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From sma...@apache.org
Subject svn commit: r1139241 [2/3] - in /incubator/airavata/core/trunk/gfac: ./ .settings/ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/ src/main/java/org/apache/airavata/ src/main/java/org/apache/airavata/core/ src/main/java/org/a...
Date Fri, 24 Jun 2011 11:01:18 GMT
Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/EC2Provider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/EC2Provider.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/EC2Provider.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/EC2Provider.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,555 @@
+package org.apache.airavata.core.gfac.provider;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.security.KeyPair;
+import java.security.KeyPairGenerator;
+import java.security.NoSuchAlgorithmException;
+import java.security.spec.InvalidKeySpecException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.TimeUnit;
+
+import javax.xml.namespace.QName;
+
+import net.schmizz.sshj.SSHClient;
+import net.schmizz.sshj.common.Base64;
+import net.schmizz.sshj.connection.channel.direct.Session;
+import net.schmizz.sshj.connection.channel.direct.Session.Command;
+import net.schmizz.sshj.xfer.scp.SCPFileTransfer;
+
+import org.apache.airavata.core.gfac.context.ExecutionContext;
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.context.impl.AmazonSecurityContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.exception.GfacException.FaultCode;
+import org.apache.airavata.core.gfac.model.ExecutionModel;
+import org.apache.airavata.core.gfac.notification.NotificationService;
+import org.apache.airavata.core.gfac.utils.GFacConstants;
+import org.apache.airavata.core.gfac.utils.GfacUtils;
+import org.apache.airavata.core.gfac.utils.OutputUtils;
+import org.bouncycastle.openssl.PEMWriter;
+
+import com.amazonaws.AmazonClientException;
+import com.amazonaws.AmazonServiceException;
+import com.amazonaws.auth.AWSCredentials;
+import com.amazonaws.auth.BasicAWSCredentials;
+import com.amazonaws.services.ec2.AmazonEC2Client;
+import com.amazonaws.services.ec2.model.AuthorizeSecurityGroupIngressRequest;
+import com.amazonaws.services.ec2.model.DeleteKeyPairRequest;
+import com.amazonaws.services.ec2.model.DescribeInstancesRequest;
+import com.amazonaws.services.ec2.model.DescribeInstancesResult;
+import com.amazonaws.services.ec2.model.DescribeKeyPairsRequest;
+import com.amazonaws.services.ec2.model.GroupIdentifier;
+import com.amazonaws.services.ec2.model.ImportKeyPairRequest;
+import com.amazonaws.services.ec2.model.Instance;
+import com.amazonaws.services.ec2.model.InstanceStateName;
+import com.amazonaws.services.ec2.model.IpPermission;
+import com.amazonaws.services.ec2.model.RunInstancesRequest;
+import com.amazonaws.services.ec2.model.RunInstancesResult;
+
+import edu.indiana.extreme.lead.workflow_tracking.common.DurationObj;
+
+
+
+public class EC2Provider extends AbstractProvider {
+	
+	public static final String AMAZON_SECURITY_CONTEXT = "amazon";
+	
+	public static final int SLEEP_TIME_SECOND = 120;
+
+	public static final String KEY_PAIR_NAME = "gfac";
+
+	public static final String KEY_PAIR_FILE = "ec2_rsa";
+	
+	private static final String privateKeyFilePath = System.getProperty("user.home") + "/.ssh/" + KEY_PAIR_FILE;
+
+	private Instance instance;	
+	
+	private static final String SPACE = " ";
+	
+	private String buildCommand(List<String> cmdList) {
+		StringBuffer buff = new StringBuffer();
+		for (String string : cmdList) {
+			buff.append(string);
+			buff.append(SPACE);
+		}
+		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();
+
+		//TODO way to read value (header or xregistry)
+		String ami_id = "";
+		String ins_type = "";
+		String ins_id = "";
+		
+		/*
+		 * Need to start EC2 instance before running it
+		 */
+		AWSCredentials credential = new BasicAWSCredentials(access_key, secret_key);
+		AmazonEC2Client ec2client = new AmazonEC2Client(credential);
+				
+		try {
+			/*
+			 * Build key pair before start instance
+			 */
+			buildKeyPair(ec2client);
+
+			// right now, we can run it on one host
+			if (ami_id != null)
+				this.instance = startInstances(ec2client, ami_id, ins_type, invocationContext.getExecutionContext().getNotificationService()).get(0);
+			else {
+
+				// already running instance
+				DescribeInstancesRequest describeInstancesRequest = new DescribeInstancesRequest();
+				DescribeInstancesResult describeInstancesResult = ec2client.describeInstances(describeInstancesRequest.withInstanceIds(ins_id));
+
+				if (describeInstancesResult.getReservations().size() == 0 || describeInstancesResult.getReservations().get(0).getInstances().size() == 0) {
+					throw new GfacException("Instance not found:" + ins_id, FaultCode.InvalidRequest);
+				}
+
+				this.instance = describeInstancesResult.getReservations().get(0).getInstances().get(0);
+
+				// check instance keypair
+				if (this.instance.getKeyName() == null || !this.instance.getKeyName().equals(KEY_PAIR_NAME))
+					throw new GfacException("Keypair for instance:" + ins_id + " is not valid", FaultCode.InvalidRequest);
+			}
+			
+			//send out instance id
+			invocationContext.getExecutionContext().getNotificationService().sendResourceMappingNotifications(this.instance.getPublicDnsName(), "EC2 Instance " + this.instance.getInstanceId() + " is running with public name " + this.instance.getPublicDnsName(), this.instance.getInstanceId());
+			
+
+			/*
+			 * Make sure port 22 is connectable
+			 */
+			for (GroupIdentifier g : this.instance.getSecurityGroups()) {
+				IpPermission ip = new IpPermission();
+				ip.setIpProtocol("tcp");
+				ip.setFromPort(22);
+				ip.setToPort(22);
+				AuthorizeSecurityGroupIngressRequest r = new AuthorizeSecurityGroupIngressRequest();
+				r = r.withIpPermissions(ip.withIpRanges("0.0.0.0/0"));
+				r.setGroupId(g.getGroupId());
+				try {
+					ec2client.authorizeSecurityGroupIngress(r);
+				} catch (AmazonServiceException as) {
+					/*
+					 * If exception is from duplicate room, ignore it.
