters // sample line is terminated by \r\n // note bytes are in reverse order in the FIFO window if (byteOne == 0x0A && byteTwo == 0x0D) { sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract just the length of the sample bytes out of the // sample buffer, and place it in the channel map as a // byte array. Then, send it to the data turbine. sampleArray = new byte[sampleByteCount]; sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // test if the sample is not just an instrument message if (this.responseString.matches("^# [0-9].*\r\n") || this.responseString.matches("^# [0-9].*\r\n") || this.responseString.matches("^ [0-9].*\r\n")) { // add the data observations string to the CTDParser object // and populate the CTDParser data fields //this.ctdParser.setData(this.responseString); //this.ctdParser.parse(); // build the channel map with all of the data and metadata channels: int channelIndex = rbnbChannelMap.Add(getRBNBChannelName()); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutTimeAuto("server"); // add the ASCII sample data field rbnbChannelMap.PutDataAsString(channelIndex, this.responseString); // add other metadata and data fields to the map if metadata was collected if (this.hasMetadata && this.ctdParser != null) { // add the samplingMode field data channelIndex = rbnbChannelMap.Add("samplingMode"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getSamplingMode()); // String // add the temperatureSerialNumber field data channelIndex = rbnbChannelMap.Add("temperatureSerialNumber"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getTemperatureSerialNumber()); // String // add the conductivitySerialNumber field data channelIndex = rbnbChannelMap.Add("conductivitySerialNumber"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getConductivitySerialNumber()); // String // add the mainBatteryVoltage field data channelIndex = rbnbChannelMap.Add("mainBatteryVoltage"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getMainBatteryVoltage() }); // double // add the lithiumBatteryVoltage field data channelIndex = rbnbChannelMap.Add("lithiumBatteryVoltage"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getLithiumBatteryVoltage() }); // double // add the operatingCurrent field data channelIndex = rbnbChannelMap.Add("operatingCurrent"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getOperatingCurrent() }); // double // add the pumpCurrent field data channelIndex = rbnbChannelMap.Add("pumpCurrent"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPumpCurrent() }); // double // add the channels01ExternalCurrent field data channelIndex = rbnbChannelMap.Add("channels01ExternalCurrent"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getChannels01ExternalCurrent() }); // double // add the channels23ExternalCurrent field data channelIndex = rbnbChannelMap.Add("channels23ExternalCurrent"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getChannels23ExternalCurrent() }); // double // add the loggingStatus field data channelIndex = rbnbChannelMap.Add("loggingStatus"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getLoggingStatus()); // String // add the numberOfScansToAverage field data channelIndex = rbnbChannelMap.Add("numberOfScansToAverage"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getNumberOfScansToAverage() }); // int // add the numberOfSamples field data channelIndex = rbnbChannelMap.Add("numberOfSamples"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getNumberOfSamples() }); // int // add the numberOfAvailableSamples field data channelIndex = rbnbChannelMap.Add("numberOfAvailableSamples"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getNumberOfAvailableSamples() }); // int // add the sampleInterval field data channelIndex = rbnbChannelMap.Add("sampleInterval"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getSampleInterval() }); // int // add the measurementsPerSample field data channelIndex = rbnbChannelMap.Add("measurementsPerSample"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getMeasurementsPerSample() }); // int // add the transmitRealtime field data channelIndex = rbnbChannelMap.Add("transmitRealtime"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getTransmitRealtime()); // String // add the numberOfCasts field data channelIndex = rbnbChannelMap.Add("numberOfCasts"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getNumberOfCasts() }); // int // add the minimumConductivityFrequency field data channelIndex = rbnbChannelMap.Add("minimumConductivityFrequency"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getMinimumConductivityFrequency() }); // int // add the pumpDelay field data channelIndex = rbnbChannelMap.Add("pumpDelay"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsInt32(channelIndex, new int[] { this.ctdParser.getPumpDelay() }); // int // add the automaticLogging field data channelIndex = rbnbChannelMap.Add("automaticLogging"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getAutomaticLogging()); // String // add the ignoreMagneticSwitch field data channelIndex = rbnbChannelMap.Add("ignoreMagneticSwitch"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getIgnoreMagneticSwitch()); // String // add the batteryType field data channelIndex = rbnbChannelMap.Add("batteryType"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getBatteryType()); // String // add the batteryCutoff field data channelIndex = rbnbChannelMap.Add("batteryCutoff"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getBatteryCutoff()); // String // add the pressureSensorType field data channelIndex = rbnbChannelMap.Add("pressureSensorType"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getPressureSensorType()); // String // add the pressureSensorRange field data channelIndex = rbnbChannelMap.Add("pressureSensorRange"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getPressureSensorRange()); // String // add the sbe38TemperatureSensor field data channelIndex = rbnbChannelMap.Add("sbe38TemperatureSensor"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getSbe38TemperatureSensor()); // String // add the gasTensionDevice field data channelIndex = rbnbChannelMap.Add("gasTensionDevice"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getGasTensionDevice()); // String // add the externalVoltageChannelZero field data channelIndex = rbnbChannelMap.Add("externalVoltageChannelZero"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getExternalVoltageChannelZero()); // String // add the externalVoltageChannelOne field data channelIndex = rbnbChannelMap.Add("externalVoltageChannelOne"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getExternalVoltageChannelOne()); // String // add the externalVoltageChannelTwo field data channelIndex = rbnbChannelMap.Add("externalVoltageChannelTwo"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getExternalVoltageChannelTwo()); // String // add the externalVoltageChannelThree field data channelIndex = rbnbChannelMap.Add("externalVoltageChannelThree"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getExternalVoltageChannelThree()); // String // add the echoCommands field data channelIndex = rbnbChannelMap.Add("echoCommands"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getEchoCommands()); // String // add the outputFormat field data channelIndex = rbnbChannelMap.Add("outputFormat"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getOutputFormat()); // String // add the temperatureCalibrationDate field data channelIndex = rbnbChannelMap.Add("temperatureCalibrationDate"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getTemperatureCalibrationDate()); // String // add the temperatureCoefficientTA0 field data channelIndex = rbnbChannelMap.Add("temperatureCoefficientTA0"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA0() }); // double // add the temperatureCoefficientTA1 field data channelIndex = rbnbChannelMap.Add("temperatureCoefficientTA1"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA1() }); // double // add the temperatureCoefficientTA2 field data channelIndex = rbnbChannelMap.Add("temperatureCoefficientTA2"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA2() }); // double // add the temperatureCoefficientTA3 field data channelIndex = rbnbChannelMap.Add("temperatureCoefficientTA3"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA3() }); // double // add the temperatureOffsetCoefficient field data channelIndex = rbnbChannelMap.Add("temperatureOffsetCoefficient"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getTemperatureOffsetCoefficient() }); // double // add the conductivityCalibrationDate field data channelIndex = rbnbChannelMap.Add("conductivityCalibrationDate"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getConductivityCalibrationDate()); // String // add the conductivityCoefficientG field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientG"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientG() }); // double // add the conductivityCoefficientH field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientH"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientH() }); // double // add the conductivityCoefficientI field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientI"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientI() }); // double // add the conductivityCoefficientJ field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientJ"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientJ() }); // double // add the conductivityCoefficientCF0 field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientCF0"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCF0() }); // double // add the conductivityCoefficientCPCOR field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientCPCOR"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCPCOR() }); // double // add the conductivityCoefficientCTCOR field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientCTCOR"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCTCOR() }); // double // add the conductivityCoefficientCSLOPE field data channelIndex = rbnbChannelMap.Add("conductivityCoefficientCSLOPE"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCSLOPE() }); // double // add the pressureSerialNumber field data channelIndex = rbnbChannelMap.Add("pressureSerialNumber"); rbnbChannelMap.PutMime(channelIndex, "text/plain"); rbnbChannelMap.PutDataAsString(channelIndex, this.ctdParser.getPressureSerialNumber()); // String // add the pressureCoefficientPA0 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPA0"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPA0() }); // double // add the pressureCoefficientPA1 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPA1"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPA1() }); // double // add the pressureCoefficientPA2 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPA2"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPA2() }); // double // add the pressureCoefficientPTCA0 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTCA0"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCA0() }); // double // add the pressureCoefficientPTCA1 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTCA1"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCA1() }); // double // add the pressureCoefficientPTCA2 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTCA2"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCA2() }); // double // add the pressureCoefficientPTCB0 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTCB0"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCB0() }); // double // add the pressureCoefficientPTCB1 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTCB1"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCB1() }); // double // add the pressureCoefficientPTCB2 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTCB2"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCB2() }); // double // add the pressureCoefficientPTEMPA0 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTEMPA0"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTEMPA0() }); // double // add the pressureCoefficientPTEMPA1 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTEMPA1"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTEMPA1() }); // double // add the pressureCoefficientPTEMPA2 field data channelIndex = rbnbChannelMap.Add("pressureCoefficientPTEMPA2"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTEMPA2() }); // double // add the pressureOffsetCoefficient field data channelIndex = rbnbChannelMap.Add("pressureOffsetCoefficient"); rbnbChannelMap.PutMime(channelIndex, "application/octet-stream"); rbnbChannelMap.PutDataAsFloat64(channelIndex, new double[] { this.ctdParser.getPressureOffsetCoefficient() }); // double } // send the sample to the data turbine getSource().Flush(rbnbChannelMap); logger.info("Sent sample to the DataTurbine: " + this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; channelIndex = 0; rbnbChannelMap.Clear(); logger.debug("Cleared b1,b2,b3,b4. Cleared sampleBuffer. Cleared rbnbChannelMap."); // check if the clock needs syncing (daily) if (this.enableSendCommands) { // get the current datetime Calendar currentCalendar = Calendar.getInstance(); currentCalendar.setTime(new Date()); Calendar lastSyncedCalendar = Calendar.getInstance(); lastSyncedCalendar.setTime(this.clockSyncDate); // round the dates to the day currentCalendar.clear(Calendar.MILLISECOND); currentCalendar.clear(Calendar.SECOND); currentCalendar.clear(Calendar.MINUTE); currentCalendar.clear(Calendar.HOUR); lastSyncedCalendar.clear(Calendar.MILLISECOND); lastSyncedCalendar.clear(Calendar.SECOND); lastSyncedCalendar.clear(Calendar.MINUTE); lastSyncedCalendar.clear(Calendar.HOUR); // sync the clock daily if (currentCalendar.before(lastSyncedCalendar)) { this.state = 8; } } // otherwise stay in state = 11 break; // the sample looks more like an instrument message, don't flush } else { logger.info("This string does not look like a sample, " + "and was not sent to the DataTurbine."); logger.info("Skipping sample: " + this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; //rbnbChannelMap.Clear(); logger.debug("Cleared b1,b2,b3,b4. Cleared sampleBuffer. Cleared rbnbChannelMap."); this.state = 11; break; } } else { // not 0x0A0D // still in the middle of the sample, keep adding bytes sampleByteCount++; // add each byte found if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); logger.debug("Compacting sampleBuffer ..."); sampleBuffer.put(byteOne); } break; } // end if for 0x0A0D EOL case 12: // alternatively use legacy DS and DCal commands if (this.enableSendCommands) { // start by getting the DS status output this.command = this.commandPrefix + this.displayStatusCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 13; break; } else { this.state = 0; break; } case 13: // handle the DS command response // command should end with the S> prompt if (byteOne == 0x7E && byteTwo == 0x53) { // handle instrument status response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount - 2]; //subtract "S>" sampleBuffer.flip(); sampleBuffer.get(sampleArray); this.responseString = new