git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@131375 82a268e6-3cf1-43bd-a215-b396298e98cf
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package org.gcube.dataanalysis.executor.job.management;
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import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.PrintStream;
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import java.nio.charset.StandardCharsets;
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import java.nio.file.Files;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.contentmanager.storageclient.model.protocol.smp.Handler;
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import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
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import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
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public class GenericWorker extends StandardLocalExternalAlgorithm{
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private static String genericWorkerDir = "/genericworker/";
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public static String AlgorithmClassParameter = "AlgorithmClass";
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public static String RightSetStartIndexParameter = "RightSetStartIndex";
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public static String NumberOfRightElementsToProcessParameter = "NumberOfRightElementsToProcess";
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public static String LeftSetStartIndexParameter = "LeftSetStartIndex";
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public static String NumberOfLeftElementsToProcessParameter = "NumberOfLeftElementsToProcess";
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public static String IsDuplicateParameter = "IsDuplicate";
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public static String SessionParameter = "Session";
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public static String ConfigurationFileParameter = "ConfigurationFile";
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public static String DeleteTemporaryFilesParameter = "DeleteTemporaryFiles";
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public static String OutputParameter = "Process_Outcome";
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public static String TASK_SUCCESS = "TASK_SUCCESS";
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public static String TASK_FAILURE = "TASK_FAILURE";
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private static void inputStreamToFile(InputStream is, String path) throws FileNotFoundException, IOException {
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FileOutputStream out = new FileOutputStream(new File(path));
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byte buf[] = new byte[1024];
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int len = 0;
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while ((len = is.read(buf)) > 0)
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out.write(buf, 0, len);
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out.close();
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}
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public void executeAlgorithm(String algorithmClass,
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int rightStartIndex,
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int numberOfRightElementsToProcess,
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int leftStartIndex,
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int numberOfLeftElementsToProcess,
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boolean isduplicate,
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String session,
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File nodeConfigurationFileObject,
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boolean deleteFiles) throws Exception {
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PrintStream origOut = System.out;
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PrintStream origErr = System.err;
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status = 0f;
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Logger logger = AnalysisLogger.getLogger();
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StringBuffer sb = new StringBuffer();
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File tempDir = null ;
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try {
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Handler.activateProtocol();
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String locDir = session;
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if (session == null)
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locDir = ("" + UUID.randomUUID()).replace("-", "");
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// invoke the algorithm
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logger.debug("GenericWorker-> Creating algorithm " + algorithmClass);
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ActorNode node = (ActorNode) Class.forName(algorithmClass).newInstance();
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logger.debug("GenericWorker-> executing algorithm " + algorithmClass +" with parameters:");
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logger.debug("GenericWorker-> rightStartIndex:" +rightStartIndex);
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logger.debug("GenericWorker-> numberOfRightElementsToProcess:" +numberOfRightElementsToProcess);
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logger.debug("GenericWorker-> leftStartIndex:" +leftStartIndex);
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logger.debug("GenericWorker-> numberOfLeftElementsToProcess:" +numberOfLeftElementsToProcess);
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logger.debug("GenericWorker-> isduplicate:" +isduplicate);
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logger.debug("GenericWorker-> execution directory:" +config.getConfigPath());
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logger.debug("GenericWorker-> nodeConfigurationFileObject.getName():" +nodeConfigurationFileObject.getName());
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File sandboxfile = new File(config.getConfigPath(),nodeConfigurationFileObject.getName());
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Files.copy(nodeConfigurationFileObject.toPath(), sandboxfile.toPath(), REPLACE_EXISTING);
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logger.debug("GenericWorker-> copied configuration file as " +sandboxfile.getAbsolutePath());
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ByteArrayOutputStream baos = new ByteArrayOutputStream();
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PrintStream ps = new PrintStream(baos);
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System.setOut(ps);
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System.setErr(ps);
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node.executeNode(rightStartIndex, numberOfRightElementsToProcess, leftStartIndex, numberOfLeftElementsToProcess, isduplicate,
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config.getConfigPath(), nodeConfigurationFileObject.getName(), "log.txt");
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String log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
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logger.debug("GenericWorker-> Execution Fulllog" );
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logger.debug("GenericWorker-> " + log);
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logger.debug("GenericWorker-> Script executed! " );
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boolean del = sandboxfile.delete();