+					 */
+					if (!as.getErrorCode().equals("InvalidPermission.Duplicate"))
+						throw as;
+				}
+			}		
+
+		} catch (Exception e) {
+			// TODO throw out
+			e.printStackTrace();
+			log.error(e.getMessage(), e);
+			throw new GfacException(e, FaultCode.InvalidRequest);
+		}		
+				
+		//set Host location
+		model.setHost(this.instance.getPublicDnsName());
+		
+		/*
+		 * Make directory
+		 */
+		SSHClient ssh = new SSHClient();
+		try {
+			ssh.loadKnownHosts();
+			ssh.connect(this.instance.getPublicDnsName());
+
+			ssh.authPublickey(privateKeyFilePath);
+			final Session session = ssh.startSession();
+			try {
+				StringBuilder command = new StringBuilder();
+				command.append("mkdir -p ");
+				command.append(model.getTmpDir());
+				command.append(" | ");
+				command.append("mkdir -p ");
+				command.append(model.getWorkingDir());
+				command.append(" | ");
+				command.append("mkdir -p ");
+				command.append(model.getInputDataDir());
+				command.append(" | ");
+				command.append("mkdir -p ");
+				command.append(model.getOutputDataDir());
+				Command cmd = session.exec(command.toString());
+				cmd.join(5, TimeUnit.SECONDS);
+			} catch (Exception e) {
+				throw e;
+			} finally {
+				try {
+					session.close();
+				} catch (Exception e) {
+				}
+			}
+		} catch (Exception e) {
+			throw new GfacException(e.getMessage(), e);
+		} finally {
+			try {
+				ssh.disconnect();
+			} catch (Exception e) {
+			}
+		}
+	}
+	
+	@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 {
+					session.close();
+				} catch (Exception e) {
+				}
+			}
+		} catch (Exception e) {
+			throw new GfacException(e.getMessage(), e);
+		} finally {
+			try {
+				ssh.disconnect();
+			} catch (Exception e) {
+			}
+		}
+	}
+
+	@Override
+	public void dispose(InvocationContext invocationContext) throws GfacException {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void abort(InvocationContext invocationContext) throws GfacException {
+		// TODO Auto-generated method stub
+		
+	}
+	
+
+	private List<Instance> startInstances(AmazonEC2Client ec2, String AMI_ID, String INS_TYPE, NotificationService notifier) throws AmazonServiceException {
+		// start only 1 instance
+		RunInstancesRequest request = new RunInstancesRequest(AMI_ID, 1, 1);
+		request.setKeyName(KEY_PAIR_NAME);
+		request.setInstanceType(INS_TYPE);
+
+		RunInstancesResult result = ec2.runInstances(request);
+
+		List<Instance> instances = result.getReservation().getInstances();
+
+		while (!allInstancesStateEqual(instances, InstanceStateName.Running)) {
+
+			// instance status should not be Terminated
+			if (anyInstancesStateEqual(instances, InstanceStateName.Terminated)) {
+				throw new AmazonClientException("Some Instance is terminated before running a job");
+			}
+			
+			// notify the status
+			for (Instance ins: instances) {
+				notifier.info("EC2 Instance " +ins.getInstanceId() + " is " + ins.getState().getName().toString());
+			}
+
+			try {
+				Thread.sleep(SLEEP_TIME_SECOND * 1000l);
+			} catch (Exception ex) {
+				// no op
+			}
+
+			DescribeInstancesRequest describeInstancesRequest = new DescribeInstancesRequest();
+			describeInstancesRequest.setInstanceIds(getInstanceIDs(instances));
+
+			DescribeInstancesResult describeInstancesResult = ec2.describeInstances(describeInstancesRequest);
+			instances = describeInstancesResult.getReservations().get(0).getInstances();
+		}
+
+		log.info("All instances is running");
+		return instances;
+	}
+
+	private void buildKeyPair(AmazonEC2Client ec2) throws NoSuchAlgorithmException, InvalidKeySpecException, AmazonServiceException, AmazonClientException, IOException {
+
+		boolean newKey = false;
+		
+		File privateKeyFile = new File(privateKeyFilePath);
+		File publicKeyFile = new File(privateKeyFilePath + ".pub");
+
+		/*
+		 * Check if Keypair already created on the server
+		 */
+		if (!privateKeyFile.exists()) {
+
+			// check folder and create if it does not exist
+			File sshDir = new File(System.getProperty("user.home") + "/.ssh/");
+			if (!sshDir.exists())
+				sshDir.mkdir();
+
+			// Generate a 1024-bit RSA key pair
+			KeyPairGenerator keyGen = KeyPairGenerator.getInstance("RSA");
+			keyGen.initialize(1024);
+			KeyPair keypair = keyGen.genKeyPair();
+
+			FileOutputStream fos = null;
+
+			// Store Public Key.
+			try {
+				fos = new FileOutputStream(privateKeyFilePath + ".pub");
+				fos.write(Base64.encodeBytes(keypair.getPublic().getEncoded()).getBytes());
+			} catch (IOException ioe) {
+				throw ioe;
+			} finally {
+				if (fos != null) {
+					try {
+						fos.close();
+						fos = null;
+					} catch (IOException ioe) {
+						throw ioe;
+					}
+				}
+			}
+
+			// Store Private Key.
+			try {
+				fos = new FileOutputStream(privateKeyFilePath);
+				StringWriter stringWriter = new StringWriter();
+				
+				/*
+				 * Write in PEM format (openssl support)
+				 */
+				PEMWriter pemFormatWriter = new PEMWriter(stringWriter);
+				pemFormatWriter.writeObject(keypair.getPrivate());
+				pemFormatWriter.close();
+				fos.write(stringWriter.toString().getBytes());
+			} catch (IOException ioe) {
+				throw ioe;
+			} finally {
+				if (fos != null) {
+					try {
+						fos.close();
+						fos = null;
+					} catch (IOException ioe) {
+						throw ioe;
+					}
+				}
+			}
+
+			privateKeyFile.setWritable(false, false);
+			privateKeyFile.setExecutable(false, false);
+			privateKeyFile.setReadable(false, false);
+			privateKeyFile.setReadable(true);
+			privateKeyFile.setWritable(true);
+
+			// set that this key is just created
+			newKey = true;
+		}
+
+		/*
+		 * Read Public Key
+		 */
+		String encodedPublicKey = null;
+		BufferedReader br = null;
+		try {
+			br = new BufferedReader(new FileReader(publicKeyFile));
+			encodedPublicKey = br.readLine();
+		} catch (IOException ioe) {
+			throw ioe;
+		} finally {
+			if (br != null) {
+				try {
+					br.close();
+					br = null;
+				} catch (IOException ioe) {
+					throw ioe;
+				}
+			}
+		}
+		
+		/*
+		 * Generate key pair in Amazon if necessary
+		 */
+		try {
+			/*
+			 * Get current key pair in Amazon
+			 */
+			DescribeKeyPairsRequest describeKeyPairsRequest = new DescribeKeyPairsRequest();
+			ec2.describeKeyPairs(describeKeyPairsRequest.withKeyNames(KEY_PAIR_NAME));
+
+			/*
+			 * If key exists and new key is created, delete old key and replace
+			 * with new one. Else, do nothing
+			 */
+
+			if (newKey) {
+				DeleteKeyPairRequest deleteKeyPairRequest = new DeleteKeyPairRequest(KEY_PAIR_NAME);
+				ec2.deleteKeyPair(deleteKeyPairRequest);
+				ImportKeyPairRequest importKeyPairRequest = new ImportKeyPairRequest(KEY_PAIR_NAME, encodedPublicKey);
+				ec2.importKeyPair(importKeyPairRequest);
+			}
+
+		} catch (AmazonServiceException ase) {
+			/*
+			 * Key doesn't exists, import new key.
