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From lah...@apache.org
Subject [2/4] moving gfac-bes classes to new package.
Date Mon, 05 May 2014 14:49:59 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
deleted file mode 100644
index 3eb020f..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
+++ /dev/null
@@ -1,288 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.gfac.context.security;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.credential.store.credential.Credential;
-import org.apache.airavata.credential.store.credential.impl.certificate.CertificateCredential;
-import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.AbstractSecurityContext;
-import org.apache.airavata.gfac.Constants;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.RequestData;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.globus.gsi.X509Credential;
-import org.globus.gsi.gssapi.GlobusGSSCredentialImpl;
-import org.globus.gsi.provider.GlobusProvider;
-import org.globus.myproxy.GetParams;
-import org.globus.myproxy.MyProxy;
-import org.globus.myproxy.MyProxyException;
-import org.gridforum.jgss.ExtendedGSSCredential;
-import org.ietf.jgss.GSSCredential;
-import org.ietf.jgss.GSSException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.security.Security;
-import java.security.cert.X509Certificate;
-
-/**
- * Handles GRID related security.
- */
-public class GSISecurityContext extends AbstractSecurityContext {
-
-    protected static final Logger log = LoggerFactory.getLogger(GSISecurityContext.class);
-    /*
-     * context name
-     */
-    public static final String GSI_SECURITY_CONTEXT = "gsi";
-
-    public static int CREDENTIAL_RENEWING_THRESH_HOLD = 10 * 90;
-
-    private GSSCredential gssCredentials = null;
-
-    private Cluster pbsCluster = null;
-
-    // Set trusted cert path and add provider
-    static {
-        Security.addProvider(new GlobusProvider());
-        try {
-			setUpTrustedCertificatePath();
-		} catch (ApplicationSettingsException e) {
-			log.error(e.getLocalizedMessage(), e);
-		}
-    }
-
-    public static void setUpTrustedCertificatePath(String trustedCertificatePath) {
-
-        File file = new File(trustedCertificatePath);
-
-        if (!file.exists() || !file.canRead()) {
-            File f = new File(".");
-            log.info("Current directory " + f.getAbsolutePath());
-            throw new RuntimeException("Cannot read trusted certificate path " + trustedCertificatePath);
-        } else {
-            System.setProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY, file.getAbsolutePath());
-        }
-    }
-
-    private static void setUpTrustedCertificatePath() throws ApplicationSettingsException {
-
-        String trustedCertificatePath  = ServerSettings.getSetting(Constants.TRUSTED_CERT_LOCATION);
-
-        setUpTrustedCertificatePath(trustedCertificatePath);
-    }
-
-    /**
-     * Gets the trusted certificate path. Trusted certificate path is stored in "X509_CERT_DIR"
-     * system property.
-     * @return The trusted certificate path as a string.
-     */
-    public static String getTrustedCertificatePath() {
-        return System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY);
-    }
-
-
-    public GSISecurityContext(CredentialReader credentialReader, RequestData requestData) {
-        super(credentialReader, requestData);
-    }
-
-
-    public GSISecurityContext(Cluster pbsCluster) {
-        this.setPbsCluster(pbsCluster);
-    }
-
-    /**
-     * Gets GSSCredentials. The process is as follows;
-     * If credentials were queried for the first time create credentials.
-     *   1. Try creating credentials using certificates stored in the credential store
-     *   2. If 1 fails use user name and password to create credentials
-     * If credentials are already created check the remaining life time of the credential. If
-     * remaining life time is less than CREDENTIAL_RENEWING_THRESH_HOLD, then renew credentials.
-     * @return GSSCredentials to be used.
-     * @throws org.apache.airavata.gfac.GFacException If an error occurred while creating credentials.
-     * @throws org.apache.airavata.common.exception.ApplicationSettingsException
-     */
-    public GSSCredential getGssCredentials() throws GFacException, ApplicationSettingsException {
-
-        if (gssCredentials == null) {
-
-            try {
-                gssCredentials = getCredentialsFromStore();
-            } catch (Exception e) {
-                log.error("An exception occurred while retrieving credentials from the credential store. " +
-                        "Will continue with my proxy user name and password.", e);
-            }
-
-            // If store does not have credentials try to get from user name and password
-            if (gssCredentials == null) {
-                gssCredentials = getDefaultCredentials();
-            }
-
-            // if still null, throw an exception
-            if (gssCredentials == null) {
-                throw new GFacException("Unable to retrieve my proxy credentials to continue operation.");
-            }
-        } else {
-            try {
-                if (gssCredentials.getRemainingLifetime() < CREDENTIAL_RENEWING_THRESH_HOLD) {
-                    return renewCredentials();
-                }
-            } catch (GSSException e) {
-                throw new GFacException("Unable to retrieve remaining life time from credentials.", e);
-            }
-        }
-
-        return gssCredentials;
-    }
-
-    /**
-     * Renews credentials. First try to renew credentials as a trusted renewer. If that failed
-     * use user name and password to renew credentials.
-     * @return Renewed credentials.
-     * @throws org.apache.airavata.gfac.GFacException If an error occurred while renewing credentials.
-     * @throws org.apache.airavata.common.exception.ApplicationSettingsException
-     */
-    public GSSCredential renewCredentials() throws GFacException, ApplicationSettingsException {
-
-        // First try to renew credentials as a trusted renewer
-        try {
-            gssCredentials = renewCredentialsAsATrustedHost();
-        } catch (Exception e) {
-            log.warn("Renewing credentials as a trusted renewer failed", e);
-            gssCredentials = getProxyCredentials();
-        }
-
-        return gssCredentials;
-    }
-
-    /**
-     * Reads the credentials from credential store.
-     * @return If token is found in the credential store, will return a valid credential. Else returns null.
-     * @throws Exception If an error occurred while retrieving credentials.
-     */
-    public GSSCredential getCredentialsFromStore() throws Exception {
-
-        if (getCredentialReader() == null) {
-            return null;
-        }
-
-        Credential credential = getCredentialReader().getCredential(getRequestData().getGatewayId(),
-                getRequestData().getTokenId());
-
-        if (credential != null) {
-            if (credential instanceof CertificateCredential) {
-
-                log.info("Successfully found credentials for token id - " + getRequestData().getTokenId() +
-                        " gateway id - " + getRequestData().getGatewayId());
-
-                CertificateCredential certificateCredential = (CertificateCredential) credential;
-
-                X509Certificate[] certificates = certificateCredential.getCertificates();
-                X509Credential newCredential = new X509Credential(certificateCredential.getPrivateKey(), certificates);
-
-                GlobusGSSCredentialImpl cred = new GlobusGSSCredentialImpl(newCredential, GSSCredential.INITIATE_AND_ACCEPT);
-                System.out.print(cred.export(ExtendedGSSCredential.IMPEXP_OPAQUE));
-                return cred;
-                //return new GlobusGSSCredentialImpl(newCredential,
-                //        GSSCredential.INITIATE_AND_ACCEPT);
-            } else {
-                log.info("Credential type is not CertificateCredential. Cannot create mapping globus credentials. " +
-                        "Credential type - " + credential.getClass().getName());
-            }
-        } else {
-            log.info("Could not find credentials for token - " + getRequestData().getTokenId() + " and "
-                    + "gateway id - " + getRequestData().getGatewayId());
-        }
-
-        return null;
-    }
-
-    /**
-     * Gets the default proxy certificate.
-     * @return Default my proxy credentials.
-     * @throws org.apache.airavata.gfac.GFacException If an error occurred while retrieving credentials.
-     * @throws org.apache.airavata.common.exception.ApplicationSettingsException
-     */
-    public GSSCredential getDefaultCredentials() throws GFacException, ApplicationSettingsException{
-        MyProxy myproxy = new MyProxy(getRequestData().getMyProxyServerUrl(), getRequestData().getMyProxyPort());
-        try {
-            return myproxy.get(getRequestData().getMyProxyUserName(), getRequestData().getMyProxyPassword(),
-                    getRequestData().getMyProxyLifeTime());
-        } catch (MyProxyException e) {
-            throw new GFacException("An error occurred while retrieving default security credentials.", e);
-        }
-    }
-
-    /**
-     * Gets a new proxy certificate given current credentials.
-     * @return The short lived GSSCredentials
-     * @throws org.apache.airavata.gfac.GFacException If an error is occurred while retrieving credentials.
-     * @throws org.apache.airavata.common.exception.ApplicationSettingsException
-     */
-    public GSSCredential getProxyCredentials() throws GFacException, ApplicationSettingsException {
-
-        MyProxy myproxy = new MyProxy(getRequestData().getMyProxyServerUrl(), getRequestData().getMyProxyPort());
-        try {
-            return myproxy.get(gssCredentials, getRequestData().getMyProxyUserName(), getRequestData().getMyProxyPassword(),
-                    getRequestData().getMyProxyLifeTime());
-        } catch (MyProxyException e) {
-            throw new GFacException("An error occurred while renewing security credentials using user/password.", e);
-        }
-    }
-
-    /**
-     * Renew GSSCredentials.
-     * Before executing we need to add current host as a trusted renewer. Note to renew credentials
-     * we dont need user name and password.