String(sampleArray, "US-ASCII"); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; // then get the instrument calibration metadata this.command = this.commandPrefix + this.displayCalibrationCommand + this.commandSuffix; this.sentCommand = queryInstrument(command); streamingThread.sleep(5000); this.state = 14; break; } else { break; // continue reading bytes } case 14: // handle the DCal command response // command should end with the S> prompt if (byteOne == 0x7E && byteTwo == 0x53) { // handle instrument status response sampleByteCount++; // add the last byte found to the count // add the last byte found to the sample buffer if (sampleBuffer.remaining() > 0) { sampleBuffer.put(byteOne); } else { sampleBuffer.compact(); sampleBuffer.put(byteOne); } // extract the sampleByteCount length from the sampleBuffer sampleArray = new byte[sampleByteCount - 2]; // subtract "S>" sampleBuffer.flip(); sampleBuffer.get(sampleArray); // append the DCal output to the DS output this.responseString = this.responseString.concat(new String(sampleArray, "US-ASCII")); // and add the data delimiter expected in the CTDParser this.responseString = this.responseString.concat("*END*\r\n\r\n"); // build the CTDParser object with legacy DS and DCal metadata this.ctdParser = new CTDParser(this.responseString); // reset variables for the next sample sampleBuffer.clear(); sampleByteCount = 0; this.state = 9; // set the clock and start sampling break; } else { break; // continue reading bytes } } // end switch statement // shift the bytes in the FIFO window byteFour = byteThree; byteThree = byteTwo; byteTwo = byteOne; } //end while (more unread bytes) // prepare the buffer to read in more bytes from the stream buffer.compact(); } // end while (more channel bytes to read) this.channel.close(); } catch (IOException e) { // handle exceptions // In the event of an i/o exception, log the exception, and allow execute() // to return false, which will prompt a retry. failed = true; this.state = 0; // close the serial or socket channel if (this.channel != null && this.channel.isOpen()) { try { this.channel.close(); } catch (IOException cioe) { logger.debug("An error occurred trying to close the byte channel. " + " The error message was: " + cioe.getMessage()); } } // disconnect from the RBNB if (isConnected()) { disconnect(); } e.printStackTrace(); return !failed; } catch (InterruptedException intde) { // in the event that the streamingThread is interrupted failed = true; this.state = 0; // close the serial or socket channel if (this.channel != null && this.channel.isOpen()) { try { this.channel.close(); } catch (IOException cioe) { logger.debug("An error occurred trying to close the byte channel. " + " The error message was: " + cioe.getMessage()); } } // disconnect from the RBNB if (isConnected()) { disconnect(); } intde.printStackTrace(); return !failed; } catch (SAPIException sapie) { // In the event of an RBNB communication exception, log the exception, // and allow execute() to return false, which will prompt a retry. //this.channel.close(); failed = true; this.state = 0; // close the serial or socket channel if (this.channel != null && this.channel.isOpen()) { try { this.channel.close(); } catch (IOException cioe) { logger.debug("An error occurred trying to close the byte channel. " + " The error message was: " + cioe.getMessage()); } } // disconnect from the RBNB if (isConnected()) { disconnect(); } sapie.printStackTrace(); return !failed; } catch (ParseException pe) { failed = true; this.state = 0; // close the serial or socket channel if (this.channel != null && this.channel.isOpen()) { try { this.channel.close(); } catch (IOException cioe) { logger.debug("An error occurred trying to close the byte channel. " + " The error message was: " + cioe.getMessage()); } } // disconnect from the RBNB if (isConnected()) { disconnect(); } logger.info("There was an error parsing the metadata response. " + "The error message was: " + pe.getMessage()); return !failed; } finally { this.state = 0; // close the serial or socket channel if (this.channel != null && this.channel.isOpen()) { try { this.channel.close(); } catch (IOException cioe) { logger.debug("An error occurred trying to close the byte channel. " + " The error message was: " + cioe.getMessage()); } } } return !failed; }
From source file:com.healthmarketscience.jackcess.Column.java
/** * Serialize an Object into a raw byte value for this column * @param obj Object to serialize/*from ww w. j av a2s . c om*/ * @param order Order in which to serialize * @return A buffer containing the bytes * @usage _advanced_method_ */ public ByteBuffer writeFixedLengthField(Object obj, ByteOrder order) throws IOException { int size = getType().getFixedSize(_columnLength); // create buffer for data ByteBuffer buffer = getPageChannel().createBuffer(size, order); // since booleans are not written by this method, it's safe to convert any // incoming boolean into an integer. obj = booleanToInteger(obj); switch (getType()) { case BOOLEAN: //Do nothing break; case BYTE: buffer.put(toNumber(obj).byteValue()); break; case INT: buffer.putShort(toNumber(obj).shortValue()); break; case LONG: buffer.putInt(toNumber(obj).intValue()); break; case MONEY: writeCurrencyValue(buffer, obj); break; case FLOAT: buffer.putFloat(toNumber(obj).floatValue()); break; case DOUBLE: buffer.putDouble(toNumber(obj).doubleValue()); break; case SHORT_DATE_TIME: writeDateValue(buffer, obj); break; case TEXT: // apparently text numeric values are also occasionally written as fixed // length... int numChars = getLengthInUnits(); // force uncompressed encoding for fixed length text buffer.put(encodeTextValue(obj, numChars, numChars, true)); break; case GUID: writeGUIDValue(buffer, obj, order); break; case NUMERIC: // yes, that's right, occasionally numeric values are written as fixed // length... writeNumericValue(buffer, obj); break; case BINARY: case UNKNOWN_0D: case UNKNOWN_11: case COMPLEX_TYPE: buffer.putInt(toNumber(obj).intValue()); break; case UNSUPPORTED_FIXEDLEN: byte[] bytes = toByteArray(obj); if (bytes.length != getLength()) { throw new IOException( "Invalid fixed size binary data, size " + getLength() + ", got " + bytes.length); } buffer.put(bytes); break; default: throw new IOException("Unsupported data type: " + getType()); } buffer.flip(); return buffer; }
From source file:edu.hawaii.soest.kilonalu.ctd.SeahorseSource.java
/** * A method that executes the streaming of data from the source to the RBNB * server after all configuration of settings, connections to hosts, and * thread initiatizing occurs. This method contains the detailed code for * streaming the data and interpreting the stream. *///from w w w .jav a 2 s .co m protected boolean execute() { logger.debug("SeahorseSource.execute() called."); // do not execute the stream if there is no connection if (!isConnected()) return false; boolean failed = false; this.socketChannel = getSocketConnection(); // while data are being sent, read them into the buffer try { // create four byte placeholders used to evaluate up to a four-byte // window. The FIFO layout looks like: // ------------------------- // in ---> | One | Two |Three|Four | ---> out // ------------------------- byte byteOne = 0x00, // set initial placeholder values byteTwo = 0x00, byteThree = 0x00, byteFour = 0x00; // define a byte array that will be used to manipulate the incoming bytes byte[] resultArray; String resultString; // Create a buffer that will store the result bytes as they are read ByteBuffer resultBuffer = ByteBuffer.allocate(getBufferSize()); // create