+			 */
+			if(ase.getErrorCode().equals("InvalidKeyPair.NotFound")){			
+				ImportKeyPairRequest importKeyPairRequest = new ImportKeyPairRequest(KEY_PAIR_NAME, encodedPublicKey);
+				ec2.importKeyPair(importKeyPairRequest);
+			}else{
+				throw ase;
+			}
+		}
+	}
+
+	private boolean anyInstancesStateEqual(List<Instance> instances, InstanceStateName name) {
+		for (Iterator<Instance> iterator = instances.iterator(); iterator.hasNext();) {
+			Instance instance = (Instance) iterator.next();
+
+			// if one of instance is not running, return false
+			if (InstanceStateName.fromValue(instance.getState().getName()) == name) {
+				return true;
+			}
+		}
+		return false;
+	}
+
+	private boolean allInstancesStateEqual(List<Instance> instances, InstanceStateName name) {
+		for (Iterator<Instance> iterator = instances.iterator(); iterator.hasNext();) {
+			Instance instance = (Instance) iterator.next();
+
+			// if one of instance is not running, return false
+			if (InstanceStateName.fromValue(instance.getState().getName()) != name) {
+				return false;
+			}
+		}
+		return true;
+	}
+
+	private List<String> getInstanceIDs(List<Instance> instances) {
+		List<String> ret = new ArrayList<String>();
+		for (Iterator<Instance> iterator = instances.iterator(); iterator.hasNext();) {
+			Instance instance = (Instance) iterator.next();
+			ret.add(instance.getInstanceId());
+		}
+		return ret;
+	}	
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/GramProvider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/GramProvider.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/GramProvider.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/GramProvider.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,275 @@
+package org.apache.airavata.core.gfac.provider;
+
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+
+import javax.xml.namespace.QName;
+
+import org.apache.airavata.core.gfac.context.ExecutionContext;
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.context.impl.GSISecurityContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.exception.JobSubmissionFault;
+import org.apache.airavata.core.gfac.exception.GfacException.FaultCode;
+import org.apache.airavata.core.gfac.external.GridFtp;
+import org.apache.airavata.core.gfac.model.ExecutionModel;
+import org.apache.airavata.core.gfac.notification.NotificationService;
+import org.apache.airavata.core.gfac.provider.utils.GramRSLGenerator;
+import org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener;
+import org.apache.airavata.core.gfac.utils.ErrorCodes;
+import org.apache.airavata.core.gfac.utils.GfacUtils;
+import org.apache.airavata.core.gfac.utils.OutputUtils;
+import org.apache.airavata.core.gfac.utils.GFacOptions.CurrentProviders;
+import org.globus.gram.GramAttributes;
+import org.globus.gram.GramException;
+import org.globus.gram.GramJob;
+import org.ietf.jgss.GSSCredential;
+import org.ietf.jgss.GSSException;
+import org.ogce.schemas.gfac.documents.GlobusGatekeeperType;
+
+import edu.indiana.extreme.lead.workflow_tracking.common.DurationObj;
+
+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();
+
+			// get Hostname
+			String hostgridFTP = null;
+
+			if (model.getHostDesc().getHostConfiguration().getGridFTPArray() != null && model.getHostDesc().getHostConfiguration().getGridFTPArray().length > 0) {
+				hostgridFTP = model.getHostDesc().getHostConfiguration().getGridFTPArray(0).getEndPointReference();
+			} else {
+				hostgridFTP = model.getHost();
+			}
+
+			URI tmpdirURI = GfacUtils.createGsiftpURI(hostgridFTP, model.getTmpDir());
+			URI workingDirURI = GfacUtils.createGsiftpURI(hostgridFTP, model.getWorkingDir());
+			URI inputURI = GfacUtils.createGsiftpURI(hostgridFTP, model.getInputDataDir());
+			URI outputURI = GfacUtils.createGsiftpURI(hostgridFTP, model.getOutputDataDir());
+
+			log.info("Host FTP = " + hostgridFTP);
+			log.info("temp directory = " + tmpdirURI);
+			log.info("Working directory = " + workingDirURI);
+			log.info("Input directory = " + inputURI);
+			log.info("Output directory = " + outputURI);
+
+			ftp.makeDir(tmpdirURI, gssCred);
+			ftp.makeDir(workingDirURI, gssCred);
+			ftp.makeDir(inputURI, gssCred);
+			ftp.makeDir(outputURI, gssCred);
+
+		} catch (Exception e) {
+			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);
+		} finally {
+			if (job != null && !jobSucsseful) {
+				try {
+					job.cancel();
+				} catch (Exception e) {
+				}
+			}
+		}
+
+	}
+
+	public void dispose(InvocationContext invocationContext) throws GfacException {
+
+	}
+
+	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);
+		} catch (GSSException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+
+	}
+
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/LocalProvider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/LocalProvider.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/LocalProvider.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/LocalProvider.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,230 @@
+package org.apache.airavata.core.gfac.provider;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.airavata.core.gfac.context.ExecutionContext;
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.exception.JobSubmissionFault;
+import org.apache.airavata.core.gfac.exception.GfacException.FaultCode;
+import org.apache.airavata.core.gfac.notification.NotificationService;
+import org.apache.airavata.core.gfac.utils.GFacConstants;
+import org.apache.airavata.core.gfac.utils.GfacUtils;
+import org.apache.airavata.core.gfac.utils.OutputUtils;
+import org.apache.airavata.core.gfac.utils.GFacOptions.CurrentProviders;
+
+import edu.indiana.extreme.lead.workflow_tracking.common.DurationObj;
+
+public class LocalProvider extends AbstractProvider {
+
+	private static final String SPACE = " ";
+
+	
+	private String buildCommand(List<String> cmdList){
+		StringBuffer buff = new StringBuffer();
+		for (String string : cmdList) {
+			buff.append(string);
+			buff.append(SPACE);
+		}
+		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();
+	}
+
+	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);
+		}
+
+	}
+
+	public void dispose(InvocationContext invocationContext) throws GfacException {
+
+	}
+
+	public void abort(InvocationContext invocationContext) throws GfacException {
+
+	}
+
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/Provider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/Provider.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/Provider.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/Provider.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,15 @@
+package org.apache.airavata.core.gfac.provider;
+
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+
+public interface Provider {
+
+	void initialize(InvocationContext invocationContext) throws GfacException;
+
+	void execute(InvocationContext invocationContext) throws GfacException;
+
+	void dispose(InvocationContext invocationContext) throws GfacException;
+
+	void abort(InvocationContext invocationContext) throws GfacException;