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logger.debug("GenericWorker-> deleted sandbox file: "+del );
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logger.debug("GenericWorker-> all done");
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if (log.contains("Exception:") && log.contains("Caused by:")){
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outputParameters.put(OutputParameter, TASK_FAILURE);
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logger.debug("GenericWorker-> Failure!");
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}
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else
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outputParameters.put(OutputParameter, TASK_SUCCESS);
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logger.debug("GenericWorker-> Success!");
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} catch (Throwable e) {
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outputParameters.put(OutputParameter, TASK_FAILURE);
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e.printStackTrace();
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logger.debug("GenericWorker-> ERROR: " + e.getLocalizedMessage());
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status = 100f;
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throw new Exception(e.getLocalizedMessage());
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}
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finally{
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System.setOut(origOut);
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System.setErr(origErr);
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try{
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if (deleteFiles && (tempDir!=null)) {
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logger.debug("GenericWorker-> ... deleting local files");
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// delete all after execution
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for (File singlefile : tempDir.listFiles()) {
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boolean del = singlefile.delete();
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if (!del)
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logger.debug("GenericWorker-> ERROR deleting " + singlefile.getName() + " " + del);
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else
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logger.debug("GenericWorker-> deleted LOCAL FILE " + singlefile.getName() + " " + del);
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}
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logger.debug("GenericWorker-> deleting temporary directory");
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tempDir.delete();
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}
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}catch(Exception e3){
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e3.printStackTrace();
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logger.debug("GenericWorker-> Error deleting files");
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}
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status = 100f;
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}
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}
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@Override
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public void init() throws Exception {
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}
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@Override
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public String getDescription() {
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return "An algorithm that executes another other algorithm";
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}
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@Override
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protected void process() throws Exception {
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AnalysisLogger.getLogger().debug("Parameters: "+config.getGeneralProperties());
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String algorithmClass = config.getParam("AlgorithmClass");
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int rightStartIndex = Integer.parseInt(config.getParam("RightSetStartIndex"));
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int numberOfRightElementsToProcess =Integer.parseInt(config.getParam("NumberOfRightElementsToProcess"));
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int leftStartIndex =Integer.parseInt(config.getParam("LeftSetStartIndex"));
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int numberOfLeftElementsToProcess =Integer.parseInt(config.getParam("NumberOfLeftElementsToProcess"));
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boolean isduplicate=Boolean.parseBoolean(config.getParam("IsDuplicate"));
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String session=config.getParam("Session");
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File nodeConfigurationFileObject=new File (config.getParam("ConfigurationFile"));
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boolean deleteFiles= Boolean.parseBoolean(config.getParam("DeleteTemporaryFiles"));
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AnalysisLogger.getLogger().debug("Executing the algorithm");
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executeAlgorithm(algorithmClass, rightStartIndex, numberOfRightElementsToProcess, leftStartIndex, numberOfLeftElementsToProcess, isduplicate, session, nodeConfigurationFileObject, deleteFiles);
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AnalysisLogger.getLogger().debug("Algorithm executed!");
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}
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@Override
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protected void setInputParameters() {
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addStringInput("AlgorithmClass", "The full class path of the algorithm", "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer");
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addIntegerInput("RightSetStartIndex", "The start index of the right set in a cartesian product of the input", "1");
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addIntegerInput("NumberOfRightElementsToProcess", "The number of elements to process in the right set", "1");
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addIntegerInput("LeftSetStartIndex", "The start index of the left set in a cartesian product of the input", "1");
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addIntegerInput("NumberOfLeftElementsToProcess", "The number of elements to process in the left set", "1");
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addBooleanInput("IsDuplicate", "Indicate if this sub computation is a duplicate of another sub-computation", "false");
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addStringInput("Session", "The session this sub-computation belongs to", "123456");
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addFileInput("ConfigurationFile", "A configuration file for the algorithm in an XML serialisation format for the AlgorithmConfiguration Object", "config.dat");
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addBooleanInput("DeleteTemporaryFiles","Delete local temporary files after the computation","true");
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}
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@Override
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public void shutdown() {
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}
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}
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