Examples of org.ogce.gfac.context.ExecutionContext

org.ogce.gfac.context.ExecutionContext

    return buff.toString();
  }


  @Override
  public void initialize(InvocationContext invocationContext) throws GfacException {
    ExecutionContext appExecContext = invocationContext.getExecutionContext();
    ExecutionModel model = appExecContext.getExecutionModel();
    
    AmazonSecurityContext amazonSecurityContext = ((AmazonSecurityContext) invocationContext.getSecurityContext(AMAZON_SECURITY_CONTEXT));
    String access_key = amazonSecurityContext.getAccessKey();
    String secret_key = amazonSecurityContext.getSecretKey();

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    }
  }
  
  @Override
  public void execute(InvocationContext invocationContext) throws GfacException {
    ExecutionContext context = invocationContext.getExecutionContext();
    ExecutionModel model = context.getExecutionModel();


    List<String> cmdList = new ArrayList<String>();


    SSHClient ssh = new SSHClient();
    try {


      /*
       * Notifier
       */
      NotificationService notifier = context.getNotificationService();


      /*
       * Builder Command
       */
      cmdList.add(context.getExecutionModel().getExecutable());
      cmdList.addAll(context.getExecutionModel().getInputParameters());


      // create process builder from command
      String command = buildCommand(cmdList);
      
      //redirect StdOut and StdErr
      command += SPACE + "1>" + SPACE + model.getStdOut();
      command += SPACE + "2>" + SPACE + model.getStderr();      


      // get the env of the host and the application
      Map<String, String> nv = context.getExecutionModel().getEnv();      


      // extra env's
      nv.put(GFacConstants.INPUT_DATA_DIR, context.getExecutionModel().getInputDataDir());
      nv.put(GFacConstants.OUTPUT_DATA_DIR, context.getExecutionModel().getOutputDataDir());
      
      // log info
      log.info("Command = " + buildCommand(cmdList));      
      for (String key : nv.keySet()) {
        log.info("Env[" + key + "] = " + nv.get(key));
      }


      // notify start
      DurationObj compObj = notifier.computationStarted();


      /*
       * Create ssh connection
       */
      ssh.loadKnownHosts();
      ssh.connect(model.getHost());
      ssh.authPublickey(privateKeyFilePath);


      final Session session = ssh.startSession();
      try {
        /*
         * Build working Directory
         */
        log.info("WorkingDir = " + model.getWorkingDir());      
        session.exec("mkdir -p " + model.getWorkingDir());
        session.exec("cd " + model.getWorkingDir());
        
        /*
         * Set environment
         */
        for (String key : nv.keySet()) {
          session.setEnvVar(key, nv.get(key));
        }
        
        /*
         * Execute
         */
        Command cmd = session.exec(command);
        log.info("stdout=" + GfacUtils.readFromStream(session.getInputStream()));
        cmd.join(5, TimeUnit.SECONDS);
        
        
        // notify end
        notifier.computationFinished(compObj);
        
        /*
         * check return value. usually not very helpful to draw conclusions
         * based on return values so don't bother. just provide warning in
         * the log messages
         */        
        if (cmd.getExitStatus() != 0) {
          log.error("Process finished with non zero return value. Process may have failed");
        } else {
          log.info("Process finished with return value of zero.");
        }                        
        
        File logDir = new File("./service_logs");
        if (!logDir.exists()) {
          logDir.mkdir();
        }        
        
        // Get the Stdouts and StdErrs
        QName x = QName.valueOf(invocationContext.getServiceName());
        String timeStampedServiceName = GfacUtils.createServiceDirName(x);
        File localStdOutFile = new File(logDir, timeStampedServiceName + ".stdout");
        File localStdErrFile = new File(logDir, timeStampedServiceName + ".stderr");
        
        SCPFileTransfer fileTransfer = ssh.newSCPFileTransfer();
        fileTransfer.download(model.getStdOut(), localStdOutFile.getAbsolutePath());
        fileTransfer.download(model.getStderr(), localStdErrFile.getAbsolutePath());        
        
        context.getExecutionModel().setStdoutStr(GfacUtils.readFile(localStdOutFile.getAbsolutePath()));
        context.getExecutionModel().setStderrStr(GfacUtils.readFile(localStdErrFile.getAbsolutePath()));
        
