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From shame...@apache.org
Subject [4/7] airavata git commit: Removed gsi related code
Date Tue, 16 Jun 2015 19:37:43 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
deleted file mode 100644
index 413b5dc..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
+++ /dev/null
@@ -1,344 +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.gsissh.provider.impl;
-
-import org.apache.airavata.registry.cpi.AppCatalogException;
-import org.apache.airavata.common.exception.AiravataException;
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.gfac.core.GFacException;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.provider.AbstractProvider;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.apache.airavata.gfac.core.GFacUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
-import org.apache.airavata.gfac.monitor.email.EmailBasedMonitor;
-import org.apache.airavata.gfac.monitor.email.EmailMonitorFactory;
-import org.apache.airavata.gfac.core.cluster.RemoteCluster;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.apache.airavata.gfac.core.JobDescriptor;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
-import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
-import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
-import org.apache.airavata.model.appcatalog.computeresource.MonitorMode;
-import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
-import org.apache.airavata.model.experiment.CorrectiveAction;
-import org.apache.airavata.model.experiment.ErrorCategory;
-import org.apache.airavata.model.experiment.JobDetails;
-import org.apache.airavata.model.experiment.JobState;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.Map;
-
-//import org.apache.airavata.schemas.gfac.GsisshHostType;
-
-public class GSISSHProvider extends AbstractProvider {
-    private static final Logger log = LoggerFactory.getLogger(GSISSHProvider.class);
-
-    public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
-
-    }
-
-    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        super.initialize(jobExecutionContext);
-        try {
-            String hostAddress = jobExecutionContext.getHostName();
-            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-        } catch (ApplicationSettingsException e) {
-            log.error(e.getMessage());
-            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-        } catch (GFacException e) {
-            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-        }
-    }
-
-    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        log.info("Invoking GSISSH Provider Invoke ...");
-        StringBuffer data = new StringBuffer();
-        ComputeResourceDescription computeResourceDescription = jobExecutionContext.getApplicationContext()
-                .getComputeResourceDescription();
-        ApplicationDeploymentDescription appDeployDesc = jobExecutionContext.getApplicationContext()
-                .getApplicationDeploymentDescription();
-        JobDetails jobDetails = new JobDetails();
-        RemoteCluster remoteCluster = null;
-
-        try {
-            if (jobExecutionContext.getSecurityContext(jobExecutionContext.getHostName()) != null) {
-                remoteCluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(jobExecutionContext.getHostName())).getRemoteCluster();
-            }
-            if (remoteCluster == null) {
-                throw new GFacProviderException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-            // This installed path is a mandetory field, because this could change based on the computing resource
-            JobDescriptor jobDescriptor = GFACGSISSHUtils.createJobDescriptor(jobExecutionContext, remoteCluster);
-            jobDetails.setJobName(jobDescriptor.getJobName());
-
-            log.info(jobDescriptor.toXML());
-            data.append("jobDesc=").append(jobDescriptor.toXML());
-            jobDetails.setJobDescription(jobDescriptor.toXML());
-            String jobID = remoteCluster.submitBatchJob(jobDescriptor);
-            jobExecutionContext.setJobDetails(jobDetails);
-            if (jobID == null) {
-                jobDetails.setJobID("none");
-                GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            } else {
-                jobDetails.setJobID(jobID.split("\\.")[0]);
-                GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.SUBMITTED);
-            }
-            data.append(",jobId=").append(jobDetails.getJobID());
-
-            // Now job has submitted to the resource, its up to the Provider to parse the information to daemon handler
-            // to perform monitoring, daemon handlers can be accessed from anywhere
-            monitor(jobExecutionContext);
-            // we know this host is type GsiSSHHostType
-        } catch (Exception e) {
-		    String error = "Error submitting the job to host " + computeResourceDescription.getHostName() + " message: " + e.getMessage();
-            log.error(error);
-            jobDetails.setJobID("none");
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            StringWriter errors = new StringWriter();
-            e.printStackTrace(new PrintWriter(errors));
-            GFacUtils.saveErrorDetails(jobExecutionContext,  errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            throw new GFacProviderException(error, e);
-        } finally {
-            log.info("Saving data for future recovery: ");
-            log.info(data.toString());
-            GFacUtils.saveHandlerData(jobExecutionContext, data, this.getClass().getName());
-        } 
-          
-    }
-
-    public void removeFromMonitorHandlers(JobExecutionContext jobExecutionContext, SSHJobSubmission sshJobSubmission, String jobID) throws GFacHandlerException {
-/*        List<ThreadedHandler> daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        if (daemonHandlers == null) {
-            daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        }
-        ThreadedHandler pullMonitorHandler = null;
-        ThreadedHandler pushMonitorHandler = null;
-        MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
-        for (ThreadedHandler threadedHandler : daemonHandlers) {
-            if ("org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pullMonitorHandler = threadedHandler;
-                if (monitorMode == null || monitorMode == MonitorMode.POLL_JOB_MANAGER) {
-                    jobExecutionContext.setProperty("cancel","true");
-                    pullMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PULL" +
-                            " to handle by the GridPullMonitorHandler");
-                }
-            } else if ("org.apache.airavata.gfac.monitor.handlers.GridPushMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pushMonitorHandler = threadedHandler;
-                if ( monitorMode == null || monitorMode == MonitorMode.XSEDE_AMQP_SUBSCRIBE) {
-                    pushMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PUSH" +
-                            " to handle by the GridPushMonitorHandler");
-                }
-            }
-            // have to handle the GridPushMonitorHandler logic
-        }
-        if (pullMonitorHandler == null && pushMonitorHandler == null && ExecutionMode.ASYNCHRONOUS.equals(jobExecutionContext.getGFacConfiguration().getExecutionMode())) {
-            log.error("No Daemon handler is configured in gfac-config.xml, either pull or push, so monitoring will not invoked" +
-                    ", execution is configured as asynchronous, so Outhandler will not be invoked");
-        }*/
-    }
-
-    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        //To change body of implemented methods use File | Settings | File Templates.