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/SSHProvider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/SSHProvider.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/SSHProvider.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/SSHProvider.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,228 @@
+package org.apache.airavata.core.gfac.provider;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.TimeUnit;
+
+import javax.xml.namespace.QName;
+
+import net.schmizz.sshj.SSHClient;
+import net.schmizz.sshj.connection.channel.direct.Session;
+import net.schmizz.sshj.connection.channel.direct.Session.Command;
+import net.schmizz.sshj.xfer.scp.SCPFileTransfer;
+
+import org.apache.airavata.core.gfac.context.ExecutionContext;
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.model.ExecutionModel;
+import org.apache.airavata.core.gfac.notification.NotificationService;
+import org.apache.airavata.core.gfac.utils.GFacConstants;
+import org.apache.airavata.core.gfac.utils.GfacUtils;
+import org.apache.airavata.core.gfac.utils.OutputUtils;
+
+import edu.indiana.extreme.lead.workflow_tracking.common.DurationObj;
+
+public class SSHProvider extends AbstractProvider {
+
+	private static final String SPACE = " ";
+	
+	private String buildCommand(List<String> cmdList) {
+		StringBuffer buff = new StringBuffer();
+		for (String string : cmdList) {
+			buff.append(string);
+			buff.append(SPACE);
+		}
+		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());
+
+			// TODO how to authenticate with system
+			ssh.authPublickey(System.getProperty("user.name"));
+			final Session session = ssh.startSession();
+			try {
+				StringBuilder command = new StringBuilder();
+				command.append("mkdir -p ");
+				command.append(model.getTmpDir());
+				command.append(" | ");
+				command.append("mkdir -p ");
+				command.append(model.getWorkingDir());
+				command.append(" | ");
+				command.append("mkdir -p ");
+				command.append(model.getInputDataDir());
+				command.append(" | ");
+				command.append("mkdir -p ");
+				command.append(model.getOutputDataDir());
+				Command cmd = session.exec(command.toString());
+				cmd.join(5, TimeUnit.SECONDS);
+			} catch (Exception e) {
+				throw e;
+			} finally {
+				try {
+					session.close();
+				} catch (Exception e) {
+				}
+			}
+		} catch (Exception e) {
+			throw new GfacException(e.getMessage(), e);
+		} finally {
+			try {
+				ssh.disconnect();
+			} catch (Exception e) {
+			}
+		}
+	}
+
+	@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 {
+					session.close();
+				} catch (Exception e) {
+				}
+			}
+		} catch (Exception e) {
+			throw new GfacException(e.getMessage(), e);
+		} finally {
+			try {
+				ssh.disconnect();
+			} catch (Exception e) {
+			}
+		}
+	}
+
+	@Override
+	public void dispose(InvocationContext invocationContext) throws GfacException {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void abort(InvocationContext invocationContext) throws GfacException {
+		// TODO Auto-generated method stub
+
+	}
+
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,145 @@
+package org.apache.airavata.core.gfac.provider.utils;
+
+import java.util.Iterator;
+import java.util.Map;
+
+import org.apache.airavata.core.gfac.context.ExecutionContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.exception.GfacException.FaultCode;
+import org.apache.airavata.core.gfac.utils.GFacConstants;
+import org.globus.gram.GramAttributes;
+import org.ogce.namespaces.x2010.x08.x30.workflowContextHeader.WorkflowContextHeaderDocument.WorkflowContextHeader;
+import org.ogce.namespaces.x2010.x08.x30.workflowResourceMapping.ResourceMappingDocument.ResourceMapping;
+import org.ogce.schemas.gfac.documents.ApplicationDescriptionType;
+import org.ogce.schemas.gfac.documents.RSLParmType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+
+public class GramRSLGenerator {
+	protected final static Logger log = LoggerFactory.getLogger(GramRSLGenerator.class);
+	private enum JobType{SINGLE,MPI,MULTIPLE,CONDOR};
+	
+	public static GramAttributes configureRemoteJob(ExecutionContext appExecContext) throws GfacException {
+		GramAttributes jobAttr = new GramAttributes();
+		jobAttr.setExecutable(appExecContext.getExecutionModel().getExecutable());
+		jobAttr.setDirectory(appExecContext.getExecutionModel().getWorkingDir());
+		jobAttr.setStdout(appExecContext.getExecutionModel().getStdOut());
+		jobAttr.setStderr(appExecContext.getExecutionModel().getStderr());
+
+		// The env here contains the env of the host and the application. i.e
+		// the env specified in
+		// the host description and application description documents
+		Map<String, String> nv = appExecContext.getExecutionModel().getEnv();
+
+		for (String key : nv.keySet()) {
+			jobAttr.addEnvVariable(key, nv.get(key));
+		}	
+
+		jobAttr.addEnvVariable(GFacConstants.INPUT_DATA_DIR, appExecContext.getExecutionModel().getInputDataDir());
+        String outputDataDir = GFacConstants.OUTPUT_DATA_DIR;
+        if(!outputDataDir.isEmpty()){
+		jobAttr.addEnvVariable(outputDataDir, appExecContext.getExecutionModel().getOutputDataDir());
+        }
+		ApplicationDescriptionType app = appExecContext.getExecutionModel().getAplicationDesc();
+		WorkflowContextHeader contextHeader = appExecContext.getWorkflowHeader();
+		ResourceMapping resourceMapping = null;
+		if (contextHeader != null) {
+			resourceMapping = contextHeader.getResourceMappings().getResourceMappingArray(0);
+		}
+
+		log.info("Configure using App Desc = " + app.xmlText());
+		if (resourceMapping != null && resourceMapping.getMaxWallTime() > 0) {
+			log.info("Header Setting Max Wall Time" + resourceMapping.getMaxWallTime());
+			jobAttr.setMaxWallTime(resourceMapping.getMaxWallTime());
+
+		} else if (app.getMaxWallTime() > 0) {
+			log.info("Setting max wall clock time to " + app.getMaxWallTime());
+
+			if (app.getMaxWallTime() > 30 && app.getQueue() != null && app.getQueue().equals("debug")) {
+				throw new GfacException("NCSA debug Queue only support jobs < 30 minutes", FaultCode.InvalidConfig);
+			}
+
+			jobAttr.setMaxWallTime(app.getMaxWallTime());
+			jobAttr.set("proxy_timeout", "1");
+		} else {
+			jobAttr.setMaxWallTime(29);
+		}
+
+		if (appExecContext.getExecutionModel().getStdIn() != null) {
+			jobAttr.setStdin(appExecContext.getExecutionModel().getStdIn());
+		} else {
+			Iterator<String> values = appExecContext.getExecutionModel().getInputParameters().iterator();
+			while (values.hasNext()) {
+				jobAttr.addArgument(values.next());
+			}
+		}
+		
+		if (resourceMapping != null && resourceMapping.getNodeCount() > 0) {
+			log.info("Setting number of procs to " + resourceMapping.getNodeCount());
+			jobAttr.set("hostCount", String.valueOf(resourceMapping.getNodeCount()));
+		}else if (app.getHostCount() > 1) {
+			jobAttr.set("hostCount", String.valueOf(app.getHostCount()));
+		}
+		if (resourceMapping != null && resourceMapping.getCpuCount() > 0) {
+			log.info("Setting host count to " + resourceMapping.getCpuCount());
+			jobAttr.setNumProcs(resourceMapping.getCpuCount());
+			
+		} else if (app.getCount() > 1) {
+			log.info("Setting number of procs to " + app.getCount());