        // set to context
        OutputUtils.fillOutputFromStdout(invocationContext.getMessageContext("output"), context.getExecutionModel().getStdoutStr(), context.getExecutionModel().getStderrStr());
        
      } catch (Exception e) {
        throw e;
      } finally {
        try {

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public class GramProvider extends AbstractProvider {


  public static final String MYPROXY_SECURITY_CONTEXT = "myproxy";


  public void initialize(InvocationContext invocationContext) throws GfacException {
    ExecutionContext appExecContext = invocationContext.getExecutionContext();
    ExecutionModel model = appExecContext.getExecutionModel();


    GridFtp ftp = new GridFtp();


    try {
      GSSCredential gssCred = ((GSISecurityContext) invocationContext.getSecurityContext(MYPROXY_SECURITY_CONTEXT)).getGssCredentails();

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      e.printStackTrace();
    }
  }


  public void execute(InvocationContext invocationContext) throws GfacException {
    ExecutionContext context = invocationContext.getExecutionContext();


    String contact = null;
    log.info("Searching for Gate Keeper");
    GlobusGatekeeperType gatekeeper = context.getExecutionModel().getGatekeeper();
    if (gatekeeper == null) {
      contact = context.getExecutionModel().getHost();
    } else {
      contact = gatekeeper.getEndPointReference();
    }
    log.info("Using Globus GateKeeper " + contact);
    GramJob job = null;
    boolean jobSucsseful = false;


    String rsl = "";
    int errCode = 0;


    try {
      GSSCredential gssCred = ((GSISecurityContext) context.getSecurityContext()).getGssCredentails();


      log.info("Host desc = " + context.getExecutionModel().getHostDesc().xmlText());


      GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(context);
      rsl = jobAttr.toRSL();
      job = new GramJob(rsl);
      job.setCredentials(gssCred);


      log.info("RSL = " + rsl);


      NotificationService notifier = context.getNotificationService();
      DurationObj compObj = notifier.computationStarted();
      StringBuffer buf = new StringBuffer();


      JobSubmissionListener listener = new JobSubmissionListener(job, context);
      job.addListener(listener);
      log.info("Request to contact:" + contact);
      // The first boolean is to specify the job is a batch job - use true
      // for interactive and false for batch.
      // the second boolean is to specify to use the full proxy and not
      // delegate a limited proxy.
      job.request(contact, false, false);


      log.info("JobID = " + job.getIDAsString());


      // Gram.request(contact, job, false, false);


      buf.append("Finished launching job, Host = ").append(context.getExecutionModel().getHost()).append(" RSL = ").append(job.getRSL()).append("working directory =").append(context.getExecutionModel().getWorkingDir()).append("tempDirectory =").append(context.getExecutionModel().getTmpDir())
          .append("Globus GateKeeper cantact = ").append(contact);
      context.getNotificationService().info(buf.toString());
      String gramJobid = job.getIDAsString();
      context.getNotificationService().info("JobID=" + gramJobid);
      log.info(buf.toString());
      // Send Audit Notifications
      notifier.appAudit(invocationContext.getServiceName(), new URI(job.getIDAsString()), contact, null, null, gssCred.getName().toString(), null, job.getRSL());


      listener.waitFor();
      job.removeListener(listener);