-     * To do that execute following command
-     * > myproxy-logon -t <LIFETIME></LIFETIME> -s <MY PROXY SERVER> -l <USER NAME>
-     * E.g :- > myproxy-logon -t 264 -s myproxy.teragrid.org -l us3
-     *          Enter MyProxy pass phrase:
-     *          A credential has been received for user us3 in /tmp/x509up_u501.
-     * > myproxy-init -A --cert /tmp/x509up_u501 --key /tmp/x509up_u501 -l ogce -s myproxy.teragrid.org
-     * @return  Renewed credentials.
-     * @throws org.apache.airavata.gfac.GFacException If an error occurred while renewing credentials.
-     * @throws org.apache.airavata.common.exception.ApplicationSettingsException
-     */
-    public GSSCredential renewCredentialsAsATrustedHost() throws GFacException, ApplicationSettingsException {
-        MyProxy myproxy = new MyProxy(getRequestData().getMyProxyServerUrl(), getRequestData().getMyProxyPort());
-        GetParams getParams = new GetParams();
-        getParams.setAuthzCreds(gssCredentials);
-        getParams.setUserName(getRequestData().getMyProxyUserName());
-        getParams.setLifetime(getRequestData().getMyProxyLifeTime());
-        try {
-            return myproxy.get(gssCredentials, getParams);
-        } catch (MyProxyException e) {
-            throw new GFacException("An error occurred while renewing security credentials.", e);
-        }
-    }
-
-    public Cluster getPbsCluster() {
-        return pbsCluster;
-    }
-
-    public void setPbsCluster(Cluster pbsCluster) {
-        this.pbsCluster = pbsCluster;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
deleted file mode 100644
index 4a531a6..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
+++ /dev/null
@@ -1,568 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.gfac.provider.impl;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.math.BigInteger;
-import java.security.InvalidKeyException;
-import java.security.KeyPair;
-import java.security.KeyPairGenerator;
-import java.security.PrivateKey;
-import java.security.cert.X509Certificate;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Random;
-import java.util.Set;
-
-import javax.security.auth.x500.X500Principal;
-
-import org.apache.airavata.gfac.Constants;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.notification.events.StatusChangeEvent;
-import org.apache.airavata.gfac.notification.events.UnicoreJobIDEvent;
-import org.apache.airavata.gfac.provider.AbstractProvider;
-import org.apache.airavata.gfac.provider.GFacProviderException;
-import org.apache.airavata.gfac.utils.DataTransferrer;
-import org.apache.airavata.gfac.utils.JSDLGenerator;
-import org.apache.airavata.gfac.utils.StorageCreator;
-import org.apache.airavata.gfac.utils.GFacUtils;
-import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.airavata.registry.api.workflow.ApplicationJob;
-import org.apache.airavata.registry.api.workflow.ApplicationJob.ApplicationJobStatus;
-import org.apache.airavata.schemas.gfac.UnicoreHostType;
-import org.apache.xmlbeans.XmlCursor;
-import org.bouncycastle.asn1.ASN1InputStream;
-import org.bouncycastle.asn1.x500.X500Name;
-import org.bouncycastle.asn1.x500.style.BCStyle;
-import org.bouncycastle.asn1.x509.AlgorithmIdentifier;
-import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo;
-import org.ggf.schemas.bes.x2006.x08.besFactory.ActivityStateEnumeration;
-import org.ggf.schemas.bes.x2006.x08.besFactory.ActivityStateEnumeration.Enum;
-import org.ggf.schemas.bes.x2006.x08.besFactory.ActivityStatusType;
-import org.ggf.schemas.bes.x2006.x08.besFactory.CreateActivityDocument;
-import org.ggf.schemas.bes.x2006.x08.besFactory.CreateActivityResponseDocument;
-import org.ggf.schemas.bes.x2006.x08.besFactory.GetActivityStatusesDocument;
-import org.ggf.schemas.bes.x2006.x08.besFactory.GetActivityStatusesResponseDocument;
-import org.ggf.schemas.jsdl.x2005.x11.jsdl.JobDefinitionDocument;
-import org.ggf.schemas.jsdl.x2005.x11.jsdl.JobDefinitionType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.w3.x2005.x08.addressing.EndpointReferenceType;
-
-import de.fzj.unicore.bes.client.FactoryClient;
-import de.fzj.unicore.bes.faults.UnknownActivityIdentifierFault;
-import de.fzj.unicore.uas.client.StorageClient;
-import de.fzj.unicore.wsrflite.xmlbeans.WSUtilities;
-import eu.emi.security.authn.x509.helpers.CertificateHelpers;
-import eu.emi.security.authn.x509.helpers.proxy.X509v3CertificateBuilder;
-import eu.emi.security.authn.x509.impl.CertificateUtils;
-import eu.emi.security.authn.x509.impl.CertificateUtils.Encoding;
-import eu.emi.security.authn.x509.impl.DirectoryCertChainValidator;
-import eu.emi.security.authn.x509.impl.KeyAndCertCredential;
-import eu.emi.security.authn.x509.impl.X500NameUtils;
-import eu.unicore.util.httpclient.DefaultClientConfiguration;
-
-
-
-public class BESProvider extends AbstractProvider {
-    protected final Logger log = LoggerFactory.getLogger(this.getClass());
-
-    private DefaultClientConfiguration secProperties;
-
-    private String jobId;
-    
-    
-        
-	public void initialize(JobExecutionContext jobExecutionContext)
-			throws GFacProviderException, GFacException {
-		log.info("Initializing UNICORE Provider");
-		super.initialize(jobExecutionContext);
-    	initSecurityProperties(jobExecutionContext);
-    	log.debug("initialized security properties");
-    }
-
-
-	public void execute(JobExecutionContext jobExecutionContext)
-			throws GFacProviderException {
-        UnicoreHostType host = (UnicoreHostType) jobExecutionContext.getApplicationContext().getHostDescription()
-                .getType();
-
-        String factoryUrl = host.getUnicoreBESEndPointArray()[0];
-
-        EndpointReferenceType eprt = EndpointReferenceType.Factory.newInstance();
-        eprt.addNewAddress().setStringValue(factoryUrl);
-
-        String userDN = getUserName(jobExecutionContext);
-
-        if (userDN == null || userDN.equalsIgnoreCase("admin")) {
-            userDN = "CN=zdv575, O=Ultrascan Gateway, C=DE";
-        }
-
-        String xlogin = getCNFromUserDN(userDN);
-        // create storage
-        StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, xlogin);
-
-        StorageClient sc = null;
-        try {
-            try {
-                sc = storageCreator.createStorage();
-            } catch (Exception e2) {
-                log.error("Cannot create storage..");
-                throw new GFacProviderException("Cannot create storage..", e2);
-            }
-
-            CreateActivityDocument cad = CreateActivityDocument.Factory.newInstance();
-            JobDefinitionDocument jobDefDoc = JobDefinitionDocument.Factory.newInstance();
-
-            JobDefinitionType jobDefinition = jobDefDoc.addNewJobDefinition();
-            try {
-                jobDefinition = JSDLGenerator.buildJSDLInstance(jobExecutionContext, sc.getUrl()).getJobDefinition();
-                cad.addNewCreateActivity().addNewActivityDocument().setJobDefinition(jobDefinition);
-
-                log.info("JSDL" + jobDefDoc.toString());
-            } catch (Exception e1) {
-                throw new GFacProviderException("Cannot generate JSDL instance from the JobExecutionContext.", e1);
-            }
-
-            // upload files if any
-            DataTransferrer dt = new DataTransferrer(jobExecutionContext, sc);
-            dt.uploadLocalFiles();
-
-            FactoryClient factory = null;
-            try {
-                factory = new FactoryClient(eprt, secProperties);
-            } catch (Exception e) {
-                throw new GFacProviderException(e.getLocalizedMessage(), e);
-            }
-
-            CreateActivityResponseDocument response = null;
-            try {
-                log.info(String.format("Activity Submitting to %s ... \n", factoryUrl));
-                response = factory.createActivity(cad);
-                log.info(String.format("Activity Submitted to %s \n", factoryUrl));
-            } catch (Exception e) {