a byte buffer to store bytes from the TCP stream ByteBuffer buffer = ByteBuffer.allocateDirect(getBufferSize()); this.rbnbChannelMap = new ChannelMap(); this.channelIndex = 0; // initiate the session with the modem, test if is network registered this.command = this.MODEM_COMMAND_PREFIX + this.REGISTRATION_STATUS_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); // while there are bytes to read from the socketChannel ... while (socketChannel.read(buffer) != -1 || buffer.position() > 0) { // prepare the buffer for reading buffer.flip(); // while there are unread bytes in the ByteBuffer while (buffer.hasRemaining()) { byteOne = buffer.get(); //logger.debug("b1: " + new String(Hex.encodeHex((new byte[]{byteOne}))) + "\t" + // "b2: " + new String(Hex.encodeHex((new byte[]{byteTwo}))) + "\t" + // "b3: " + new String(Hex.encodeHex((new byte[]{byteThree}))) + "\t" + // "b4: " + new String(Hex.encodeHex((new byte[]{byteFour}))) + "\t" + // "result pos: " + resultBuffer.position() + "\t" + // "result rem: " + resultBuffer.remaining() + "\t" + // "result cnt: " + resultByteCount + "\t" + // "buffer pos: " + buffer.position() + "\t" + // "buffer rem: " + buffer.remaining() + "\t" + // "state: " + state //); // Use a State Machine to process the byte stream. // Start building an rbnb frame for the entire sample, first by // inserting a timestamp into the channelMap. This time is merely // the time of insert into the data turbine, not the time of // observations of the measurements. That time should be parsed out // of the sample in the Sink client code switch (state) { case 0: // the network registration status should end in OK\r\n // note bytes are in reverse order in the FIFO window if (byteOne == 0x0A && byteTwo == 0x0D && byteThree == 0x4B && byteFour == 0x4F) { logger.debug("Received the registration status result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the network registration status string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("Network Registration Result: " + resultString.trim()); resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // send a request for the signal strength this.command = this.MODEM_COMMAND_PREFIX + this.SIGNAL_STRENGTH_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 1; break; } else { this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } break; } case 1: // report the signal strength of the Iridium modem // the signal strength status should end in OK\r\n // note bytes are in reverse order in the FIFO window if (byteOne == 0x0A && byteTwo == 0x0D && byteThree == 0x4B && byteFour == 0x4F) { logger.debug("Received the signal strength result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the signal strength status string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("Signal Strength Result: " + resultString.trim()); int signalStrengthIndex = resultString.indexOf(this.SIGNAL_STRENGTH) + 5; int signalStrength = new Integer( resultString.substring(signalStrengthIndex, signalStrengthIndex + 1)) .intValue(); // test if the signal strength is above the threshold if (signalStrength > SIGNAL_THRESHOLD) { resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 2; break; // the signal strength is too low, check again } else { resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // resend a request for the signal strength this.command = this.MODEM_COMMAND_PREFIX + this.SIGNAL_STRENGTH_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 1; break; } } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 2: // handle the RING command from the instrument // listen for the RING command // note bytes are in reverse order in the FIFO window if (byteOne == 0x47 && byteTwo == 0x4E && byteThree == 0x49 && byteFour == 0x52) { logger.debug("Received the RING command."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // answer the call this.command = this.MODEM_COMMAND_PREFIX + this.ANSWER_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 3; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 3: // acknowledge the connection // the ready status string should end in READY\r // note bytes are in reverse order in the FIFO window if (byteOne == 0x0D && byteTwo == 0x59 && byteThree == 0x44 && byteFour == 0x41) { logger.debug("Received the ready status result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the connect rate and ready status string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); // test the connect rate logger.debug("Result from ATA: " + resultString); if (resultString.indexOf(this.CONNECT_RATE) > 0) { logger.debug("Connect Rate Result: " + this.CONNECT_RATE); // test the ready status if (resultString.indexOf(this.READY_STATUS) > 0) { logger.debug("Connect Rate Result: " + this.READY_STATUS); resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // acknowledge the ready status this.command = this.ACKNOWLEDGE_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to receive the ACK streamingThread.sleep(this.SLEEP_INTERVAL); // query the instrument id this.command = this.ID_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 4; break; } else { logger.debug("The ready status differs from: " + this.READY_STATUS); // throw an exception here? break; } } else { logger.debug("The connect rate differs from: " + this.CONNECT_RATE); // throw an exception here? break; } } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 4: // get the instrument id // the instrument ID string should end in \r if (byteOne == 0x0D) { logger.debug("Received the instrument ID result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the instrument ID string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("Seahorse Instrument ID: " + resultString.trim()); // set the platformID variable this.platformID = resultString.substring(0, resultString.length() - 1); resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // query the battery voltage this.command = this.BATTERY_VOLTAGE_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 5; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 5: // get the seahorse battery voltage // the battery voltage string should end in \r if (byteOne == 0x0D) { logger.debug("Received the instrument battery voltage result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the battery voltage string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("Seahorse Battery Voltage: " + resultString.trim()); resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // query the GPS location this.command = this.GPRMC_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 6; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 6: // the GPRMC string should end in END\r // note bytes are in reverse order in the FIFO window if (byteOne == 0x0D && byteTwo == 0x44 && byteThree == 0x4E && byteFour == 0x45) { logger.debug("Received the GPRMS result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the GPRMC string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("Seahorse GPRMC string: " + resultString.trim()); resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; // query the file name for transfer this.command = this.FILENAME_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); state = 7; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 7: // the file name string should end in .Z\r // note bytes are in reverse order in the FIFO window if (byteOne == 0x0D && byteTwo == 0x5A && byteThree == 0x2E) { logger.debug("Received the file name result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the file name string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("File name result: " + resultString.trim()); resultString = resultString.trim(); int fileNameIndex = resultString.indexOf(this.FILENAME_PREFIX); //extract just the filename from the result (excise the "FILE=") this.fileNameToDownload = resultString.substring( (fileNameIndex + (this.FILENAME_PREFIX).length()), resultString.length()); logger.debug("File name to download: " + this.fileNameToDownload); // test to see if the GFN command returns FILES=NONE if (!