+			jobAttr.setNumProcs(app.getCount());
+		}
+
+		if (app.getProject() != null && app.getProject().getProjectName() != null) {
+			log.info("Setting project to " + app.getProject());
+			jobAttr.setProject(app.getProject().getProjectName());
+		}
+
+		if (resourceMapping != null && resourceMapping.getQueueName() != null) {
+			jobAttr.setQueue(resourceMapping.getQueueName());
+		} else if (app.getQueue() != null && app.getQueue().getQueueName() != null) {
+			log.info("Setting job queue to " + app.getQueue());
+			jobAttr.setQueue(app.getQueue().getQueueName());
+		}
+		String jobType = JobType.SINGLE.toString() ;
+
+		if (app.getJobType() != null) {
+			jobType = app.getJobType().toString();
+		}
+		if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
+			log.info("Setting job type to single");
+			jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
+		} else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
+			log.info("Setting job type to mpi");
+			jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
+		} else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
+			log.info("Setting job type to multiple");
+			jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
+		} else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
+			jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
+		}
+
+		// Support to add the Additional RSL parameters
+		RSLParmType[] rslParams = app.getRslparmArray();
+		if (rslParams.length > 0) {
+			for (RSLParmType rslType : rslParams) {
+				log.info("Adding rsl param of [" + rslType.getName() + "," + rslType.getStringValue() + "]");
+				if (rslType.getName() != "") {
+					jobAttr.set(rslType.getName(), rslType.getStringValue());
+				}
+			}
+		}
+
+		// support urgency/SPRUCE case
+		// only add spruce rsl parameter if this host has a spruce jobmanager
+		// configured
+		if (appExecContext.getWorkflowHeader() != null && appExecContext.getWorkflowHeader().getURGENCY() != null
+				//&& GfacUtils.getSpruceGatekeeper(appExecContext) != null
+				) {
+			jobAttr.set("urgency", appExecContext.getWorkflowHeader().getURGENCY());
+		}
+
+		return jobAttr;
+	}
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,93 @@
+package org.apache.airavata.core.gfac.provider.utils;
+
+import org.apache.airavata.core.gfac.context.ExecutionContext;
+import org.apache.airavata.core.gfac.context.impl.GSISecurityContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.utils.GfacUtils;
+import org.globus.gram.GramException;
+import org.globus.gram.GramJob;
+import org.globus.gram.GramJobListener;
+import org.ietf.jgss.GSSCredential;
+import org.ietf.jgss.GSSException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+public class JobSubmissionListener implements GramJobListener {
+
+	private boolean finished;
+	private int error;
+	private int status;
+	private ExecutionContext executionContext;
+	private GramJob job;
+	protected final Logger log = LoggerFactory.getLogger(JobSubmissionListener.class);
+
+	public JobSubmissionListener(GramJob job, ExecutionContext executionContext) {
+		this.job = job;
+		this.executionContext = executionContext;
+	}
+	// waits for DONE or FAILED status
+	public void waitFor() throws InterruptedException,GSSException, GfacException, GramException {
+		while (!finished) {
+			int proxyExpTime = job.getCredentials().getRemainingLifetime();
+			if(proxyExpTime < 900){
+				log.info("Job proxy expired. Trying to renew proxy");
+				GSSCredential newgssCred = ((GSISecurityContext)executionContext.getSecurityContext()).getGssCredentails();
+				job.renew(newgssCred);
+			}
+			// job status is changed but method isn't invoked
+			if (status != 0) {
+				if (job.getStatus() != status) {
+					log.info("invoke method manually");
+					statusChanged(job);
+				} else {
+					log.info("job " + job.getIDAsString() + " have same status: " + GramJob.getStatusAsString(status));
+				}
+			} else {
+				log.info("Status is zero");
+			}
+			
+			synchronized (this) {
+				wait(60 * 1000l);
+			}			
+		}
+	}
+	
+	public synchronized void statusChanged(GramJob job) {
+		int jobStatus = job.getStatus();
+		String jobId = job.getIDAsString();
+		String statusString = job.getStatusAsString();
+		 String jobStatusMessage = GfacUtils.formatJobStatus(jobId,  statusString);
+        log.info(jobStatusMessage);
+        status = jobStatus;
+    	executionContext.getNotificationService().info(jobStatusMessage);
+	    if (jobStatus == GramJob.STATUS_DONE) {
+			finished = true;
+		} else if (jobStatus == GramJob.STATUS_FAILED) {
+			finished = true;
+			error = job.getError();
+			log.info("Job Error Code: " + error);
+		}
+	
+		if (finished) {
+			notify();
+		}
+	}
+
+	
+	public int getError() {
+		return error;
+	}
+
+	public int getStatus() {
+		return status;
+	}
+
+	public void wakeup() {
+		try {
+			notify();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/RegistryService.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/RegistryService.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/RegistryService.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/RegistryService.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,46 @@
+
+package org.apache.airavata.core.gfac.registry;
+
+import javax.xml.namespace.QName;
+
+import org.apache.airavata.core.gfac.exception.GfacException;
+
+
+public interface RegistryService {
+
+	public void registerConcreteWsdl(String wsdlAsStr,int lifetimeAsSeconds)throws GfacException;
+    public String getConcreateWsdl(String wsdlQName)throws GfacException;
+    public void removeConcreteWsdl(String wsdlQName)throws GfacException;
+    
+    public String getAbstractWsdl(String wsdlQName) throws GfacException;
+    public void removeAwsdl(String wsdlQName) throws GfacException;
+    
+    public void registerServiceMap(String serviceMapAsStr,String abstractWsdlAsString)throws GfacException;
+    public void removeServiceMap(String serviceQName)throws GfacException;
+    public String getServiceMap(String serviceQName)throws GfacException;
+    
+    public void registerHostDesc(String hostDescAsStr)throws GfacException;
+    public String getHostDesc(String hostName)throws GfacException;
+    public void removeHostDesc(String hostName)throws GfacException;
+    
+    public void registerAppDesc(String appDescAsStr)throws GfacException;
+    public String getAppDesc(String appQName,String hostName)throws GfacException;
+    public void removeAppDesc(String appQName,String hostName)throws GfacException;
+    
+    public void registerOutputFiles(QName resourceId, String resourceName, String resourceType, 
+    		String resourceDesc, String resourceDocument, String resourceParentTypedID, 
+    		String owner)throws GfacException;
+    
+    public String[] findService(String serviceName)throws GfacException;
+    public String[] findServiceDesc(String serviceName)throws GfacException;
+    public String[] findAppDesc(String query) throws GfacException;
+    
+    public String[] listHosts()throws GfacException;
+    public String[] listApps()throws GfacException;
+    public String[] app2Hosts(String appName)throws GfacException;