-                throw new GFacProviderException("Cannot create activity.", e);
-            }
-            EndpointReferenceType activityEpr = response.getCreateActivityResponse().getActivityIdentifier();
-
-            log.info("Activity : " + activityEpr.getAddress().getStringValue() + " Submitted.");
-
-            // factory.waitWhileActivityIsDone(activityEpr, 1000);
-            jobId = WSUtilities.extractResourceID(activityEpr);
-            if (jobId == null) {
-                jobId = new Long(Calendar.getInstance().getTimeInMillis()).toString();
-            }
-            log.info("JobID: " + jobId);
-            jobExecutionContext.getNotifier().publish(new UnicoreJobIDEvent(jobId));
-            saveApplicationJob(jobExecutionContext, jobDefinition, activityEpr.toString());
-
-            factory.getActivityStatus(activityEpr);
-            log.info(formatStatusMessage(activityEpr.getAddress().getStringValue(),
-                    factory.getActivityStatus(activityEpr).toString()));
-
-            // TODO publish the status messages to the message bus
-            while ((factory.getActivityStatus(activityEpr) != ActivityStateEnumeration.FINISHED)
-                    && (factory.getActivityStatus(activityEpr) != ActivityStateEnumeration.FAILED)
-                    && (factory.getActivityStatus(activityEpr) != ActivityStateEnumeration.CANCELLED)) {
-
-                ActivityStatusType activityStatus = null;
-                try {
-                    activityStatus = getStatus(factory, activityEpr);
-                    JobState jobStatus = getApplicationJobStatus(activityStatus);
-                    String jobStatusMessage = "Status of job " + jobId + "is " + jobStatus;
-                    jobExecutionContext.getNotifier().publish(new StatusChangeEvent(jobStatusMessage));
-                    details.setJobID(jobId);
-                    GFacUtils.updateJobStatus(jobExecutionContext, details, jobStatus);
-                } catch (UnknownActivityIdentifierFault e) {
-                    throw new GFacProviderException(e.getMessage(), e.getCause());
-                }catch (GFacException e) {
-                    throw new GFacProviderException(e.getMessage(), e.getCause());
-                }
-
-                try {
-                    Thread.sleep(5000);
-                } catch (InterruptedException e) {
-                }
-                continue;
-            }
-
-            ActivityStatusType activityStatus = null;
-            try {
-                activityStatus = getStatus(factory, activityEpr);
-            } catch (UnknownActivityIdentifierFault e) {
-                throw new GFacProviderException(e.getMessage(), e.getCause());
-            }
-
-            log.info(formatStatusMessage(activityEpr.getAddress().getStringValue(), activityStatus.getState()
-                    .toString()));
-
-            if ((activityStatus.getState() == ActivityStateEnumeration.FAILED)) {
-                String error = activityStatus.getFault().getFaultcode().getLocalPart() + "\n"
-                        + activityStatus.getFault().getFaultstring() + "\n EXITCODE: " + activityStatus.getExitCode();
-                log.info(error);
-                try {
-                    Thread.sleep(5000);
-                } catch (InterruptedException e) {
-                }
-                dt.downloadStdOuts();
-            } else if (activityStatus.getState() == ActivityStateEnumeration.CANCELLED) {
-                String experimentID = (String) jobExecutionContext.getProperty(Constants.PROP_TOPIC);
-                JobState jobStatus = JobState.CANCELED;
-                String jobStatusMessage = "Status of job " + jobId + "is " + jobStatus;
-                jobExecutionContext.getNotifier().publish(new StatusChangeEvent(jobStatusMessage));
-                details.setJobID(jobId);
-                try {
-					GFacUtils.saveJobStatus(jobExecutionContext,details, jobStatus);
-				} catch (GFacException e) {
-					 throw new GFacProviderException(e.getLocalizedMessage(),e);
-				}
-                throw new GFacProviderException(experimentID + "Job Canceled");
-            }
-
-            else if (activityStatus.getState() == ActivityStateEnumeration.FINISHED) {
-                try {
-                    Thread.sleep(5000);
-                } catch (InterruptedException e) {
-                }
-                if (activityStatus.getExitCode() == 0) {
-                    dt.downloadRemoteFiles();
-                } else {
-                    dt.downloadStdOuts();
-                }
-            }
-
-        } catch (UnknownActivityIdentifierFault e1) {
-            throw new GFacProviderException(e1.getLocalizedMessage(), e1);
-        } finally {
-            // destroy sms instance
-            try {
-                if (sc != null) {
-                    sc.destroy();
-                }
-            } catch (Exception e) {
-                log.warn("Cannot destroy temporary SMS instance:" + sc.getUrl(), e);
-            }
-        }
-    }
-
-	private JobState getApplicationJobStatus(ActivityStatusType activityStatus){
-        if (activityStatus == null) {
-            return JobState.UNKNOWN;
-        }
-        Enum state = activityStatus.getState();
-        String status = null;
-        XmlCursor acursor = activityStatus.newCursor();
-        try {
-            if (acursor.toFirstChild()) {
-                if (acursor.getName().getNamespaceURI().equals("http://schemas.ogf.org/hpcp/2007/01/fs")) {
-                    status = acursor.getName().getLocalPart();
-                }
-            }
-            if (status != null) {
-                if (status.equalsIgnoreCase("Queued") || status.equalsIgnoreCase("Starting")
-                        || status.equalsIgnoreCase("Ready")) {
-                    return JobState.QUEUED;
-                } else if (status.equalsIgnoreCase("Staging-In")) {
-                    return JobState.SUBMITTED;
-                } else if (status.equalsIgnoreCase("Staging-Out") || status.equalsIgnoreCase("FINISHED")) {
-                    return JobState.COMPLETE;
-                } else if (status.equalsIgnoreCase("Executing")) {
-                    return JobState.ACTIVE;
-                } else if (status.equalsIgnoreCase("FAILED")) {
-                    return JobState.FAILED;
-                } else if (status.equalsIgnoreCase("CANCELLED")) {
-                    return JobState.CANCELED;
-                }
-            } else {
-                if (ActivityStateEnumeration.CANCELLED.equals(state)) {
-                    return JobState.CANCELED;
-                } else if (ActivityStateEnumeration.FAILED.equals(state)) {
-                    return JobState.FAILED;
-                } else if (ActivityStateEnumeration.FINISHED.equals(state)) {
-                    return JobState.COMPLETE;
-                } else if (ActivityStateEnumeration.RUNNING.equals(state)) {
-                    return JobState.ACTIVE;
-                }
-            }
-        } finally {
-            if (acursor != null)
-                acursor.dispose();
-        }
-        return JobState.UNKNOWN;
-    }
-
-    private void saveApplicationJob(JobExecutionContext jobExecutionContext, JobDefinitionType jobDefinition,
-                                    String metadata) {
-        ApplicationJob appJob = GFacUtils.createApplicationJob(jobExecutionContext);
-        appJob.setJobId(jobId);
-        appJob.setJobData(jobDefinition.toString());
-        appJob.setSubmittedTime(Calendar.getInstance().getTime());
-        appJob.setStatus(ApplicationJobStatus.SUBMITTED);
-        appJob.setStatusUpdateTime(appJob.getSubmittedTime());
-        appJob.setMetadata(metadata);
-        GFacUtils.recordApplicationJob(jobExecutionContext, appJob);
-    }
-
-    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        secProperties = null;
-    }
-
-    /**
-     * EndpointReference need to be saved to make cancel work.