      int jobStatus = listener.getStatus();
      if (jobStatus == GramJob.STATUS_FAILED) {
        errCode = listener.getError();
        // Adding retry for error code to properties files as
        // gfac.retryonJobErrorCodes with comma separated
        if (context.getServiceContext().getGlobalConfiguration().getRetryonErrorCodes().contains(Integer.toString(errCode))) {
          try {
            log.info("Job Failed with Error code " + errCode + " and job id: " + gramJobid);
            log.info("Retry job sumttion one more time for error code" + errCode);
            job = new GramJob(rsl);
            job.setCredentials(gssCred);
            listener = new JobSubmissionListener(job, context);
            job.addListener(listener);
            job.request(contact, false, false);
            String newGramJobid = job.getIDAsString();
            String jobStatusMessage = GfacUtils.formatJobStatus(newGramJobid, "RETRY");
            context.getNotificationService().info(jobStatusMessage);
            context.getNotificationService().info("JobID=" + newGramJobid);
            notifier.appAudit(context.getServiceContext().getService().getService().getServiceName().getStringValue(), new URI(job.getIDAsString()), contact, null, null, gssCred.getName().toString(), null, job.getRSL());
            listener.waitFor();
            job.removeListener(listener);
            int jobStatus1 = listener.getStatus();
            if (jobStatus1 == GramJob.STATUS_FAILED) {
              int errCode1 = listener.getError();
              String errorMsg = "Job " + job.getID() + " on host " + context.getExecutionModel().getHost() + " Error Code = " + errCode1;
              String localHost = context.getServiceContext().getGlobalConfiguration().getLocalHost();
              throw new JobSubmissionFault(new Exception(errorMsg), localHost, "", "", CurrentProviders.Gram);
            }
          } catch (Exception e) {
            String localHost = context.getServiceContext().getGlobalConfiguration().getLocalHost();
            throw new JobSubmissionFault(e, localHost, "", "", CurrentProviders.Gram);
          }
        } else {
          String errorMsg = "Job " + job.getID() + " on host " + context.getExecutionModel().getHost() + " Error Code = " + errCode;
          String localHost = context.getServiceContext().getGlobalConfiguration().getLocalHost();
          GfacException error = new JobSubmissionFault(new Exception(errorMsg), localHost, contact, rsl, CurrentProviders.Gram);
          if (errCode == 8) {
            error.setFaultCode(ErrorCodes.JOB_CANCELED);
          } else {
            error.setFaultCode(ErrorCodes.JOB_FAILED);
          }
          // error.addProperty(ErrorCodes.JOB_TYPE,
          // ErrorCodes.JobType.Gram.toString());
          // error.addProperty(ErrorCodes.CONTACT, contact);
          throw error;
        }
      }
      notifier.computationFinished(compObj);      


      /*
       * Stdout and Stderror
       */
      GridFtp ftp = new GridFtp();


      // get Hostname
      String hostgridFTP = null;


      if (invocationContext.getExecutionContext().getExecutionModel().getHostDesc().getHostConfiguration().getGridFTPArray() != null && invocationContext.getExecutionContext().getExecutionModel().getHostDesc().getHostConfiguration().getGridFTPArray().length > 0) {
        hostgridFTP = invocationContext.getExecutionContext().getExecutionModel().getHostDesc().getHostConfiguration().getGridFTPArray(0).getEndPointReference();
      } else {
        hostgridFTP = invocationContext.getExecutionContext().getExecutionModel().getHost();
      }      


      URI stdoutURI = GfacUtils.createGsiftpURI(hostgridFTP, invocationContext.getExecutionContext().getExecutionModel().getStdOut());
      URI stderrURI = GfacUtils.createGsiftpURI(hostgridFTP, invocationContext.getExecutionContext().getExecutionModel().getStderr());
      
      System.out.println(stdoutURI);
      System.out.println(stderrURI);
      
      File logDir = new File("./service_logs");
      if (!logDir.exists()) {
        logDir.mkdir();
      }


      // Get the Stdouts and StdErrs
      QName x = QName.valueOf(invocationContext.getServiceName());
      String timeStampedServiceName = GfacUtils.createServiceDirName(x);
      File localStdOutFile = new File(logDir, timeStampedServiceName + ".stdout");
      File localStdErrFile = new File(logDir, timeStampedServiceName + ".stderr");
      
      String stdout = ftp.readRemoteFile(stdoutURI, gssCred, localStdOutFile);
      String stderr = ftp.readRemoteFile(stderrURI, gssCred, localStdErrFile);
      
