Java tutorial
/** * Global Sensor Networks (GSN) Source Code * Copyright (c) 2006-2014, Ecole Polytechnique Federale de Lausanne (EPFL) * * This file is part of GSN. * * GSN is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * GSN is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with GSN. If not, see <http://www.gnu.org/licenses/>. * * File: src/gsn/vsensor/RVirtualSensor.java * * @author sp3dy * @author Ali Salehi * @author Mehdi Riahi * */ package gsn.vsensor; import gsn.beans.DataField; import gsn.beans.DataTypes; import gsn.beans.StreamElement; import java.io.File; import java.io.Serializable; import java.util.Hashtable; import java.util.TreeMap; import java.util.concurrent.ArrayBlockingQueue; import org.apache.commons.io.FileUtils; import org.slf4j.LoggerFactory; import org.slf4j.Logger; import org.rosuda.REngine.REXP; import org.rosuda.REngine.Rserve.RConnection; public class RVirtualSensor extends AbstractVirtualSensor { private static final String WINDOW_SIZE = "window_size"; private static final String STEP_SIZE = "step_size"; private static final String OUTPUT_PLOT = "gsn_plot"; private static final String SCRIPT = "script"; private static final String SERVER = "server"; private static final String PORT = "port"; public String script = null; public String stype = null; private static transient Logger logger = LoggerFactory.getLogger(RVirtualSensor.class); private Hashtable<String, ArrayBlockingQueue<StreamElement>> circularBuffers; private int windowSize = -1; private int stepSize = -1; public RConnection rc; public REXP xp; public TreeMap<String, String> params = null; public boolean initialize() { params = getVirtualSensorConfiguration().getMainClassInitialParams(); circularBuffers = new Hashtable<String, ArrayBlockingQueue<StreamElement>>(); // Get the parameters from the XML configuration file String param = null; param = params.get(WINDOW_SIZE); if (param != null) { windowSize = Integer.parseInt(param); } else { logger.error("The required parameter: >" + WINDOW_SIZE + "<+ is missing.from the virtual sensor configuration file."); return false; } param = params.get("script_type"); if (param != null) { stype = param; } else { stype = "computation"; } param = params.get(STEP_SIZE); if (param != null) { stepSize = Integer.parseInt(param); } else { logger.error("The required parameter: >" + STEP_SIZE + "<+ is missing.from the virtual sensor configuration file."); return false; } if (windowSize < stepSize) { logger.error( "The parameter " + WINDOW_SIZE + " must be greater or equal to the parameter " + STEP_SIZE); return false; } return true; } public void dataAvailable(String inputStreamName, StreamElement streamElement) { ArrayBlockingQueue<StreamElement> circularBuffer = circularBuffers.get(inputStreamName); // Get the circular buffer that matches the input stream. Create a new one // if none exists if (circularBuffer == null) { circularBuffer = new ArrayBlockingQueue<StreamElement>(windowSize); circularBuffers.put(inputStreamName, circularBuffer); } try { circularBuffer.put(streamElement); logger.debug( "Window for " + inputStreamName + " contains: " + circularBuffer.size() + " of " + windowSize); if (circularBuffer.size() == windowSize) { logger.info("Window for " + inputStreamName + " contains: " + circularBuffer.size() + " of " + windowSize); // Connect to Rserve and assign global variables try { rc = new RConnection(params.get(SERVER), Integer.parseInt(params.get(PORT))); logger.info("Connected to R server " + params.get(SERVER) + ":" + params.get(PORT)); String[] fieldname = streamElement.getFieldNames(); logger.info("Sending " + fieldname.length + " data attributes to R server."); // Assign R vector variables prior the script for (int n = 0; n < fieldname.length; n++) { // Build the window double[] values = new double[windowSize]; StreamElement elt = null; // convert the circular buffer to an array Object[] elts = circularBuffer.toArray(); for (int i = 0; i < elts.length; i++) { elt = (StreamElement) elts[i]; values[i] = ((Number) elt.getData()[n]).doubleValue(); // } // assign vectors as R variables rc.assign("gsn_" + fieldname[n].toLowerCase(), values); } logger.info("Done."); // read the R script // open the script file every time we do some processing (this can be // improved). File file = new File(params.get(SCRIPT).toString()); script = FileUtils.readFileToString(file, "UTF-8"); logger.info("Sending R script."); // evaluate the R script rc.voidEval(script); logger.info("Done."); // get the output timestamp logger.info("Performing computation in R server (please wait)."); // collect vector values after computation DataField[] outStructure = null; outStructure = getVirtualSensorConfiguration().getOutputStructure(); String[] plotFieldName = new String[outStructure.length]; Byte[] plotFieldType = new Byte[outStructure.length]; for (int w = 0; w < outStructure.length; w++) { plotFieldName[w] = outStructure[w].getName(); plotFieldType[w] = outStructure[w].getDataTypeID(); } Serializable[] outputData = null; StreamElement se = null; Byte[] fieldType = streamElement.getFieldTypes(); // check if we have defined more attributes in the output structure if (outStructure.length > fieldname.length) { outputData = new Serializable[outStructure.length]; } else { outputData = new Serializable[fieldname.length]; } for (int n = 0; n < fieldname.length; n++) { // evaluate/get attribute data from R server xp = rc.parseAndEval(fieldname[n].toLowerCase()); if (fieldType[n] == DataTypes.DOUBLE) { double[] b1 = xp.asDoubles(); outputData[n] = b1[b1.length - 1]; } if (fieldType[n] == DataTypes.INTEGER) { int[] b1 = xp.asIntegers(); outputData[n] = b1[b1.length - 1]; } if (fieldType[n] == DataTypes.BIGINT) { int[] b1 = xp.asIntegers(); outputData[n] = (long) b1[b1.length - 1]; } } int len1 = outStructure.length; int len2 = fieldname.length; // check if we have defined more attributes in the output structure if (len1 > len2) { if (stype.equals("plot")) { xp = rc.parseAndEval("gsn_plot"); outputData[len2] = xp.asBytes(); se = new StreamElement(plotFieldName, plotFieldType, outputData); } } else { se = new StreamElement(fieldname, fieldType, outputData); } logger.info("Computation finished."); dataProduced(se); logger.debug("Stream published: " + se.toString().toLowerCase()); // Close connection to R server rc.close(); logger.info("Connection to R server closed."); } catch (Exception e) { logger.warn(e.getMessage()); // Close connection to R server logger.info("Connection to R server closed."); rc.close(); } // Remove step size elements from the beginning of the buffer for (int i = 0; i < stepSize; i++) { try { circularBuffer.take(); } catch (InterruptedException e) { logger.warn(e.getMessage(), e); } } } // end if if for window } catch (InterruptedException e) { logger.warn(e.getMessage(), e); } } public void dispose() { } public int getPredicateValueAsIntWithException(String parameter) { String param = getVirtualSensorConfiguration().getMainClassInitialParams().get(parameter); if (param == null) throw new java.lang.RuntimeException("The required parameter: >" + parameter + "<+ is missing.from the virtual sensor configuration file."); else return Integer.parseInt(param); } }