-     *
-     * @param activityEpr
-     * @param jobExecutionContext
-     * @throws GFacProviderException
-     */
-    public void cancelJob(String activityEpr, JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        try {
-            initSecurityProperties(jobExecutionContext);
-            EndpointReferenceType eprt = EndpointReferenceType.Factory.parse(activityEpr);
-            UnicoreHostType host = (UnicoreHostType) jobExecutionContext.getApplicationContext().getHostDescription()
-                    .getType();
-
-            String factoryUrl = host.getUnicoreBESEndPointArray()[0];
-            EndpointReferenceType epr = EndpointReferenceType.Factory.newInstance();
-            epr.addNewAddress().setStringValue(factoryUrl);
-
-            FactoryClient factory = new FactoryClient(epr, secProperties);
-            factory.terminateActivity(eprt);
-        } catch (Exception e) {
-            throw new GFacProviderException(e.getLocalizedMessage(),e);
-        }
-
-    }
-
-    protected void downloadOffline(String smsEpr, JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        try {
-            initSecurityProperties(jobExecutionContext);
-            EndpointReferenceType eprt = EndpointReferenceType.Factory.parse(smsEpr);
-            StorageClient sms = new StorageClient(eprt, secProperties);
-            DataTransferrer dt = new DataTransferrer(jobExecutionContext, sms);
-            // there must be output files there
-            // this is also possible if client is re-connected, the jobs are
-            // still
-            // running and no output is produced
-            dt.downloadRemoteFiles();
-
-            // may be use the below method before downloading for checking
-            // the number of entries
-            // sms.listDirectory(".");
-
-        } catch (Exception e) {
-            throw new GFacProviderException(e.getLocalizedMessage(), e);
-        }
-    }
-
-    protected void initSecurityProperties(JobExecutionContext jobExecutionContext) throws GFacProviderException,
-            GFacException {
-
-        if (secProperties != null)
-            return;
-
-        GSISecurityContext gssContext = (GSISecurityContext) jobExecutionContext
-                .getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT);
-
-        try {
-            String certLocation = gssContext.getTrustedCertificatePath();
-            List<String> trustedCert = new ArrayList<String>();
-            trustedCert.add(certLocation + "/*.0");
-            trustedCert.add(certLocation + "/*.pem");
-
-            DirectoryCertChainValidator dcValidator = new DirectoryCertChainValidator(trustedCert, Encoding.PEM, -1,
-                    60000, null);
-
-            String userID = getUserName(jobExecutionContext);
-
-            if ( userID == null || "".equals(userID) || userID.equalsIgnoreCase("admin") ) {
-                userID = "CN=zdv575, O=Ultrascan Gateway, C=DE";
-            }
-
-            String userDN = userID.replaceAll("^\"|\"$", "");
-
-            // TODO: should be changed to default airavata server locations
-            KeyAndCertCredential cred = generateShortLivedCertificate(userDN, certLocation
-                    + "/cacert.pem", certLocation
-                    + "/cakey.pem", "ultrascan3");
-            secProperties = new DefaultClientConfiguration(dcValidator, cred);
-
-            // secProperties.doSSLAuthn();
-            secProperties.getETDSettings().setExtendTrustDelegation(true);
-
-            secProperties.setDoSignMessage(true);
-
-            String[] outHandlers = secProperties.getOutHandlerClassNames();
-
-            Set<String> outHandlerLst = null;
-
-            // timeout in milliseconds
-            Properties p = secProperties.getExtraSettings();
-            p.setProperty("http.connection.timeout", "300000");
-            p.setProperty("http.socket.timeout", "300000");
-
-            if (outHandlers == null) {
-                outHandlerLst = new HashSet<String>();
-            } else {
-                outHandlerLst = new HashSet<String>(Arrays.asList(outHandlers));
-            }
-
-            outHandlerLst.add("de.fzj.unicore.uas.security.ProxyCertOutHandler");
-
-            secProperties.setOutHandlerClassNames(outHandlerLst.toArray(new String[outHandlerLst.size()]));
-
-        } catch (Exception e) {
-            throw new GFacProviderException(e.getMessage(), e);
-        }
-    }
-
-    //FIXME: Get user details
-    private String getUserName(JobExecutionContext context) {
-//        if (context.getConfigurationData()!= null) {
-//            return context.getConfigurationData().getBasicMetadata().getUserName();
-//        } else {
-           return "";
-//        }
-    }
-
-    protected ActivityStatusType getStatus(FactoryClient fc, EndpointReferenceType activityEpr)
-            throws UnknownActivityIdentifierFault {
-
-        GetActivityStatusesDocument stats = GetActivityStatusesDocument.Factory.newInstance();
-
-        stats.addNewGetActivityStatuses().setActivityIdentifierArray(new EndpointReferenceType[] { activityEpr });
-
-        GetActivityStatusesResponseDocument resDoc = fc.getActivityStatuses(stats);
-
-        ActivityStatusType activityStatus = resDoc.getGetActivityStatusesResponse().getResponseArray()[0]
-                .getActivityStatus();
-        return activityStatus;
-    }
-
-    protected String formatStatusMessage(String activityUrl, String status) {
-        return String.format("Activity %s is %s.\n", activityUrl, status);
-    }
-
-    protected String subStatusAsString(ActivityStatusType statusType) {
-
-        StringBuffer sb = new StringBuffer();
-
-        sb.append(statusType.getState().toString());
-
-        XmlCursor acursor = statusType.newCursor();
-        if (acursor.toFirstChild()) {
-            do {
-                if (acursor.getName().getNamespaceURI().equals("http://schemas.ogf.org/hpcp/2007/01/fs")) {
-                    sb.append(":");
-                    sb.append(acursor.getName().getLocalPart());
-                }
-            } while (acursor.toNextSibling());
-            acursor.dispose();
-            return sb.toString();
-        } else {
-            acursor.dispose();
-            return sb.toString();
-        }
-
-    }
-
-    public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
-
-    }
-
-    protected KeyAndCertCredential generateShortLivedCertificate(String userDN, String caCertPath, String caKeyPath,
-                                                                 String caPwd) throws Exception {
-        final long CredentialGoodFromOffset = 1000L * 60L * 15L; // 15 minutes
-        // ago
-
-        final long startTime = System.currentTimeMillis() - CredentialGoodFromOffset;
-        final long endTime = startTime + 30 * 3600 * 1000;
-
-        String keyLengthProp = "1024";
-        int keyLength = Integer.parseInt(keyLengthProp);
-        String signatureAlgorithm = "SHA1withRSA";
-
-        KeyAndCertCredential caCred = getCACredential(caCertPath, caKeyPath, caPwd);
-
-        KeyPairGenerator kpg = KeyPairGenerator.getInstance(caCred.getKey().getAlgorithm());
-        kpg.initialize(keyLength);
-        KeyPair pair = kpg.generateKeyPair();
-
-        X500Principal subjectDN = new X500Principal(userDN);
-        Random rand = new Random();
-
-        SubjectPublicKeyInfo publicKeyInfo;
-        try {
-            publicKeyInfo = SubjectPublicKeyInfo.getInstance(new ASN1InputStream(pair.getPublic().getEncoded())
-                    .readObject());
-        } catch (IOException e) {
-            throw new InvalidKeyException("Can not parse the public key"
-                    + "being included in the short lived certificate", e);
-        }
-
-        X500Name issuerX500Name = CertificateHelpers.toX500Name(caCred.getCertificate().getSubjectX500Principal());
-
-        X500Name subjectX500Name = CertificateHelpers.toX500Name(subjectDN);
-
-        X509v3CertificateBuilder certBuilder = new X509v3CertificateBuilder(issuerX500Name, new BigInteger(20, rand),
-                new Date(startTime), new Date(endTime), subjectX500Name, publicKeyInfo);
-
-        AlgorithmIdentifier sigAlgId = X509v3CertificateBuilder.extractAlgorithmId(caCred.getCertificate());
-
-        X509Certificate certificate = certBuilder.build(caCred.getKey(), sigAlgId, signatureAlgorithm, null, null);
-
-        certificate.checkValidity(new Date());
-        certificate.verify(caCred.getCertificate().getPublicKey());
-        KeyAndCertCredential result = new KeyAndCertCredential(pair.getPrivate(), new X509Certificate[] { certificate,
-                caCred.getCertificate() });
-
-        return result;
-    }
-
-    private KeyAndCertCredential getCACredential(String caCertPath, String caKeyPath, String password) throws Exception {
-        InputStream isKey = new FileInputStream(caKeyPath);
-        PrivateKey pk = CertificateUtils.loadPrivateKey(isKey, Encoding.PEM, password.toCharArray());
-
-        InputStream isCert = new FileInputStream(caCertPath);
-        X509Certificate caCert = CertificateUtils.loadCertificate(isCert, Encoding.PEM);
-
-        if (isKey != null)
-            isKey.close();
-        if (isCert != null)
-            isCert.close();
-
-        return new KeyAndCertCredential(pk, new X509Certificate[] { caCert });
-    }
-
-    private String getCNFromUserDN(String userDN) {
-        return X500NameUtils.getAttributeValues(userDN, BCStyle.CN)[0];
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/ApplicationProcessor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/ApplicationProcessor.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/ApplicationProcessor.java
deleted file mode 100644