(resultString.indexOf(this.END_OF_FILES) > 0)) { // there is a file to download. parse the file name, // get the number of blocks to transfer this.command = this.NUMBER_OF_BLOCKS_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 8; break; } else { // We have downloaded all files. Parse the data string, // build the channel map, and flush the data to the Dataturbine // by iterating through the data matrix. The metadata and // ASCII data strings are flushed once with the first matrix // row. // Parse the data file, not the cast file. try { // parse the CTD data file this.ctdParser = new CTDParser(this.dataFileString); // convert the raw frequencies and voltages to engineering // units and return the data as a matrix CTDConverter ctdConverter = new CTDConverter(this.ctdParser); ctdConverter.convert(); RealMatrix convertedDataMatrix = ctdConverter.getConvertedDataValuesMatrix(); // Register the data and metadata channels; failed = register(); if (!failed) { // format the first sample date and use it as the first insert // date. Add the sampleInterval on each iteration to insert // subsequent data rows. Sample interval is by default // 4 scans/second for the CTD. DATE_FORMAT.setTimeZone(TZ); this.sampleDateTime = Calendar.getInstance(); this.sampleDateTime .setTime(DATE_FORMAT.parse(ctdParser.getFirstSampleTime())); for (int row = 0; row < convertedDataMatrix.getRowDimension(); row++) { // Only insert the metadata fields and full ASCII text strings // with the first row of data if (row == 0) { // Add the samplingMode data to the channel map this.channelIndex = this.rbnbChannelMap.Add("samplingMode"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getSamplingMode()); // Add the firstSampleTime data to the channel map this.channelIndex = this.rbnbChannelMap.Add("firstSampleTime"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getFirstSampleTime()); // Add the fileName data to the channel map this.channelIndex = this.rbnbChannelMap.Add("fileName"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getFileName()); // Add the temperatureSerialNumber data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureSerialNumber"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getTemperatureSerialNumber()); // Add the conductivitySerialNumber data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivitySerialNumber"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getConductivitySerialNumber()); // Add the systemUpLoadTime data to the channel map this.channelIndex = this.rbnbChannelMap.Add("systemUpLoadTime"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getSystemUpLoadTime()); // Add the cruiseInformation data to the channel map this.channelIndex = this.rbnbChannelMap.Add("cruiseInformation"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getCruiseInformation()); // Add the stationInformation data to the channel map this.channelIndex = this.rbnbChannelMap.Add("stationInformation"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getStationInformation()); // Add the shipInformation data to the channel map this.channelIndex = this.rbnbChannelMap.Add("shipInformation"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getShipInformation()); // Add the chiefScientist data to the channel map this.channelIndex = this.rbnbChannelMap.Add("chiefScientist"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getChiefScientist()); // Add the organization data to the channel map this.channelIndex = this.rbnbChannelMap.Add("organization"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getOrganization()); // Add the areaOfOperation data to the channel map this.channelIndex = this.rbnbChannelMap.Add("areaOfOperation"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getAreaOfOperation()); // Add the instrumentPackage data to the channel map this.channelIndex = this.rbnbChannelMap.Add("instrumentPackage"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getInstrumentPackage()); // Add the mooringNumber data to the channel map this.channelIndex = this.rbnbChannelMap.Add("mooringNumber"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getMooringNumber()); // Add the instrumentLatitude data to the channel map this.channelIndex = this.rbnbChannelMap.Add("instrumentLatitude"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getInstrumentLatitude() }); // Add the instrumentLongitude data to the channel map this.channelIndex = this.rbnbChannelMap.Add("instrumentLongitude"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getInstrumentLongitude() }); // Add the depthSounding data to the channel map this.channelIndex = this.rbnbChannelMap.Add("depthSounding"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getDepthSounding() }); // Add the profileNumber data to the channel map this.channelIndex = this.rbnbChannelMap.Add("profileNumber"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getProfileNumber()); // Add the profileDirection data to the channel map this.channelIndex = this.rbnbChannelMap.Add("profileDirection"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getProfileDirection()); // Add the deploymentNotes data to the channel map this.channelIndex = this.rbnbChannelMap.Add("deploymentNotes"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getDeploymentNotes()); // Add the mainBatteryVoltage data to the channel map this.channelIndex = this.rbnbChannelMap.Add("mainBatteryVoltage"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getMainBatteryVoltage() }); // Add the lithiumBatteryVoltage data to the channel map this.channelIndex = this.rbnbChannelMap .Add("lithiumBatteryVoltage"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getLithiumBatteryVoltage() }); // Add the operatingCurrent data to the channel map this.channelIndex = this.rbnbChannelMap.Add("operatingCurrent"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getOperatingCurrent() }); // Add the pumpCurrent data to the channel map this.channelIndex = this.rbnbChannelMap.Add("pumpCurrent"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPumpCurrent() }); // Add the channels01ExternalCurrent data to the channel map this.channelIndex = this.rbnbChannelMap .Add("channels01ExternalCurrent"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getChannels01ExternalCurrent() }); // Add the channels23ExternalCurrent data to the channel map this.channelIndex = this.rbnbChannelMap .Add("channels23ExternalCurrent"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getChannels23ExternalCurrent() }); // Add the loggingStatus data to the channel map this.channelIndex = this.rbnbChannelMap.Add("loggingStatus"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getLoggingStatus()); // Add the numberOfScansToAverage data to the channel map this.channelIndex = this.rbnbChannelMap .Add("numberOfScansToAverage"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getNumberOfScansToAverage() }); // Add the numberOfSamples data to the channel map this.channelIndex = this.rbnbChannelMap.Add("numberOfSamples"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getNumberOfSamples() }); // Add the numberOfAvailableSamples data to the channel