+    public String[] listAwsdl()throws GfacException;
+    
+    public boolean isAuthorizedToAcsses(String resourceID, String actor, String action) throws GfacException;
+    
+}
+

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/impl/XregistryServiceWrapper.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/impl/XregistryServiceWrapper.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/impl/XregistryServiceWrapper.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/registry/impl/XregistryServiceWrapper.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,397 @@
+package org.apache.airavata.core.gfac.registry.impl;
+
+import java.io.File;
+import java.security.cert.X509Certificate;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.namespace.QName;
+
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.exception.GfacException.FaultCode;
+import org.apache.airavata.core.gfac.registry.RegistryService;
+import org.apache.xmlbeans.impl.values.XmlValueOutOfRangeException;
+import org.globus.gsi.TrustedCertificates;
+import org.ietf.jgss.GSSCredential;
+import org.ogce.xregistry.client.XRegistryClient;
+import org.ogce.xregistry.doc.AppData;
+import org.ogce.xregistry.doc.DocData;
+import org.ogce.xregistry.utils.XRegistryClientException;
+
+import xregistry.generated.CapabilityToken;
+import xregistry.generated.FindAppDescResponseDocument;
+import xregistry.generated.HostDescData;
+import xregistry.generated.ServiceDescData;
+import xregistry.generated.WsdlData;
+
+public class XregistryServiceWrapper implements RegistryService {
+
+	private XRegistryClient xregistryClient;
+
+	public XregistryServiceWrapper(String xregistryUrl, String trustedCertFile, GSSCredential sessionCredentail) throws GfacException {
+		try {
+			if (sessionCredentail != null && trustedCertFile != null) {
+				if (new File(trustedCertFile).isFile()) {
+					this.xregistryClient = new XRegistryClient(sessionCredentail, trustedCertFile, xregistryUrl);
+				} else {
+					TrustedCertificates certificates = TrustedCertificates.load(trustedCertFile);
+					TrustedCertificates.setDefaultTrustedCertificates(certificates);
+					X509Certificate[] trustedCertificates = certificates.getCertificates();
+					System.out.println("xregistryUrl=" + xregistryUrl);
+					System.out.println("trustedCertificates=" + trustedCertificates);
+					this.xregistryClient = new XRegistryClient(sessionCredentail, trustedCertificates, xregistryUrl);
+				}
+			} else {
+				throw new GfacException("Neither host certificate of gss credential is set", FaultCode.ErrorAtDependentService);
+			}
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+	
+	public XregistryServiceWrapper(String xregistryUrl, String trustedCertFile, String hostcertsKeyFile) throws GfacException {
+		try {
+			if (hostcertsKeyFile != null && trustedCertFile != null) {
+				if (new File(trustedCertFile).isFile()) {
+					this.xregistryClient = new XRegistryClient(hostcertsKeyFile, trustedCertFile, xregistryUrl);
+				} else {
+					TrustedCertificates certificates = TrustedCertificates.load(trustedCertFile);
+					TrustedCertificates.setDefaultTrustedCertificates(certificates);
+					X509Certificate[] trustedCertificates = certificates.getCertificates();
+					System.out.println("xregistryUrl=" + xregistryUrl);
+					System.out.println("hostcertsKeyFile=" + hostcertsKeyFile);
+					System.out.println("trustedCertificates=" + trustedCertificates);
+					this.xregistryClient = new XRegistryClient(hostcertsKeyFile, trustedCertificates, xregistryUrl);
+				}
+			} else {
+				throw new GfacException("Neither host certificate of gss credential is set", FaultCode.ErrorAtDependentService);
+			}
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String[] app2Hosts(String appName) throws GfacException {
+		try {
+			return xregistryClient.app2Hosts(appName);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String[] findAppDesc(String query) throws GfacException {
+		try {
+
+			FindAppDescResponseDocument.FindAppDescResponse.AppData[] xregAppDesc = xregistryClient.findAppDesc(query);
+			AppData[] appDesc = null;
+			if (xregAppDesc != null) {
+				List<AppData> appDescList = new ArrayList<AppData>();
+				for (int i = 0; i < xregAppDesc.length; i++) {
+					try {
+						FindAppDescResponseDocument.FindAppDescResponse.AppData xbeansData = xregAppDesc[i];
+						AppData resultAppData = new AppData(xbeansData.getName(), xbeansData.getOwner(), xbeansData.getHostName());
+						resultAppData.allowedAction = xbeansData.getAllowedAction();
+						resultAppData.resourceID = xbeansData.getName();
+						appDescList.add(resultAppData);
+					} catch (XmlValueOutOfRangeException e) {
+						throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+					}
+				}
+				appDesc = appDescList.toArray(new AppData[0]);
+			} else {
+				return null;
+			}
+
+			String[] finalResults = new String[appDesc.length];
+			for (int i = 0; i < appDesc.length; i++) {
+				finalResults[i] = appDesc[i].name + "#" + appDesc[i].secondryName;
+			}
+			return finalResults;
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String[] findService(String serviceName) throws GfacException {
+		try {
+			WsdlData[] serviceInstanceData = xregistryClient.findServiceInstance(serviceName);
+			String[] results = new String[serviceInstanceData.length];
+			for (int i = 0; i < serviceInstanceData.length; i++) {
+				try {
+					results[i] = serviceInstanceData[i].getName().toString();
+				} catch (XmlValueOutOfRangeException e) {
+					throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+				}
+			}
+			return results;
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String[] findServiceDesc(String serviceName) throws GfacException {
+		try {
+			ServiceDescData[] serviceDescData = xregistryClient.findServiceDesc(serviceName);
+			String[] results = new String[serviceDescData.length];
+			for (int i = 0; i < serviceDescData.length; i++) {
+				try {
+					results[i] = serviceDescData[i].getName().toString();
+				} catch (XmlValueOutOfRangeException e) {
+					throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+				}
+			}
+			return results;
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String getAbstractWsdl(String wsdlQName) throws GfacException {
+		try {
+			return xregistryClient.getAbstractWsdl(QName.valueOf(wsdlQName));
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String getAppDesc(String appQName, String hostName) throws GfacException {
+		try {
+			return xregistryClient.getAppDesc(appQName, hostName);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String getConcreateWsdl(String wsdlQName) throws GfacException {
+		try {
+			return xregistryClient.getConcreateWsdl(QName.valueOf(wsdlQName));
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String getHostDesc(String hostName) throws GfacException {
+		try {
+			return xregistryClient.getHostDesc(hostName);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String getServiceMap(String serviceQName) throws GfacException {
+		try {
+			return xregistryClient.getServiceDesc(QName.valueOf(serviceQName));