index 76e9818..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/ApplicationProcessor.java
+++ /dev/null
@@ -1,252 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.utils;
-
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.schemas.gfac.ExtendedKeyValueType;
-import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.JobTypeType;
-import org.apache.airavata.schemas.gfac.NameValuePairType;
-import org.ggf.schemas.jsdl.x2005.x11.jsdl.ApplicationType;
-import org.ggf.schemas.jsdl.x2005.x11.jsdl.JobDefinitionType;
-import org.ggf.schemas.jsdl.x2005.x11.jsdlPosix.EnvironmentType;
-import org.ggf.schemas.jsdl.x2005.x11.jsdlPosix.FileNameType;
-import org.ggf.schemas.jsdl.x2005.x11.jsdlPosix.UserNameType;
-import org.ogf.schemas.jsdl.x2007.x02.jsdlSpmd.NumberOfProcessesType;
-import org.ogf.schemas.jsdl.x2007.x02.jsdlSpmd.ProcessesPerHostType;
-import org.ogf.schemas.jsdl.x2007.x02.jsdlSpmd.ThreadsPerProcessType;
-
-import java.io.File;
-
-
-public class ApplicationProcessor {
-	
-	public static void generateJobSpecificAppElements(JobDefinitionType value, JobExecutionContext context){
-		
-		String userName = getUserNameFromContext(context);
-		if (userName.equalsIgnoreCase("admin")){
-			userName = "CN=zdv575, O=Ultrascan Gateway, C=DE";
-		}
-		
-		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) context
-				.getApplicationContext().getApplicationDeploymentDescription()
-				.getType();
-		
-		createGenericApplication(value, appDepType);
-		
-		if (appDepType.getApplicationEnvironmentArray().length > 0) {
-			createApplicationEnvironment(value,
-					appDepType.getApplicationEnvironmentArray(), appDepType);
-		}
-
-		
-		if (appDepType.getExecutableLocation() != null) {
-			FileNameType fNameType = FileNameType.Factory.newInstance();
-			fNameType.setStringValue(appDepType.getExecutableLocation());
-			if(isParallelJob(appDepType)) {
-				JSDLUtils.getOrCreateSPMDApplication(value).setExecutable(fNameType);
-				JSDLUtils.getSPMDApplication(value).setSPMDVariation(getSPMDVariation(appDepType));
-				
-				if(getValueFromMap(appDepType, JSDLUtils.NUMBEROFPROCESSES)!=null){
-					NumberOfProcessesType num = NumberOfProcessesType.Factory.newInstance();
-					num.setStringValue(getValueFromMap(appDepType, JSDLUtils.NUMBEROFPROCESSES));
-					JSDLUtils.getSPMDApplication(value).setNumberOfProcesses(num);
-				}
-							
-				if(getValueFromMap(appDepType, JSDLUtils.PROCESSESPERHOST)!=null){
-					ProcessesPerHostType pph = ProcessesPerHostType.Factory.newInstance();
-					pph.setStringValue(getValueFromMap(appDepType, JSDLUtils.PROCESSESPERHOST));
-					JSDLUtils.getSPMDApplication(value).setProcessesPerHost(pph);
-				}
-				
-				if(getValueFromMap(appDepType, JSDLUtils.THREADSPERHOST)!=null){
-					ThreadsPerProcessType tpp = ThreadsPerProcessType.Factory.newInstance();
-					tpp.setStringValue(getValueFromMap(appDepType, JSDLUtils.THREADSPERHOST));
-					JSDLUtils.getSPMDApplication(value).setThreadsPerProcess(tpp);
-					
-				}
-				
-				if(userName != null) {
-					UserNameType userNameType = UserNameType.Factory.newInstance();
-					userNameType.setStringValue(userName);
-					JSDLUtils.getSPMDApplication(value).setUserName(userNameType);
-				}
-			}
-			else {
-				JSDLUtils.getOrCreatePOSIXApplication(value).setExecutable(fNameType);
-				if(userName != null) {
-					UserNameType userNameType = UserNameType.Factory.newInstance();
-					userNameType.setStringValue(userName);
-					JSDLUtils.getOrCreatePOSIXApplication(value).setUserName(userNameType);
-				}
-			}
-		}
-		
-
-		String stdout = (appDepType.getStandardOutput() != null) ? new File(appDepType.getStandardOutput()).getName(): "stdout"; 
-		ApplicationProcessor.setApplicationStdOut(value, appDepType, stdout);
-		
-	
-		String stderr = (appDepType.getStandardError() != null) ? new File(appDepType.getStandardError()).getName() : "stderr"; 
-		ApplicationProcessor.setApplicationStdErr(value, appDepType, stderr);
-	
-	}
-	
-	public static String getUserNameFromContext(JobExecutionContext jobContext) {
-		if(jobContext.getTaskData() == null)
-			return null;
-		//FIXME: Discuss to get user and change this
-		return "admin";
-	}
-	public static boolean isParallelJob(HpcApplicationDeploymentType appDepType) {
-		
-		boolean isParallel = false;
-		
-		if (appDepType.getJobType() != null) {
-			// TODO set data output directory
-			int status = appDepType.getJobType().intValue();
-
-			switch (status) {
-			// TODO: this check should be done outside this class
-			case JobTypeType.INT_MPI:
-			case JobTypeType.INT_OPEN_MP:
-				isParallel = true;
-				break;
-				
-			case JobTypeType.INT_SERIAL:
-			case JobTypeType.INT_SINGLE:
-				isParallel = false;
-				break;
-
-			default:
-				isParallel = false;
-				break;
-			}
-		}
-		return isParallel;
-	}
-
-	
-	public static void createApplicationEnvironment(JobDefinitionType value, NameValuePairType[] nameValuePairs, HpcApplicationDeploymentType appDepType) {
-		
-		if(isParallelJob(appDepType)) {
-			for (NameValuePairType nv : nameValuePairs) {
-				EnvironmentType envType = JSDLUtils.getOrCreateSPMDApplication(value).addNewEnvironment();
-				envType.setName(nv.getName());
-				envType.setStringValue(nv.getValue());
-			}
-		}
-		else {
-			for (NameValuePairType nv : nameValuePairs) {
-				EnvironmentType envType = JSDLUtils.getOrCreatePOSIXApplication(value).addNewEnvironment();
-				envType.setName(nv.getName());
-				envType.setStringValue(nv.getValue());
-			}
-		}
-
-	}
-	
-	
-	public static String getSPMDVariation (HpcApplicationDeploymentType appDepType) {
-		
-		String variation = null;
-		
-		if (appDepType.getJobType() != null) {
-			// TODO set data output directory
-			int status = appDepType.getJobType().intValue();
-
-			switch (status) {
-			// TODO: this check should be done outside this class
-			case JobTypeType.INT_MPI:
-				variation = SPMDVariations.MPI.value();				
-				break;
-				
-			case JobTypeType.INT_OPEN_MP:
-				variation = SPMDVariations.OpenMPI.value();
-				break;
-				
-			}
-		}
-		return variation;
-	}
-	
-	
-	public static void addApplicationArgument(JobDefinitionType value, HpcApplicationDeploymentType appDepType, String stringPrm) {
-		if(isParallelJob(appDepType)) 		
-			JSDLUtils.getOrCreateSPMDApplication(value)
-			.addNewArgument().setStringValue(stringPrm);
-		else 
-		    JSDLUtils.getOrCreatePOSIXApplication(value)
-				.addNewArgument().setStringValue(stringPrm);
-
-	}
-	
-	public static void setApplicationStdErr(JobDefinitionType value, HpcApplicationDeploymentType appDepType, String stderr) {
-		FileNameType fName = FileNameType.Factory.newInstance();
-		fName.setStringValue(stderr);
-		if (isParallelJob(appDepType)) 
-			JSDLUtils.getOrCreateSPMDApplication(value).setError(fName);
-		else 
-			JSDLUtils.getOrCreatePOSIXApplication(value).setError(fName);
-	}
-	
-	public static void setApplicationStdOut(JobDefinitionType value, HpcApplicationDeploymentType appDepType, String stderr) {
-		FileNameType fName = FileNameType.Factory.newInstance();
-		fName.setStringValue(stderr);
-		if (isParallelJob(appDepType)) 
-			JSDLUtils.getOrCreateSPMDApplication(value).setOutput(fName);
-		else 
-			JSDLUtils.getOrCreatePOSIXApplication(value).setOutput(fName);
-	}
-	
-	public static String getApplicationStdOut(JobDefinitionType value, HpcApplicationDeploymentType appDepType) throws RuntimeException {
-		if (isParallelJob(appDepType)) return JSDLUtils.getOrCreateSPMDApplication(value).getOutput().getStringValue();
-		else return JSDLUtils.getOrCreatePOSIXApplication(value).getOutput().getStringValue();
-	}
-	
-	public static String getApplicationStdErr(JobDefinitionType value, HpcApplicationDeploymentType appDepType) throws RuntimeException {
-		if (isParallelJob(appDepType)) return JSDLUtils.getOrCreateSPMDApplication(value).getError().getStringValue();
-		else return JSDLUtils.getOrCreatePOSIXApplication(value).getError().getStringValue();
-	}
-	
-	public static void createGenericApplication(JobDefinitionType value, HpcApplicationDeploymentType appDepType) {
-		if (appDepType.getApplicationName() != null) {
-			ApplicationType appType = JSDLUtils.getOrCreateApplication(value);
-			String appName = appDepType.getApplicationName()
-					.getStringValue();
-			appType.setApplicationName(appName);
-			JSDLUtils.getOrCreateJobIdentification(value).setJobName(appName);
-		}
-	}
-	
-	
-	public static String getValueFromMap(HpcApplicationDeploymentType appDepType, String name) {
-		ExtendedKeyValueType[] extended = appDepType.getKeyValuePairsArray();
-		for(ExtendedKeyValueType e: extended) {
-			if(e.getName().equalsIgnoreCase(name)) {
-				return e.getStringValue();
-			}
-		}
-		return null;
-	}
-	
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataStagingProcessor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataStagingProcessor.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataStagingProcessor.java
deleted file mode 100644
index adf6836..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataStagingProcessor.java
+++ /dev/null
@@ -1,235 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.utils;
-
-import java.io.File;
-import java.net.URI;
-import java.util.Map;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.StringArrayType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.apache.airavata.schemas.gfac.UnicoreHostType;
-import org.ggf.schemas.jsdl.x2005.x11.jsdl.JobDefinitionType;
-
-public class DataStagingProcessor {
-	
-	public static void generateDataStagingElements(JobDefinitionType value, JobExecutionContext context) throws Exception{
-		
-		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) context
-				.getApplicationContext().getApplicationDeploymentDescription()
-				.getType();
-
-		