map this.channelIndex = this.rbnbChannelMap .Add("numberOfAvailableSamples"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getNumberOfAvailableSamples() }); // Add the sampleInterval data to the channel map this.channelIndex = this.rbnbChannelMap.Add("sampleInterval"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getSampleInterval() }); // Add the measurementsPerSample data to the channel map this.channelIndex = this.rbnbChannelMap .Add("measurementsPerSample"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getMeasurementsPerSample() }); // Add the transmitRealtime data to the channel map this.channelIndex = this.rbnbChannelMap.Add("transmitRealtime"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getTransmitRealtime()); // Add the numberOfCasts data to the channel map this.channelIndex = this.rbnbChannelMap.Add("numberOfCasts"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getNumberOfCasts() }); // Add the minimumConductivityFrequency data to the channel map this.channelIndex = this.rbnbChannelMap .Add("minimumConductivityFrequency"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getMinimumConductivityFrequency() }); // Add the pumpDelay data to the channel map this.channelIndex = this.rbnbChannelMap.Add("pumpDelay"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsInt32(this.channelIndex, new int[] { this.ctdParser.getPumpDelay() }); // Add the automaticLogging data to the channel map this.channelIndex = this.rbnbChannelMap.Add("automaticLogging"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getAutomaticLogging()); // Add the ignoreMagneticSwitch data to the channel map this.channelIndex = this.rbnbChannelMap.Add("ignoreMagneticSwitch"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getIgnoreMagneticSwitch()); // Add the batteryType data to the channel map this.channelIndex = this.rbnbChannelMap.Add("batteryType"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getBatteryType()); // Add the batteryCutoff data to the channel map this.channelIndex = this.rbnbChannelMap.Add("batteryCutoff"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getBatteryCutoff()); // Add the pressureSensorType data to the channel map this.channelIndex = this.rbnbChannelMap.Add("pressureSensorType"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getPressureSensorType()); // Add the pressureSensorRange data to the channel map this.channelIndex = this.rbnbChannelMap.Add("pressureSensorRange"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getPressureSensorRange()); // Add the sbe38TemperatureSensor data to the channel map this.channelIndex = this.rbnbChannelMap .Add("sbe38TemperatureSensor"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getSbe38TemperatureSensor()); // Add the gasTensionDevice data to the channel map this.channelIndex = this.rbnbChannelMap.Add("gasTensionDevice"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getGasTensionDevice()); // Add the externalVoltageChannelZero data to the channel map this.channelIndex = this.rbnbChannelMap .Add("externalVoltageChannelZero"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getExternalVoltageChannelZero()); // Add the externalVoltageChannelOne data to the channel map this.channelIndex = this.rbnbChannelMap .Add("externalVoltageChannelOne"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getExternalVoltageChannelOne()); // Add the externalVoltageChannelTwo data to the channel map this.channelIndex = this.rbnbChannelMap .Add("externalVoltageChannelTwo"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getExternalVoltageChannelTwo()); // Add the externalVoltageChannelThree data to the channel map this.channelIndex = this.rbnbChannelMap .Add("externalVoltageChannelThree"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getExternalVoltageChannelThree()); // Add the echoCommands data to the channel map this.channelIndex = this.rbnbChannelMap.Add("echoCommands"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getEchoCommands()); // Add the outputFormat data to the channel map this.channelIndex = this.rbnbChannelMap.Add("outputFormat"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getOutputFormat()); // Add the temperatureCalibrationDate data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureCalibrationDate"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getTemperatureCalibrationDate()); // Add the temperatureCoefficientTA0 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureCoefficientTA0"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA0() }); // Add the temperatureCoefficientTA1 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureCoefficientTA1"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA1() }); // Add the temperatureCoefficientTA2 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureCoefficientTA2"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA2() }); // Add the temperatureCoefficientTA3 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureCoefficientTA3"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getTemperatureCoefficientTA3() }); // Add the temperatureOffsetCoefficient data to the channel map this.channelIndex = this.rbnbChannelMap .Add("temperatureOffsetCoefficient"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getTemperatureOffsetCoefficient() }); // Add the conductivityCalibrationDate data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCalibrationDate"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getConductivityCalibrationDate()); // Add the conductivityCoefficientG data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientG"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientG() }); // Add the conductivityCoefficientH data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientH"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientH() }); // Add the conductivityCoefficientI data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientI"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientI() }); // Add the conductivityCoefficientJ data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientJ"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientJ() }); // Add the conductivityCoefficientCF0 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientCF0"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCF0() }); // Add the conductivityCoefficientCPCOR data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientCPCOR"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCPCOR() }); // Add the conductivityCoefficientCTCOR data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientCTCOR"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getConductivityCoefficientCTCOR() }); // Add the conductivityCoefficientCSLOPE data to the channel map this.channelIndex = this.rbnbChannelMap .Add("conductivityCoefficientCSLOPE"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser .getConductivityCoefficientCSLOPE() }); // Add the pressureSerialNumber data to the channel map this.channelIndex = this.rbnbChannelMap.Add("pressureSerialNumber"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.ctdParser.getPressureSerialNumber()); // Add the pressureCoefficientPA0 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPA0"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPA0() }); // Add the pressureCoefficientPA1 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPA1"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPA1() }); // Add the pressureCoefficientPA2 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPA2"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPA2() }); // Add