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public String[] listApps() throws GfacException {
+		return findAppDesc("");
+	}
+
+	public String[] listAwsdl() throws GfacException {
+		return findServiceDesc("");
+	}
+
+	public String[] listHosts() throws GfacException {
+		try {
+			HostDescData[] hostDescData = xregistryClient.findHosts("");
+			String[] results = new String[hostDescData.length];
+			for (int i = 0; i < hostDescData.length; i++) {
+				try {
+					results[i] = hostDescData[i].getName().toString();
+				} catch (XmlValueOutOfRangeException e) {
+					throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+				}
+			}
+			return results;
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void registerAppDesc(String appDescAsStr) throws GfacException {
+		try {
+			xregistryClient.registerAppDesc(appDescAsStr);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void registerConcreteWsdl(String wsdlAsStr, int lifetimeAsSeconds) throws GfacException {
+		try {
+			xregistryClient.registerConcreteWsdl(wsdlAsStr, lifetimeAsSeconds);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void registerOutputFiles(QName resourceId, String resourceName, String resourceType, String resourceDesc, String resourceDocument, String resourceParentTypedID, String owner) throws GfacException {
+		try {
+			xregistryClient.registerOGCEResource(resourceId, resourceName, resourceType, resourceDesc, resourceDocument, resourceParentTypedID, owner);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void registerHostDesc(String hostDescAsStr) throws GfacException {
+		try {
+			xregistryClient.registerHostDesc(hostDescAsStr);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void registerServiceMap(String serviceMapAsStr, String abstractWsdlAsString) throws GfacException {
+		try {
+			xregistryClient.registerServiceDesc(serviceMapAsStr, abstractWsdlAsString);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void removeAppDesc(String appQName, String hostName) throws GfacException {
+		try {
+			xregistryClient.removeAppDesc(QName.valueOf(appQName), hostName);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void removeAwsdl(String wsdlQName) throws GfacException {
+		throw new UnsupportedOperationException();
+	}
+
+	public void removeConcreteWsdl(String wsdlQName) throws GfacException {
+		try {
+			xregistryClient.removeConcreteWsdl(QName.valueOf(wsdlQName));
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void removeHostDesc(String hostName) throws GfacException {
+		try {
+			xregistryClient.removeHostDesc(hostName);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void removeServiceMap(String serviceQName) throws GfacException {
+		try {
+			xregistryClient.removeServiceDesc(QName.valueOf(serviceQName));
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public boolean isAuthorizedToAcsses(String resourceID, String actor, String action) throws GfacException {
+		try {
+			return xregistryClient.isAuthorizedToAcsses(null, resourceID, actor, action);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void addCapability(String resource, String actor, boolean isUser, String action) throws GfacException {
+		try {
+			xregistryClient.addCapability(resource, actor, isUser, action);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public CapabilityToken[] getCapability(String resource, String actor, boolean isUser, String action) throws GfacException {
+		try {
+			return xregistryClient.findCapability(resource, actor, isUser, action);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public void removeCapability(String resourceID, String actor) throws GfacException {
+		try {
+			xregistryClient.removeCapability(resourceID, actor);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public AppData[] xfindAppDesc(String query) throws GfacException {
+		try {
+			xregistry.generated.FindAppDescResponseDocument.FindAppDescResponse.AppData[] xregAppDesc = xregistryClient.findAppDesc(query);
+			AppData[] appDesc = null;
+			if (xregAppDesc != null) {
+				List<AppData> appDescList = new ArrayList<AppData>();
+				for (int i = 0; i < xregAppDesc.length; i++) {
+					try {
+						xregistry.generated.FindAppDescResponseDocument.FindAppDescResponse.AppData xbeansData = xregAppDesc[i];
+						AppData resultAppData = new AppData(xbeansData.getName(), xbeansData.getOwner(), xbeansData.getHostName());
+						resultAppData.allowedAction = xbeansData.getAllowedAction();
+						resultAppData.resourceID = xbeansData.getName();
+						appDescList.add(resultAppData);
+					} catch (XmlValueOutOfRangeException e) {
+						throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+					}
+				}
+				appDesc = appDescList.toArray(new AppData[0]);
+			} else {
+				return null;
+			}
+			return appDesc;
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public DocData[] xfindHostDesc(String query) throws GfacException {
+		try {
+			HostDescData[] hostDescData = xregistryClient.findHosts(query);
+			if (hostDescData == null) {
+				return null;
+			}
+
+			List<DocData> results = new ArrayList<DocData>();
+			for (int i = 0; i < hostDescData.length; i++) {
+				try {
+					HostDescData host = hostDescData[i];
+					DocData data = new DocData(new QName(host.getResourceID()), host.getOwner());
+					data.allowedAction = host.getAllowedAction();
+					data.resourceID = new QName(host.getResourceID());
+					results.add(data);
+				} catch (XmlValueOutOfRangeException e) {
+					throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+				}
+			}
+			return results.toArray(new DocData[0]);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+	public DocData[] xfindServiceDesc(String query) throws GfacException {
+		try {
+			ServiceDescData[] serviceDescData = xregistryClient.findServiceDesc(query);
+			if (serviceDescData == null) {
+				return null;
+			}
+			List<DocData> results = new ArrayList<DocData>();
+			for (int i = 0; i < serviceDescData.length; i++) {
+				try {
+					DocData data = new DocData(serviceDescData[i].getName(), serviceDescData[i].getOwner());
+					data.allowedAction = serviceDescData[i].getAllowedAction();
+					data.resourceID = serviceDescData[i].getName();
+					results.add(data);
+				} catch (XmlValueOutOfRangeException e) {
+					throw new GfacException("Problem with retrieving object : " + e.getLocalizedMessage(), FaultCode.ErrorAtDependentService);
+				}
+			}
+			return results.toArray(new DocData[0]);
+		} catch (XRegistryClientException e) {
+			throw new GfacException(e, FaultCode.ErrorAtDependentService);
+		}
+	}
+
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/Scheduler.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/Scheduler.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/Scheduler.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/Scheduler.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,9 @@
+package org.apache.airavata.core.gfac.scheduler;
+
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.provider.Provider;
+
+public interface Scheduler {
+	public Provider schedule(InvocationContext context) throws GfacException;