      //set to context
      OutputUtils.fillOutputFromStdout(invocationContext.getMessageContext("output"), stdout, stderr);
      
      
      jobSucsseful = true;      
    } catch (GramException e) {
      String localHost = "xxxx";
      GfacException error = new JobSubmissionFault(e, localHost, contact, rsl, CurrentProviders.Gram);
      if (errCode == 8) {
        error.setFaultCode(ErrorCodes.JOB_CANCELED);
      } else {
        error.setFaultCode(ErrorCodes.JOB_FAILED);
      }
      // error.addProperty(ErrorCodes.JOB_TYPE,
      // ErrorCodes.JobType.Gram.toString());
      // error.addProperty(ErrorCodes.CONTACT, contact);
      throw error;
    } catch (GSSException e) {
      String localHost = context.getServiceContext().getGlobalConfiguration().getLocalHost();
      throw new JobSubmissionFault(e, localHost, contact, rsl, CurrentProviders.Gram);
    } catch (URISyntaxException e) {
      throw new GfacException(e, FaultCode.ErrorAtDependentService);
    } catch (InterruptedException e) {
      throw new GfacException(e, FaultCode.ErrorAtDependentService);

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  }


  public void abort(InvocationContext invocationContext) throws GfacException {
    try {
      ExecutionContext context = invocationContext.getExecutionContext();
      GramJob job = new GramJob("");
      job.setID(context.getExecutionModel().getJobID());
      job.setCredentials(((GSISecurityContext) context.getSecurityContext()).getGssCredentails());
      job.cancel();
    } catch (MalformedURLException e) {
      throw new GfacException(e, FaultCode.ErrorAtDependentService);
    } catch (GramException e) {
      throw new GfacException(e, FaultCode.ErrorAtDependentService);

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    }
    return buff.toString();
  }
  
  public void initialize(InvocationContext invocationContext) throws GfacException {
    ExecutionContext context = invocationContext.getExecutionContext();
    
    log.info("working diectroy = " + context.getExecutionModel().getWorkingDir());
    log.info("temp directory = " + context.getExecutionModel().getTmpDir());
    new File(context.getExecutionModel().getWorkingDir()).mkdir();
    new File(context.getExecutionModel().getTmpDir()).mkdir();
    new File(context.getExecutionModel().getInputDataDir()).mkdir();
    new File(context.getExecutionModel().getOutputDataDir()).mkdir();
  }

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    new File(context.getExecutionModel().getInputDataDir()).mkdir();
    new File(context.getExecutionModel().getOutputDataDir()).mkdir();
  }


  public void execute(InvocationContext invocationContext) throws GfacException {
    ExecutionContext context = invocationContext.getExecutionContext();
    
    List<String> cmdList = new ArrayList<String>();
    
    try {
      /*
       * Notifier
       */
      NotificationService notifier = context.getNotificationService();
      
      /*
       * Builder Command
       */          
      cmdList.add(context.getExecutionModel().getExecutable());
      cmdList.addAll(context.getExecutionModel().getInputParameters());
      
      //create process builder from command
      ProcessBuilder builder = new  ProcessBuilder(cmdList);
      
      
      // get the env of the host and the application
      Map<String, String> nv = context.getExecutionModel().getEnv();      
      builder.environment().putAll(nv);
      
      // extra env's      
      builder.environment().put(GFacConstants.INPUT_DATA_DIR, context.getExecutionModel().getInputDataDir());
      builder.environment().put(GFacConstants.OUTPUT_DATA_DIR, context.getExecutionModel().getOutputDataDir());
      
      //working directory
      builder.directory(new File(context.getExecutionModel().getWorkingDir()));
            
      
      //log info
      log.info("Command = " + buildCommand(cmdList));
      log.info("Working dir = " + builder.directory());
      for (String key : builder.environment().keySet()) {
        log.info("Env[" + key + "] = " + builder.environment().get(key));
      }
      
      //notify start      
      DurationObj compObj = notifier.computationStarted();    
      