-		String gridftpEndpoint = ((UnicoreHostType) context.getApplicationContext().getHostDescription().getType())
-				.getGridFTPEndPointArray()[0];
-
-
-		if (context.getInMessageContext().getParameters().size() > 0) {
-			buildDataStagingFromInputContext(context, value, gridftpEndpoint, appDepType);
-		}
-
-		if (context.getOutMessageContext().getParameters().size() > 0) {
-			buildFromOutputContext(context, value, gridftpEndpoint, appDepType);
-		}
-
-		createStdOutURIs(value, appDepType, gridftpEndpoint, isUnicoreEndpoint(context));
-
-	}
-	
-	private static void createInURIElement(JobDefinitionType value,
-			String endpoint, String inputDir, ActualParameter inParam)
-			throws Exception {
-
-		String uri = ((URIParameterType) inParam.getType()).getValue();
-		String fileName = new File(uri).getName();
-		if (uri.startsWith("file")) {
-			URI gridFTPInputDirURI = URIUtils.createGsiftpURI(endpoint,
-					inputDir);
-			String filePath = gridFTPInputDirURI.toString() + File.separator
-					+ fileName;
-			JSDLUtils
-					.addDataStagingSourceElement(value, filePath, null, fileName);
-		} else if (uri.startsWith("gsiftp") || uri.startsWith("http")
-				|| uri.startsWith("rns")) {
-			// no need to stage-in those files to the input
-			// directory
-			JSDLUtils.addDataStagingSourceElement(value, uri, null, fileName);
-		}
-
-	}
-
-	private static void createStdOutURIs(JobDefinitionType value,
-			HpcApplicationDeploymentType appDepType, String endpoint,
-			boolean isUnicore) throws Exception {
-
-		URI remoteOutputDir = URIUtils.createGsiftpURI(endpoint,
-				appDepType.getOutputDataDirectory());
-		
-		String stdout = ApplicationProcessor.getApplicationStdOut(value, appDepType);
-		
-		String stderr = ApplicationProcessor.getApplicationStdErr(value, appDepType);
-		
-		String stdoutFileName = (stdout == null || stdout.equals("")) ? "stdout"
-				: stdout;
-		String stdoutURI = GFacUtils.createGsiftpURIAsString(
-				remoteOutputDir.toString(), stdoutFileName);
-		JSDLUtils.addDataStagingTargetElement(value, null, stdoutFileName,
-				stdoutURI);
-
-		String stderrFileName = (stdout == null || stderr.equals("")) ? "stderr"
-				: stderr;
-		String stderrURI = GFacUtils.createGsiftpURIAsString(
-				remoteOutputDir.toString(), stderrFileName);
-		JSDLUtils.addDataStagingTargetElement(value, null, stderrFileName,
-				stderrURI);
-		
-		if(isUnicore) {
-			String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE";
-			String scriptExitCode = GFacUtils.createGsiftpURIAsString(
-					remoteOutputDir.toString(), scriptExitCodeFName);
-			JSDLUtils.addDataStagingTargetElement(value, null,
-					scriptExitCodeFName, scriptExitCode.toString());
-		}
-
-	}
-
-	
-	private static void createOutStringElements(JobDefinitionType value,
-			HpcApplicationDeploymentType appDeptype, String endpoint, String prmValue) throws Exception {
-		
-		if(prmValue == null || "".equals(prmValue)) return;
-		
-		
-		String outputUri = GFacUtils.createGsiftpURIAsString(endpoint, appDeptype.getOutputDataDirectory());
-		
-		URI finalOutputUri = URIUtils.createGsiftpURI(outputUri, prmValue);
-		JSDLUtils.addDataStagingTargetElement(value, null, prmValue,	finalOutputUri.toString());
-	}
-
-	
-	private static void createOutURIElement(JobDefinitionType value,
-			String prmValue) throws Exception {
-		String fileName = new File(prmValue.toString()).getName();
-		JSDLUtils.addDataStagingTargetElement(value, null, fileName, prmValue);
-	}
-
-	
-	private static JobDefinitionType buildFromOutputContext(JobExecutionContext context,
-			JobDefinitionType value, String gridftpEndpoint,
-			HpcApplicationDeploymentType appDepType) throws Exception {
-		
-		Map<String, Object> outputParams = context.getOutMessageContext()
-				.getParameters();
-
-		for (String paramKey : outputParams.keySet()) {
-
-			ActualParameter outParam = (ActualParameter) outputParams
-					.get(paramKey);
-
-			// if single urls then convert each url into jsdl source
-			// elements,
-			// that are formed by concat of gridftpurl+inputdir+filename
-
-			String paramDataType = outParam.getType().getType().toString();
-
-			if ("URI".equals(paramDataType)) {
-				String uriPrm = ((URIParameterType) outParam.getType())
-						.getValue();
-				createOutURIElement(value, uriPrm);
-			}
-
-			// string params are converted into the job arguments
-
-			else if (("URIArray").equals(paramDataType)) {
-				String[] uriArray = ((URIArrayType) outParam.getType())
-						.getValueArray();
-				for (String u : uriArray) {
-					
-					createOutURIElement(value, u);
-				}
-
-			}
-			else if ("String".equals(paramDataType)) {
-				String stringPrm = ((StringParameterType) outParam
-						.getType()).getValue();
-				createOutStringElements(value, appDepType, gridftpEndpoint, stringPrm);
-			}
-
-			else if ("StringArray".equals(paramDataType)) {
-				String[] valueArray = ((StringArrayType) outParam.getType())
-						.getValueArray();
-				for (String v : valueArray) {
-					createOutStringElements(value, appDepType, gridftpEndpoint, v);
-				}
-			}
-		}
-		
-		return value;
-	}
-
-	
-	private static void buildDataStagingFromInputContext(JobExecutionContext context, JobDefinitionType value, String gridftpEndpoint, HpcApplicationDeploymentType appDepType) 
-			throws Exception {
-		
-		// TODO set data directory
-		Map<String, Object> inputParams = context.getInMessageContext()
-				.getParameters();
-
-		for (String paramKey : inputParams.keySet()) {
-
-			ActualParameter inParam = (ActualParameter) inputParams
-					.get(paramKey);
-
-			// if single urls then convert each url into jsdl source
-			// elements,
-			// that are formed by concat of gridftpurl+inputdir+filename
-
-			String paramDataType = inParam.getType().getType().toString();
-
-			if ("URI".equals(paramDataType)) {
-				createInURIElement(value, gridftpEndpoint,
-						appDepType.getInputDataDirectory(), inParam);
-			}
-
-			// string params are converted into the job arguments
-
-			else if ("String".equals(paramDataType)) {
-				String stringPrm = ((StringParameterType) inParam.getType())
-						.getValue();
-				ApplicationProcessor.addApplicationArgument(value, appDepType, stringPrm);
-			}
-		}
-		
-	}
-	
-	
-	public static boolean isUnicoreEndpoint(JobExecutionContext context) {
-		return ( (context.getApplicationContext().getHostDescription().getType() instanceof UnicoreHostType)?true:false );
-	}
-
-	
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataTransferrer.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataTransferrer.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataTransferrer.java
deleted file mode 100644
index 6f844c7..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/DataTransferrer.java
+++ /dev/null
@@ -1,241 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.utils;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.gfac.Constants;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.provider.GFacProviderException;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.StringArrayType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import de.fzj.unicore.uas.client.StorageClient;
-
-
-public class DataTransferrer {
-    protected final Logger log = LoggerFactory.getLogger(this.getClass());
-
-	private JobExecutionContext jobContext;
-	
-	private StorageClient storageClient;
-	
-	public DataTransferrer(JobExecutionContext jobContext, StorageClient storageClient) {
-		this.jobContext = jobContext;
-		this.storageClient = storageClient;
-	}
-	
-	
-	public void uploadLocalFiles() throws GFacProviderException {
-		Map<String, Object> inputParams = jobContext.getInMessageContext()
-				.getParameters();
-		for (String paramKey : inputParams.keySet()) {
-			ActualParameter inParam = (ActualParameter) inputParams
-					.get(paramKey);
-			String paramDataType = inParam.getType().getType().toString();
-			if("URI".equals(paramDataType)) {
-				String uri = ((URIParameterType) inParam.getType()).getValue();
-				String fileName = new File(uri).getName();
-				if (uri.startsWith("file")) {
-					try {
-						String uriWithoutProtocol = uri.substring(
-								uri.lastIndexOf("://") + 1, uri.length());
-						FileUploader fileUploader = new FileUploader(
-								uriWithoutProtocol, "input/" + fileName,
-								Mode.overwrite);
-						fileUploader.perform(storageClient);
-					} catch (FileNotFoundException e3) {
-						throw new GFacProviderException(
-								"Error while staging-in, local file "+fileName+" not found", e3);
-					} catch (Exception e) {
-						throw new GFacProviderException("Cannot upload files", e);
-
-					}
-
-				}
-			}
-		}
-		
-	}
-	
-	/**
-	 * This method will download all the remote files specified according to the output 
-	 * context of a job.  
-	 * */
-	public void downloadRemoteFiles() throws GFacProviderException {
-		
-		String downloadLocation = getDownloadLocation();
-		
-		File file = new File(downloadLocation);
-		if(!file.exists()){
-			file.mkdirs();	
-		}
-		
-		Map<String, ActualParameter> stringMap = new HashMap<String, ActualParameter>();
-		     
-		Map<String, Object> outputParams = jobContext.getOutMessageContext()
-				.getParameters();
-
-		for (String paramKey : outputParams.keySet()) {
-
-			ActualParameter outParam = (ActualParameter) outputParams
-					.get(paramKey);
-
-			// if single urls then convert each url into jsdl source
-			// elements,
-			// that are formed by concat of gridftpurl+inputdir+filename
-
-			String paramDataType = outParam.getType().getType().toString();
-
-			if ("String".equals(paramDataType)) {
-				String stringPrm = ((StringParameterType) outParam
-						.getType()).getValue();
-				String localFileName = null;
-				//TODO: why analysis.tar? it wont scale to gateways..