the pressureCoefficientPTCA0 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTCA0"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCA0() }); // Add the pressureCoefficientPTCA1 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTCA1"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCA1() }); // Add the pressureCoefficientPTCA2 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTCA2"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCA2() }); // Add the pressureCoefficientPTCB0 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTCB0"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCB0() }); // Add the pressureCoefficientPTCB1 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTCB1"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCB1() }); // Add the pressureCoefficientPTCB2 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTCB2"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTCB2() }); // Add the pressureCoefficientPTEMPA0 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTEMPA0"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTEMPA0() }); // Add the pressureCoefficientPTEMPA1 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTEMPA1"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTEMPA1() }); // Add the pressureCoefficientPTEMPA2 data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureCoefficientPTEMPA2"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureCoefficientPTEMPA2() }); // Add the pressureOffsetCoefficient data to the channel map this.channelIndex = this.rbnbChannelMap .Add("pressureOffsetCoefficient"); this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { this.ctdParser.getPressureOffsetCoefficient() }); // Insert the file into the channel map. this.channelIndex = this.rbnbChannelMap.Add(this.rbnbChannelName); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.dataFileString); this.channelIndex = this.rbnbChannelMap.Add("ASCIICastData"); this.rbnbChannelMap.PutMime(this.channelIndex, "text/plain"); this.rbnbChannelMap.PutDataAsString(this.channelIndex, this.castFileString); } // Add in the matrix data row to the map here List<String> variableNames = ctdParser.getDataVariableNames(); List<String> variableUnits = ctdParser.getDataVariableUnits(); // iterate through the variable names and add them to // the channel map. for (int variableIndex = 0; variableIndex < variableNames .size(); variableIndex++) { // Add the variable name to the channel map this.channelIndex = this.rbnbChannelMap .Add(variableNames.get(variableIndex)); // The matrix is a double array, so set the data type below this.rbnbChannelMap.PutMime(this.channelIndex, "application/octet-stream"); // add the data to the map from the [row,column] of the // matrix (row is from the outer for loop) this.rbnbChannelMap.PutDataAsFloat64(this.channelIndex, new double[] { convertedDataMatrix.getEntry(row, variableIndex) }); } // Flush the channel map to the RBNB double sampleTimeAsSecondsSinceEpoch = (double) (this.sampleDateTime .getTimeInMillis() / 1000); this.rbnbChannelMap.PutTime(sampleTimeAsSecondsSinceEpoch, 0d); getSource().Flush(this.rbnbChannelMap); logger.info("Flushed data to the DataTurbine."); this.rbnbChannelMap.Clear(); // samples are taken 4x per second, so increment the // sample time by 250 milliseconds for the next insert this.sampleDateTime.add(Calendar.MILLISECOND, 250); } // end for loop } // end if !failed } catch (Exception e) { logger.debug("Failed to parse the CTD data file: " + e.getMessage()); } // there are no more files to read. close the Tx session. this.command = this.CLOSE_TRANSFER_SESSION_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); // clean up resultBuffer.clear(); this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 10; break; } } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 8: // the number of blocks string should end in \r if (byteOne == 0x0D) { logger.debug("Received the number of blocks result."); this.resultByteCount++; // add the last byte found to the count // add the last byte found to the result buffer if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); resultBuffer.put(byteOne); } // report the number of blocks string resultArray = new byte[this.resultByteCount]; resultBuffer.flip(); resultBuffer.get(resultArray); resultString = new String(resultArray, "US-ASCII"); logger.debug("Number of bytes reported: " + resultString.trim()); int numberOfBlocksIndex = resultString.indexOf(this.BLOCKSIZE_PREFIX); // If 'BLOCKSIZE=' is not found, set the index to 0 if (numberOfBlocksIndex == -1) { numberOfBlocksIndex = 0; } resultString = resultString.substring( (numberOfBlocksIndex + (this.BLOCKSIZE_PREFIX).length()), resultString.length()); // convert the string to an integer try { this.numberOfBlocks = new Integer(resultString.trim()).intValue(); logger.debug("Number of bytes to download: " + this.numberOfBlocks); } catch (java.lang.NumberFormatException nfe) { failed = true; nfe.printStackTrace(); logger.debug("Failed to convert returned string value " + "to an integer value. The returned string is: " + this.numberOfBlocks); } // test to see if the GNB command returns DONE\r if (!(resultString.indexOf(this.TRANSFER_COMPLETE) > 0)) { // there are bytes to transfer. send the transfer command this.command = this.TRANSFER_BLOCKS_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); //resultBuffer.clear(); dont clear the buffer this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 9; break; } else { // there are no more bytes to transfer. // Decompress the file, which is under zlib compression. Inflater inflater = new Inflater(); inflater.setInput(resultBuffer.array()); byte[] output = new byte[resultBuffer.capacity()]; int numDecompressed = inflater.inflate(output); // set the appropriate string variable if (this.fileNameToDownload.indexOf(DATA_FILE_PREFIX) > 0) { this.dataFileString = new String(output); //report the file contents to the log logger.debug("File " + this.fileNameToDownload + ": "); logger.debug(this.dataFileString); } else { this.castFileString = new String(output); //report the file contents to the log logger.debug("File " + this.fileNameToDownload + ": "); logger.debug(this.castFileString); } // Ask for the next file. this.command = this.FILENAME_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); //resultBuffer.clear(); dont clear the buffer this.resultByteCount = 0; resultArray = new byte[0]; resultString = ""; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 7; //back to the file name state break; } } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 9: // transfer up to the reported number of bytes if (this.resultByteCount == this.numberOfBlocks) { // we have downloaded the reported bytes. get the next section. // get the number of blocks to transfer this.command = this.NUMBER_OF_BLOCKS_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); //resultBuffer.clear(); this.resultByteCount = 0; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 8; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 10: // the response from the modem should end in BYE\r // note bytes are in reverse order in the FIFO window if (byteOne == 0x0D && byteTwo == 0x45 && byteThree == 0x59 && byteFour == 0x42) { logger.debug("Received the BYE command."); // continue to disconnect. send the escape sequence this.command = this.ESCAPE_SEQUENCE_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); resultBuffer.clear(); this.resultByteCount = 0; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 11; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 