      //running cmd
      Process process = builder.start();                


      final BufferedReader in = new BufferedReader(new InputStreamReader(process.getInputStream()));
      final BufferedReader err = new BufferedReader(new InputStreamReader(process.getErrorStream()));
      final BufferedWriter stdoutWtiter = new BufferedWriter(new FileWriter(context.getExecutionModel().getStdOut()));
      final BufferedWriter stdErrWtiter =  new BufferedWriter(new FileWriter(context.getExecutionModel().getStderr()));


      Thread t1 = new Thread(new Runnable() {
        
        public void run() {
          try {
            String line=null;
                  while ( (line = in.readLine()) != null){
                    log.debug(line);
                    stdoutWtiter.write(line);
                    stdoutWtiter.newLine();        
                  }
          } catch (Exception e) {
            e.printStackTrace();
          } finally {
            if (in != null){
              try {
                in.close();
              } catch (Exception e) {
                e.printStackTrace();
              }              
            }
            if (stdoutWtiter != null) {
              try {
                stdoutWtiter.close();
              } catch (Exception e) {
                e.printStackTrace();
              }
            }
          }
        }


      });


      Thread t2 = new Thread(new Runnable() {


        public void run() {
          try {
            String line=null;
            while ((line = err.readLine()) != null){
                    log.debug(line);
                    stdErrWtiter.write(line);
                    stdErrWtiter.newLine();        
                  }
          } catch (Exception e) {
            e.printStackTrace();
          } finally {
            if (err != null){
              try {
                err.close();
              } catch (Exception e) {
                e.printStackTrace();
              }              
            }
            if (stdErrWtiter != null) {
              try {
                stdErrWtiter.close();
              } catch (Exception e) {
                e.printStackTrace();
              }
            }
          }


        }


      });
      
      //start output threads
      t1.setDaemon(true);
      t2.setDaemon(true);      
      t1.start();
      t2.start();


      
      // wait for the process (application) to finish executing
      int returnValue = process.waitFor();
      
      // notify end
      notifier.computationFinished(compObj);
      
      // make sure other two threads are done
      t1.join();
      t2.join();


      /*
       * check return value. usually not very helpful to draw conclusions
       * based on return values so don't bother. just provide warning in
       * the log messages
       */
      if (returnValue != 0) {
        log.error("Process finished with non zero return value. Process may have failed");
      } else {
        log.info("Process finished with return value of zero.");
      }


      StringBuffer buf = new StringBuffer();
      buf.append("Executed ")
        .append(buildCommand(cmdList))
        .append(" on the localHost, working directory =")
        .append(context.getExecutionModel().getWorkingDir())
        .append("tempDirectory =")
        .append(context.getExecutionModel().getTmpDir())
        .append("With the status")
        .append(String.valueOf(returnValue));  
      context.getNotificationService().info(buf.toString());
      
      log.info(buf.toString());
      
      context.getExecutionModel().setStdoutStr(GfacUtils.readFile(context.getExecutionModel().getStdOut()));
      context.getExecutionModel().setStderrStr(GfacUtils.readFile(context.getExecutionModel().getStderr()));
      
      //set to context
      OutputUtils.fillOutputFromStdout(invocationContext.getMessageContext("output"), context.getExecutionModel().getStdoutStr(), context.getExecutionModel().getStderrStr());


    } catch (IOException e) {      
      throw new JobSubmissionFault(e, "", "", buildCommand(cmdList), CurrentProviders.Local);
    } catch (InterruptedException e) {
      throw new GfacException(e, FaultCode.LocalError);

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    return buff.toString();
  }


  @Override
  public void initialize(InvocationContext invocationContext) throws GfacException {
    ExecutionContext appExecContext = invocationContext.getExecutionContext();
    ExecutionModel model = appExecContext.getExecutionModel();


    SSHClient ssh = new SSHClient();
    try {
      ssh.loadKnownHosts();
      ssh.connect(model.getHost());

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    }
  }


  @Override
  public void execute(InvocationContext invocationContext) throws GfacException {
    ExecutionContext context = invocationContext.getExecutionContext();
    ExecutionModel model = context.getExecutionModel();