-				if(stringPrm == null || stringPrm.isEmpty()){
-					localFileName = "analysis-results.tar";
-				}else{
-					localFileName = stringPrm.substring(stringPrm.lastIndexOf("/")+1);
-				}
-				String outputLocation = downloadLocation+File.separator+localFileName;
-				FileDownloader fileDownloader = new FileDownloader("output/"+stringPrm,outputLocation, Mode.overwrite);
-				try {
-					fileDownloader.perform(storageClient);
-					 ((StringParameterType) outParam.getType()).setValue(outputLocation);
-						stringMap.put(paramKey, outParam);
-				} catch (Exception e) {
-					throw new GFacProviderException(e.getLocalizedMessage(),e);
-				}
-			}
-
-			else if ("StringArray".equals(paramDataType)) {
-				String[] valueArray = ((StringArrayType) outParam.getType())
-						.getValueArray();
-				for (String v : valueArray) {
-					String localFileName = v.substring(v.lastIndexOf("/")+1);;
-					String outputLocation = downloadLocation+File.separator+localFileName;
-					FileDownloader fileDownloader = new FileDownloader("output/"+v,outputLocation, Mode.overwrite);
-					try {
-						fileDownloader.perform(storageClient);
-						 ((StringParameterType) outParam.getType()).setValue(outputLocation);
-						stringMap.put(paramKey, outParam);
-					} catch (Exception e) {
-						throw new GFacProviderException(e.getLocalizedMessage(),e);
-					}
-				}
-			}
-		}
-		 if (stringMap == null || stringMap.isEmpty()) {
-             throw new GFacProviderException("Empty Output returned from the Application, Double check the application" +
-                     "and ApplicationDescriptor output Parameter Names");
-         }
-		
-		downloadStdOuts();
-	}
-	
-	
-	public void downloadStdOuts()  throws GFacProviderException{
-		String downloadLocation = getDownloadLocation();
-		File file = new File(downloadLocation);
-		if(!file.exists()){
-			file.mkdirs();	
-		}
-		
-		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) jobContext
-				.getApplicationContext().getApplicationDeploymentDescription()
-				.getType();
-		
-		String stdout = appDepType.getStandardOutput();
-		String stderr = appDepType.getStandardError();
-		if(stdout != null) {
-			stdout = stdout.substring(stdout.lastIndexOf('/')+1);
-		}
-		
-		if(stderr != null) {
-			stderr = stderr.substring(stderr.lastIndexOf('/')+1);
-		}
-		
-		String stdoutFileName = (stdout == null || stdout.equals("")) ? "stdout"
-				: stdout;
-		String stderrFileName = (stdout == null || stderr.equals("")) ? "stderr"
-				: stderr;
-		
-		ApplicationDescription application = jobContext.getApplicationContext().getApplicationDeploymentDescription();
-		ApplicationDeploymentDescriptionType appDesc = application.getType();
-	
-		String stdoutLocation = downloadLocation+File.separator+stdoutFileName;
-		FileDownloader f1 = new FileDownloader("output/"+stdoutFileName,stdoutLocation, Mode.overwrite);
-		try {
-			f1.perform(storageClient);
-			String stdoutput = readFile(stdoutLocation);
-			appDesc.setStandardOutput(stdoutput);
-		} catch (Exception e) {
-			throw new GFacProviderException(e.getLocalizedMessage(),e);
-		}
-		String stderrLocation = downloadLocation+File.separator+stderrFileName;
-		FileDownloader f2 = new FileDownloader("output/"+stderrFileName,stderrLocation, Mode.overwrite);
-		try {
-			f2.perform(storageClient);
-			String stderror = readFile(stderrLocation);
-			appDesc.setStandardError(stderror);
-		} catch (Exception e) {
-			throw new GFacProviderException(e.getLocalizedMessage(),e);
-		}
-	}
-
-	private String readFile(String localFile) throws IOException {
-		BufferedReader instream = new BufferedReader(new FileReader(localFile));
-		StringBuffer buff = new StringBuffer();
-		String temp = null;
-		while ((temp = instream.readLine()) != null) {
-			buff.append(temp);
-			buff.append(Constants.NEWLINE);
-		}
-
-		log.info("finish read file:" + localFile);
-
-		return buff.toString();
-	}
-	
-	private String getDownloadLocation() {
-		TaskDetails taskData = jobContext.getTaskData();
-		if (taskData != null && taskData.getAdvancedOutputDataHandling() != null) {
-			String outputDataDirectory = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
-			return outputDataDirectory;
-		}
-		return null;
-	}
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileDownloader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileDownloader.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileDownloader.java
deleted file mode 100644
index 1eabb12..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileDownloader.java
+++ /dev/null
@@ -1,256 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.utils;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.Map;
-
-import org.unigrids.services.atomic.types.GridFileType;
-import org.unigrids.services.atomic.types.ProtocolType;
-
-import de.fzj.unicore.uas.client.FileTransferClient;
-import de.fzj.unicore.uas.client.StorageClient;
-import de.fzj.unicore.uas.client.UFTPConstants;
-import de.fzj.unicore.uas.client.UFTPFileTransferClient;
-import de.fzj.unicore.uas.fts.FiletransferOptions.IMonitorable;
-import de.fzj.unicore.uas.fts.FiletransferOptions.SupportsPartialRead;
-
-/**
- * helper that exports remote files from a UNICORE Storage 
- * to the local client machine.<br/>
- * Simple wildcards ("*" and "?") and download of 
- * directories are supported.
- * 
- * TODO this should be refactored so the single-file download logic 
- * is separated from the wildcard/directory/provided outputStream logic
- * 
- * @author schuller
- */
-public class FileDownloader extends FileTransferBase{
-
-	private boolean showProgress=true;
-
-	private boolean forceFileOnly=false;
-	
-	private OutputStream targetStream=null;
-	
-	public FileDownloader(String from, String to, Mode mode){
-		this(from,to,mode,true);
-	}
-	
-	public FileDownloader(String from, String to, Mode mode, boolean failOnError){
-		this.to=to;
-		this.from=from;
-		this.mode=mode;
-		this.failOnError=failOnError;
-	}
-	
-	public void perform(StorageClient sms)throws Exception{
-		boolean isWildcard=hasWildCards(from);
-		boolean isDirectory=false;
-		GridFileType gridSource=null;
-		if(isWildcard){
-			performWildCardExport(sms);
-		}
-		else {
-			//check if source is a directory
-			gridSource=sms.listProperties(from);
-			isDirectory=gridSource.getIsDirectory();
-			if(isDirectory){
-				if(forceFileOnly){
-					throw new IOException("Source is a directory");
-				}
-				performDirectoryExport(gridSource, new File(to), sms);
-			}
-			else{
-				download(gridSource,new File(to),sms);
-			}
-		}	
-	}
-	
-	protected void performDirectoryExport(GridFileType directory, File targetDirectory, StorageClient sms)throws Exception{
-		if(!targetDirectory.exists()|| !targetDirectory.canWrite()){
-			throw new IOException("Target directory <"+to+"> does not exist or is not writable!");
-		}
-		if(!targetDirectory.isDirectory()){
-			throw new IOException("Target <"+to+"> is not a directory!");
-		}
-		GridFileType[]gridFiles=sms.listDirectory(directory.getPath());
-		for(GridFileType file: gridFiles){
-			if(file.getIsDirectory()){
-				if(!recurse) {
-					System.out.println("Skipping directory "+file.getPath());
-					continue;
-				}
-				else{
-					File newTargetDirectory=new File(targetDirectory,getName(file.getPath()));
-					boolean success=newTargetDirectory.mkdirs();
-					if(!success)throw new IOException("Can create directory: "+newTargetDirectory.getAbsolutePath());
-					performDirectoryExport(file, newTargetDirectory, sms);
-					continue;
-				}
-			}
-			download(file, new File(targetDirectory,getName(file.getPath())), sms);
-		}
-	}
-	
-	protected void performWildCardExport(StorageClient sms)throws Exception{
-		String dir=getDir(from);
-		if(dir==null)dir="/";
-		GridFileType[] files=sms.find(dir, false, from, false, null, null);
-		File targetDir=targetStream==null?new File(to):null;
-		if(targetStream==null){
-			if(!targetDir.isDirectory())throw new IOException("Target is not a directory.");
-		}
-		for(GridFileType f: files){
-			download(f, targetDir, sms);
-		}
-	}	
-	
-	private String getDir(String path){
-		return new File(path).getParent();
-	}
-	
-	private String getName(String path){
-		return new File(path).getName();
-	}
-	
-	/**
-	 * download a single regular file
-	 * 
-	 * @param source - grid file descriptor
-	 * @param localFile - local file or directory to write to
-	 * @param sms
-	 * @throws Exception
-	 */
-	private void download(GridFileType source, File localFile, StorageClient sms)throws Exception{
-		if(source==null || source.getIsDirectory()){
-			throw new IllegalStateException("Source="+source); 