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/impl/SchedulerImpl.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/impl/SchedulerImpl.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/impl/SchedulerImpl.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/scheduler/impl/SchedulerImpl.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,83 @@
+package org.apache.airavata.core.gfac.scheduler.impl;
+
+import javax.xml.namespace.QName;
+
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.exception.GfacException.FaultCode;
+import org.apache.airavata.core.gfac.provider.GramProvider;
+import org.apache.airavata.core.gfac.provider.LocalProvider;
+import org.apache.airavata.core.gfac.provider.Provider;
+import org.apache.airavata.core.gfac.registry.RegistryService;
+import org.apache.airavata.core.gfac.scheduler.Scheduler;
+import org.apache.airavata.core.gfac.utils.GfacUtils;
+import org.apache.xmlbeans.XmlException;
+import org.ogce.schemas.gfac.documents.ServiceMapDocument;
+import org.ogce.schemas.gfac.documents.ServiceMapType;
+
+public class SchedulerImpl implements Scheduler {
+
+	public Provider schedule(InvocationContext context) throws GfacException {
+
+		String hostName = null;
+
+		/*
+		 * Load host and app description from registry
+		 */
+		RegistryService registryService = context.getExecutionContext().getRegistryService();
+		String serviceMapStr = registryService.getServiceMap(context.getServiceName());
+
+		if (serviceMapStr != null) {
+			try {
+				
+				ServiceMapType serviceMap = ServiceMapDocument.Factory.parse(serviceMapStr).getServiceMap();
+				QName appName = GfacUtils.findApplcationName(serviceMap);				
+
+				// host name
+				hostName = findHostFromServiceMap(registryService, appName);			
+				
+			} catch (XmlException e) {
+				throw new GfacException(e, FaultCode.InitalizationError);
+			}
+		} else {
+			throw new GfacException("Service Map for " + context.getServiceName() + " does not found on resource Catalog " + registryService, FaultCode.InvalidRequest);
+		}
+
+		
+		/*
+		 * Determine provider
+		 */
+		if (GfacUtils.isLocalHost(hostName)) {
+			return new LocalProvider();
+		} else {
+			// set Security context for executionContext
+			if (context.getSecurityContext(GramProvider.MYPROXY_SECURITY_CONTEXT) != null) {
+				context.getExecutionContext().setSecurityContext(context.getSecurityContext(GramProvider.MYPROXY_SECURITY_CONTEXT));
+			} else {
+				throw new GfacException("Cannot get security context to run on Gram", FaultCode.InvalidRequest);
+			}
+
+			return new GramProvider();
+		}
+	}
+
+	private String findHostFromServiceMap(RegistryService regService, QName appName) throws GfacException {
+
+		System.out.println("Searching registry for some deployed application hosts\n");
+		String[] hosts = regService.app2Hosts(appName.toString());
+		if (hosts.length > 1) {
+			String hostNames = "";
+			for (int i = 0; i < hosts.length; i++) {
+				hostNames = hostNames + hosts[i];
+			}
+			System.out.println("Application deployed on more than one machine. The full Host list is " + hostNames + "\n");
+		}
+		if (hosts.length >= 1) {
+			System.out.println("Found Host = " + hosts[0]);
+			return hosts[0];
+		} else {
+			System.out.println("Applcation  " + appName.getLocalPart() + " not found in registry");
+			return null;
+		}
+	}
+}

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/GenericService.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/GenericService.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/GenericService.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/GenericService.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,13 @@
+package org.apache.airavata.core.gfac.services;
+
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+
+public interface GenericService {
+	
+	public void init() throws GfacException;
+	
+	public void execute(InvocationContext context) throws GfacException;
+	
+	public void dispose() throws GfacException;	
+}
\ No newline at end of file

Added: incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java
URL: http://svn.apache.org/viewvc/incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java?rev=1139241&view=auto
==============================================================================
--- incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java (added)
+++ incubator/airavata/core/trunk/gfac/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java Fri Jun 24 11:01:15 2011
@@ -0,0 +1,95 @@
+package org.apache.airavata.core.gfac.services.impl;
+
+import org.apache.airavata.core.gfac.context.InvocationContext;
+import org.apache.airavata.core.gfac.exception.GfacException;
+import org.apache.airavata.core.gfac.extension.DataServiceChain;
+import org.apache.airavata.core.gfac.extension.ExitableChain;
+import org.apache.airavata.core.gfac.extension.PostExecuteChain;
+import org.apache.airavata.core.gfac.extension.PreExecuteChain;
+import org.apache.airavata.core.gfac.provider.Provider;
+import org.apache.airavata.core.gfac.scheduler.Scheduler;
+import org.apache.airavata.core.gfac.services.GenericService;
+
+public abstract class AbstractSimpleService implements GenericService {
+
+	public abstract void preProcess(InvocationContext context) throws GfacException;
+	
+	public abstract void postProcess(InvocationContext context) throws GfacException;
+	
+	public abstract Scheduler getScheduler(InvocationContext context) throws GfacException;
+
+	public abstract PreExecuteChain[] getPreExecutionSteps(InvocationContext context) throws GfacException;
+
+	public abstract PostExecuteChain[] getPostExecuteSteps(InvocationContext context) throws GfacException;
+
+	public abstract DataServiceChain[] getDataChains(InvocationContext context) throws GfacException;
+
+	public final void execute(InvocationContext context) throws GfacException {
+		
+		/*
+		 * Pre-Process
+		 */
+		preProcess(context);
+		
+		/*
+		 * Determine provider
+		 */
+		Provider provider = getScheduler(context).schedule(context);
+
+		/*
+		 * Load data necessary data
+		 */
+		buildChains(getDataChains(context)).start(context);
+
+		/*
+		 * Init
+		 */
+		provider.initialize(context);
+
+		/*
+		 * Pre-Execution
+		 */
+		buildChains(getPreExecutionSteps(context)).start(context);
+
+		/*
+		 * Execute
+		 */
+		provider.execute(context);
+
+		/*
+		 * Post-Execution
+		 */
+		buildChains(getPostExecuteSteps(context)).start(context);
+
+		/*
+		 * Destroy
+		 */
+		provider.dispose(context);
+		
+		/*
+		 * Pre-Process
+		 */
+		postProcess(context);
+	}
+
+	private ExitableChain buildChains(ExitableChain[] list) {
+
+		/*
+		 * Validation check and return doing-nothing chain object
+		 */
+		if (list == null || list.length == 0) {
+			return new ExitableChain() {
+				@Override
+				protected boolean execute(InvocationContext context) {
+					return true;
+				}
+			};
+		}
+
+		ExitableChain currentPoint = list[0];
+		for (int i = 1; i < list.length; i++) {
+			currentPoint = currentPoint.setNext(list[i]);
+		}
+		return currentPoint;
+	}
+}



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