    List<String> cmdList = new ArrayList<String>();


    SSHClient ssh = new SSHClient();
    try {


      /*
       * Notifier
       */
      NotificationService notifier = context.getNotificationService();


      /*
       * Builder Command
       */
      cmdList.add(context.getExecutionModel().getExecutable());
      cmdList.addAll(context.getExecutionModel().getInputParameters());


      // create process builder from command
      String command = buildCommand(cmdList);
      
      //redirect StdOut and StdErr
      command += SPACE + "1>" + SPACE + model.getStdOut();
      command += SPACE + "2>" + SPACE + model.getStderr();      


      // get the env of the host and the application
      Map<String, String> nv = context.getExecutionModel().getEnv();      


      // extra env's
      nv.put(GFacConstants.INPUT_DATA_DIR, context.getExecutionModel().getInputDataDir());
      nv.put(GFacConstants.OUTPUT_DATA_DIR, context.getExecutionModel().getOutputDataDir());
      
      // log info
      log.info("Command = " + buildCommand(cmdList));      
      for (String key : nv.keySet()) {
        log.info("Env[" + key + "] = " + nv.get(key));
      }


      // notify start
      DurationObj compObj = notifier.computationStarted();


      /*
       * Create ssh connection
       */
      ssh.loadKnownHosts();
      ssh.connect(model.getHost());


      // TODO how to authenticate with system
      ssh.authPublickey(System.getProperty("user.name"));


      final Session session = ssh.startSession();
      try {
        /*
         * Build working Directory
         */
        log.info("WorkingDir = " + model.getWorkingDir());      
        session.exec("mkdir -p " + model.getWorkingDir());
        session.exec("cd " + model.getWorkingDir());
        
        /*
         * Set environment
         */
        for (String key : nv.keySet()) {
          session.setEnvVar(key, nv.get(key));
        }
        
        /*
         * Execute
         */
        Command cmd = session.exec(command);
        log.info("stdout=" + GfacUtils.readFromStream(session.getInputStream()));
        cmd.join(5, TimeUnit.SECONDS);
        
        
        // notify end
        notifier.computationFinished(compObj);
        
        /*
         * check return value. usually not very helpful to draw conclusions
         * based on return values so don't bother. just provide warning in
         * the log messages
         */        
        if (cmd.getExitStatus() != 0) {
          log.error("Process finished with non zero return value. Process may have failed");
        } else {
          log.info("Process finished with return value of zero.");
        }                        
        
        File logDir = new File("./service_logs");
        if (!logDir.exists()) {
          logDir.mkdir();
        }        
        
        // Get the Stdouts and StdErrs
        QName x = QName.valueOf(invocationContext.getServiceName());
        String timeStampedServiceName = GfacUtils.createServiceDirName(x);
        File localStdOutFile = new File(logDir, timeStampedServiceName + ".stdout");
        File localStdErrFile = new File(logDir, timeStampedServiceName + ".stderr");
        
        SCPFileTransfer fileTransfer = ssh.newSCPFileTransfer();
        fileTransfer.download(model.getStdOut(), localStdOutFile.getAbsolutePath());
        fileTransfer.download(model.getStderr(), localStdErrFile.getAbsolutePath());        
        
        context.getExecutionModel().setStdoutStr(GfacUtils.readFile(localStdOutFile.getAbsolutePath()));
        context.getExecutionModel().setStderrStr(GfacUtils.readFile(localStdErrFile.getAbsolutePath()));
        
        // set to context
        OutputUtils.fillOutputFromStdout(invocationContext.getMessageContext("output"), context.getExecutionModel().getStdoutStr(), context.getExecutionModel().getStderrStr());
        
      } catch (Exception e) {
        throw e;
      } finally {
        try {

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Related Classes of org.ogce.gfac.context.ExecutionContext

org.ogce.gfac.provider.EC2Provider

org.ogce.gfac.provider.GramProvider

org.ogce.gfac.provider.LocalProvider

org.ogce.gfac.provider.SSHProvider

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