-		}
-		
-		OutputStream os=targetStream!=null?targetStream:null;
-		FileTransferClient ftc=null;
-		try{
-			String path=source.getPath();
-			if(targetStream==null){
-				if(localFile.isDirectory()){
-					localFile=new File(localFile,getName(source.getPath()));
-				}
-				if(mode.equals(Mode.nooverwrite) && localFile.exists()){
-					System.out.println("File exists and creation mode was set to 'nooverwrite'.");
-					return; 
-				}
-				System.out.println("Downloading remote file '"+sms.getUrl()+"#/"+path+"' -> "+localFile.getAbsolutePath());
-				os=new FileOutputStream(localFile.getAbsolutePath(), mode.equals(Mode.append));
-			}
-			
-			chosenProtocol=sms.findSupportedProtocol(preferredProtocols.toArray(new ProtocolType.Enum[preferredProtocols.size()]));
-			Map<String,String>extraParameters=makeExtraParameters(chosenProtocol);
-			ftc=sms.getExport(path,extraParameters,chosenProtocol);
-			configure(ftc, extraParameters);
-			System.out.println("DEB:File transfer URL : "+ftc.getUrl());
-//			ProgressBar p=null;
-			if(ftc instanceof IMonitorable  && showProgress){
-				long size=ftc.getSourceFileSize();
-				if(isRange()){
-					size=getRangeSize();
-				}
-//				p=new ProgressBar(localFile.getName(),size,msg);
-//				((IMonitorable) ftc).setProgressListener(p);
-			}
-			long startTime=System.currentTimeMillis();
-			if(isRange()){
-				if(!(ftc instanceof SupportsPartialRead)){
-					throw new Exception("Byte range is defined but protocol does not allow " +
-							"partial read! Please choose a different protocol!");
-				}
-				System.out.println("Byte range: "+startByte+" - "+(getRangeSize()>0?endByte:""));
-				SupportsPartialRead pReader=(SupportsPartialRead)ftc;
-				pReader.readPartial(startByte, endByte-startByte+1, os);
-			}
-			else{
-				ftc.readAllData(os);
-			}
-//			if(p!=null){
-//				p.finish();
-//			}
-			if(timing){
-				long duration=System.currentTimeMillis()-startTime;
-				double rate=(double)localFile.length()/(double)duration;
-				System.out.println("Rate: " +rate+ " kB/sec.");
-			}
-			if(targetStream==null)copyProperties(source, localFile);
-		}
-		finally{
-			try{ 
-				if(targetStream==null && os!=null){
-					os.close();
-				}
-			}catch(Exception ignored){}
-			if(ftc!=null){
-				try{
-					ftc.destroy();
-				}catch(Exception e1){
-//					System.out.println("Could not destroy the filetransfer client",e1);
-				}
-			}
-		}
-	}
-
-	/**
-	 * if possible, copy the remote executable flag to the local file
-	 * @throws Exception
-	 */
-	private void copyProperties(GridFileType source, File localFile)throws Exception{
-		try{
-			localFile.setExecutable(source.getPermissions().getExecutable());
-		}
-		catch(Exception ex){
-			//TODO: logging
-//			("Can't set 'executable' flag for "+localFile.getName(), ex);
-		}
-	}
-	
-	private void configure(FileTransferClient ftc, Map<String,String>params){
-		if(ftc instanceof UFTPFileTransferClient){
-			UFTPFileTransferClient u=(UFTPFileTransferClient)ftc;
-			String secret=params.get(UFTPConstants.PARAM_SECRET);
-			u.setSecret(secret);
-		}
-	}
-
-	public void setShowProgress(boolean showProgress) {
-		this.showProgress = showProgress;
-	}
-
-	public void setForceFileOnly(boolean forceFileOnly) {
-		this.forceFileOnly = forceFileOnly;
-	}
-
-	public void setTargetStream(OutputStream targetStream) {
-		this.targetStream = targetStream;
-	}
-	
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/49b6987f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileTransferBase.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileTransferBase.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileTransferBase.java
deleted file mode 100644
index 114ee57..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/utils/FileTransferBase.java
+++ /dev/null
@@ -1,227 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.utils;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.regex.Pattern;
-
-import org.unigrids.services.atomic.types.GridFileType;
-import org.unigrids.services.atomic.types.ProtocolType;
-
-import de.fzj.unicore.uas.client.StorageClient;
-import de.fzj.unicore.uas.util.PropertyHelper;
-public class FileTransferBase {
-
-	protected Properties extraParameterSource;
-
-	protected boolean timing=false;
-
-	protected boolean recurse=false;
-
-	protected String from;
-
-	protected String to;
-
-	//index of first byte to download
-	protected Long startByte;
-	
-	//index of last byte to download
-	protected Long endByte;
-	
-	/**
-	 * the creation mode
-	 */
-	protected Mode mode;
-
-	/**
-	 * whether the job processing should fail if an error occurs
-	 */
-	protected boolean failOnError;
-
-	protected List<ProtocolType.Enum> preferredProtocols=new ArrayList<ProtocolType.Enum>();
-
-	public FileTransferBase(){
-		preferredProtocols.add(ProtocolType.BFT);
-	}
-
-	protected Map<String,String>makeExtraParameters(ProtocolType.Enum protocol){
-		Map<String, String> res;
-		if(extraParameterSource==null){
-			res=new HashMap<String, String>();
-		}
-		else{
-			String p=String.valueOf(protocol);
-			PropertyHelper ph=new PropertyHelper(extraParameterSource, new String[]{p,p.toLowerCase()});
-			res= ph.getFilteredMap();
-		}
-		if(res.size()>0){
-			// TODO: change it to logger 
-			System.out.println("Have "+res.size()+" extra parameters for protocol "+protocol);
-		}
-		return res;
-	}
-	
-	
-	public String getTo() {
-		return to;
-	}
-
-	public String getFrom() {
-		return from;
-	}
-
-	public void setTo(String to) {
-		this.to = to;
-	}
-
-	public void setFrom(String from) {
-		this.from = from;
-	}
-
-	public Mode getMode() {
-		return mode;
-	}
-
-	public boolean isFailOnError() {
-		return failOnError;
-	}
-
-	public boolean isTiming() {
-		return timing;
-	}
-
-	public void setTiming(boolean timing) {
-		this.timing = timing;
-	}
-
-	public void setFailOnError(boolean failOnError) {
-		this.failOnError = failOnError;
-	}
-
-	public List<ProtocolType.Enum> getPreferredProtocols() {
-		return preferredProtocols;
-	}
-
-	public void setPreferredProtocols(List<ProtocolType.Enum> preferredProtocols) {
-		this.preferredProtocols = preferredProtocols;
-	}
-
-	public void setExtraParameterSource(Properties properties){
-		this.extraParameterSource=properties;
-	}
-
-	public void setRecurse(boolean recurse) {
-		this.recurse = recurse;
-	}
-	/**
-	 * check if the given path denotes a valid remote directory
-	 * @param remotePath - the path
-	 * @param sms - the storage
-	 * @return <code>true</code> if the remote directory exists and is a directory
-	 */
-	protected boolean isValidDirectory(String remotePath, StorageClient sms){
-		boolean result=false;
-		if(! ("/".equals(remotePath) || ".".equals(remotePath)) ){
-			try{
-				GridFileType gft=sms.listProperties(remotePath);
-				result=gft.getIsDirectory();
-			}catch(Exception ex){
-				result=false;
-			}
-		}
-		else result=true;
-		
-		return result;
-	}
-	
-	public File[] resolveWildCards(File original){
-		final String name=original.getName();
-		if(!hasWildCards(original))return new File[]{original};
-		File parent=original.getParentFile();
-		if(parent==null)parent=new File(".");
-		FilenameFilter filter=new FilenameFilter(){
-			Pattern p=createPattern(name);
-			public boolean accept(File file, String name){
-				return p.matcher(name).matches();
-			}
-		};
-		return parent.listFiles(filter);
-	}
-
-	protected boolean hasWildCards(File file){
-		return hasWildCards(file.getName());
-	}
-
-	public boolean hasWildCards(String name){
-		return name.contains("*") || name.contains("?");
-	}
-
-	private Pattern createPattern(String nameWithWildcards){
-		String regex=nameWithWildcards.replace("?",".").replace("*", ".*");
-		return Pattern.compile(regex);
-	}
-	
-	protected ProtocolType.Enum chosenProtocol=null;
-	
-	public ProtocolType.Enum getChosenProtocol(){
-		return chosenProtocol;
-	}
-
-	public Long getStartByte() {
-		return startByte;
-	}
-
-	public void setStartByte(Long startByte) {
-		this.startByte = startByte;
-	}
-
-	public Long getEndByte() {
-		return endByte;
-	}
-
-	public void setEndByte(Long endByte) {
-		this.endByte = endByte;
-	}
-	
-	/**
-	 * checks if a byte range is defined
-	 * @return <code>true</code> iff both startByte and endByte are defined
-	 */
-	protected boolean isRange(){
-		return startByte!=null && endByte!=null;
-	}
-	
-	/**
-	 * get the number of bytes in the byte range, or "-1" if the range is open-ended
-	 * @return
-	 */
-	protected long getRangeSize(){
-		if(Long.MAX_VALUE==endByte)return -1;
-		return endByte-startByte;
-	}
-}


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