11: // the response from the modem should end in OK\r\n // note bytes are in reverse order in the FIFO window if (byteOne == 0x0D && byteTwo == 0x0A && byteThree == 0x4B && byteFour == 0x4F) { // now hang up. this.command = this.MODEM_COMMAND_PREFIX + this.HANGUP_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); resultBuffer.clear(); this.resultByteCount = 0; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 12; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } case 12: // the response from the modem should end in OK\r\n // note bytes are in reverse order in the FIFO window if (byteOne == 0x0D && byteTwo == 0x0A && byteThree == 0x4B && byteFour == 0x4F) { // we are done. re-test if is network registered this.command = this.MODEM_COMMAND_PREFIX + this.REGISTRATION_STATUS_COMMAND + this.MODEM_COMMAND_SUFFIX; this.sentCommand = queryInstrument(this.command); // allow time for the modem to respond streamingThread.sleep(this.SLEEP_INTERVAL); resultBuffer.clear(); this.resultByteCount = 0; byteOne = 0x00; byteTwo = 0x00; byteThree = 0x00; byteFour = 0x00; state = 0; break; } else { // still in the middle of the result, keep adding bytes this.resultByteCount++; // add each byte found if (resultBuffer.remaining() > 0) { resultBuffer.put(byteOne); } else { resultBuffer.compact(); logger.debug("Compacting resultBuffer ..."); resultBuffer.put(byteOne); } break; } } // end switch statement // shift the bytes in the FIFO window byteFour = byteThree; byteThree = byteTwo; byteTwo = byteOne; } //end while (more unread bytes) // prepare the buffer to read in more bytes from the stream buffer.compact(); } // end while (more socketChannel bytes to read) socketChannel.close(); } catch (IOException e) { // handle exceptions // In the event of an i/o exception, log the exception, and allow execute() // to return false, which will prompt a retry. failed = true; e.printStackTrace(); return !failed; } catch (java.lang.InterruptedException ine) { failed = true; ine.printStackTrace(); return !failed; } catch (java.util.zip.DataFormatException dfe) { failed = true; dfe.printStackTrace(); return !failed; } return !failed; }
From source file:edu.umass.cs.gigapaxos.paxospackets.RequestPacket.java
/** * The weird constant above is to try to avoid mistakes in the painful (but * totally worth it) byte'ification method below. Using bytes as opposed to * json strings makes a non-trivial difference (~2x over json-smart and >4x * over org.json. So we just chuck json libraries and use our own byte[] * serializer for select packets./*from w ww.ja va 2s .c om*/ * * The serialization overhead really matters most for RequestPacket and * AcceptPacket. Every request, even with batching, must be deserialized by * the coordinator and must be serialized back while sending out the * AcceptPacket. The critical path is the following at a coordinator and is * incurred at least in part even with batching for every request: (1) * receive request, (2) send accept, (3) receive accept_replies, (4) send * commit Accordingly, we use byteification for {@link RequestPacket}, * {@link AcceptPacket}, {@link BatchedAcceptReply} and * {@link BatchedCommit}. * * */ protected byte[] toBytes(boolean instrument) { // return cached value if already present if ((this.getType() == PaxosPacketType.REQUEST || this.getType() == PaxosPacketType.ACCEPT) && this.byteifiedSelf != null && !instrument) return this.byteifiedSelf; // check if we can use byteification at all; if not, use toString() if (!((BYTEIFICATION && IntegerMap.allInt()) || instrument)) { try { if (this.getType() == PaxosPacketType.REQUEST || this.getType() == PaxosPacketType.ACCEPT) return this.byteifiedSelf = this.toString().getBytes(CHARSET); // cache return this.toString().getBytes(CHARSET); } catch (UnsupportedEncodingException e1) { e1.printStackTrace(); return null; } } // else byteify try { int exactLength = 0; byte[] array = new byte[this.lengthEstimate()]; ByteBuffer bbuf = ByteBuffer.wrap(array); assert (bbuf.position() == 0); // paxospacket stuff super.toBytes(bbuf); int ppPos = bbuf.position(); // for assertion assert (bbuf.position() == ByteBuffer.wrap(array, SIZEOF_PAXOSPACKET_FIXED - 1, 1).get() + SIZEOF_PAXOSPACKET_FIXED) : bbuf.position() + " != " + ByteBuffer.wrap(array, SIZEOF_PAXOSPACKET_FIXED - 1, 1).get() + SIZEOF_PAXOSPACKET_FIXED; exactLength += (bbuf.position()); bbuf.putLong(this.requestID); bbuf.put(this.stop ? (byte) 1 : (byte) 0); exactLength += (Long.BYTES + 1); // addresses /* Note: 0 is ambiguous with wildcard address, but that's okay * because an incoming packet will never come with a wildcard * address. */ bbuf.put(this.clientAddress != null ? this.clientAddress.getAddress().getAddress() : new byte[4]); // 0 (not -1) means invalid port bbuf.putShort(this.clientAddress != null ? (short) this.clientAddress.getPort() : 0); /* Note: 0 is an ambiguous wildcard address that could also be a * legitimate value of the listening socket address. If the request * happens to have no listening address, we will end up assuming it * was received on the wildcard address. At worst, the matching for * the corresponding response back to the client can fail. */ bbuf.put(this.listenAddress != null ? this.listenAddress.getAddress().getAddress() : new byte[4]); // 0 (not -1) means invalid port bbuf.putShort(this.listenAddress != null ? (short) this.listenAddress.getPort() : 0); exactLength += 2 * (Integer.BYTES + Short.BYTES); // other non-final fields bbuf.putInt(this.entryReplica); bbuf.putLong(this.entryTime); bbuf.put(this.shouldReturnRequestValue ? (byte) 1 : (byte) 0); bbuf.putInt(this.forwardCount); exactLength += (Integer.BYTES + Long.BYTES + 1 + Integer.BYTES); // digest related fields: broadcasted, digest // whether this request was already broadcasted bbuf.put(this.broadcasted ? (byte) 1 : (byte) 0); exactLength += 1; assert (exactLength == // where parent left us off ppPos + SIZEOF_REQUEST_FIXED // for the three int fields not yet filled - 4 * Integer.BYTES) : exactLength + " != [" + ppPos + " + " + SIZEOF_REQUEST_FIXED + " - " + 4 * Integer.BYTES + "]"; // digest length and digest iteself bbuf.putInt(this.digest != null ? this.digest.length : 0); exactLength += Integer.BYTES; if (this.digest != null) bbuf.put(this.digest); exactLength += (this.digest != null ? this.digest.length : 0); // /////////// end of digest related fields ////////// // highly variable length fields // requestValue byte[] reqValBytes = this.requestValue != null ? this.requestValue.getBytes(CHARSET) : new byte[0]; bbuf.putInt(reqValBytes != null ? reqValBytes.length : 0); bbuf.put(reqValBytes); exactLength += (4 + reqValBytes.length); // responseValue byte[] respValBytes = this.responseValue != null ? this.responseValue.getBytes(CHARSET) : new byte[0]; bbuf.putInt(respValBytes != null ? respValBytes.length : 0); bbuf.put(respValBytes); exactLength += (4 + respValBytes.length); // batched requests batchSize|(length:batchedReqBytes)+ bbuf.putInt(this.batchSize()); exactLength += (4); if (this.batchSize() > 0) for (RequestPacket req : this.batched) { byte[] element = req.toBytes(); bbuf.putInt(element.length); bbuf.put(element); exactLength += (4 + element.length); } // bbuf.array() was a generous allocation byte[] exactBytes = new byte[exactLength]; bbuf.flip(); assert (bbuf.remaining() == exactLength) : bbuf.remaining() + " != " + exactLength; bbuf.get(exactBytes); if (this.getType() == PaxosPacketType.REQUEST) this.byteifiedSelf = exactBytes; return exactBytes; } catch (UnsupportedEncodingException e) { e.printStackTrace(); } return null; }