-    }
-
-    public boolean cancelJob(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
-        //To change body of implemented methods use File | Settings | File Templates.
-        log.info("canceling the job status in GSISSHProvider!!!!!");
-        JobDetails jobDetails = jobExecutionContext.getJobDetails();
-        String hostName = jobExecutionContext.getHostName();
-        try {
-            RemoteCluster remoteCluster = null;
-            if (jobExecutionContext.getSecurityContext(hostName) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-            remoteCluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostName)).getRemoteCluster();
-            if (remoteCluster == null) {
-                throw new GFacProviderException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-            // This installed path is a mandetory field, because this could change based on the computing resource
-            if(jobDetails == null) {
-                log.error("There is not JobDetails so cancelations cannot perform !!!");
-                return false;
-            }
-            if (jobDetails.getJobID() != null) {
-                // if this operation success without any exceptions, we can assume cancel operation succeeded.
-                remoteCluster.cancelJob(jobDetails.getJobID());
-            } else {
-                log.error("No Job Id is set, so cannot perform the cancel operation !!!");
-                return false;
-            }
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.CANCELED);
-            return true;
-            // we know this host is type GsiSSHHostType
-        } catch (SSHApiException e) {
-            String error = "Error submitting the job to host " + jobExecutionContext.getHostName() + " message: " + e.getMessage();
-            log.error(error);
-            jobDetails.setJobID("none");
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            throw new GFacProviderException(error, e);
-        } catch (Exception e) {
-            String error = "Error submitting the job to host " + jobExecutionContext.getHostName() + " message: " + e.getMessage();
-            log.error(error);
-            jobDetails.setJobID("none");
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            throw new GFacProviderException(error, e);
-        }
-    }
-
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
-        // have to implement the logic to recover a gfac failure
-        log.info("Invoking Recovering for the Experiment: " + jobExecutionContext.getExperimentID());
-        ComputeResourceDescription computeResourceDescription = jobExecutionContext.getApplicationContext()
-                .getComputeResourceDescription();
-        String hostName = jobExecutionContext.getHostName();
-        String jobId = "";
-        String jobDesc = "";
-        try {
-            String pluginData = GFacUtils.getHandlerData(jobExecutionContext, this.getClass().getName());
-            String[] split = pluginData.split(",");
-            if (split.length < 2) {
-                try {
-                    this.execute(jobExecutionContext);
-                } catch (GFacException e) {
-                    log.error("Error while  recovering provider", e);
-                    throw new GFacProviderException("Error recovering provider", e);
-                }
-                return;
-            }
-            jobDesc = split[0].substring(7);
-            jobId = split[1].substring(6);
-
-            log.info("Following data have recovered: ");
-            log.info("Job Description: " + jobDesc);
-            log.info("Job Id: " + jobId);
-            if (jobId == null || "none".equals(jobId) ||
-                    "".equals(jobId)) {
-                try {
-                    this.execute(jobExecutionContext);
-                } catch (GFacException e) {
-                    log.error("Error while  recovering provider", e);
-                    throw new GFacProviderException("Error recovering provider", e);
-                }
-                return;
-            }
-        } catch (Exception e) {
-            log.error("Error while  recovering provider", e);
-        }
-        try {
-            // Now we are we have enough data to recover
-            JobDetails jobDetails = new JobDetails();
-            jobDetails.setJobDescription(jobDesc);
-            jobDetails.setJobID(jobId);
-            jobExecutionContext.setJobDetails(jobDetails);
-            if (jobExecutionContext.getSecurityContext(hostName) == null) {
-                try {
-                    GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-                } catch (ApplicationSettingsException e) {
-                    log.error(e.getMessage());
-                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-                }
-            }
-            monitor(jobExecutionContext);
-        } catch (Exception e) {
-            log.error("Error while recover the job", e);
-            throw new GFacProviderException("Error delegating already ran job to Monitoring", e);
-        }
-    }
-
-    @Override
-    public void monitor(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        String jobSubmissionInterfaceId = jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionInterfaceId();
-        SSHJobSubmission sshJobSubmission = null;
-        try {
-            sshJobSubmission = jobExecutionContext.getAppCatalog().getComputeResource().getSSHJobSubmission(jobSubmissionInterfaceId);
-        } catch (AppCatalogException e) {
-            throw new GFacException("Error while reading compute resource", e);
-        }
-        if (jobExecutionContext.getPreferredJobSubmissionProtocol() == JobSubmissionProtocol.SSH) {
-            MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
-            if (monitorMode != null && monitorMode == MonitorMode.JOB_EMAIL_NOTIFICATION_MONITOR) {
-                try {
-                    EmailBasedMonitor emailBasedMonitor = EmailMonitorFactory.getEmailBasedMonitor(
-                            sshJobSubmission.getResourceJobManager().getResourceJobManagerType());
-                    emailBasedMonitor.addToJobMonitorMap(jobExecutionContext);
-                } catch (AiravataException e) {
-                    throw new GFacHandlerException("Error while activating email job monitoring ", e);
-                }
-                return;
-            }
-        }
-/*
-        // if email monitor is not activeated or not configure we use pull or push monitor
-        List<ThreadedHandler> daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        if (daemonHandlers == null) {
-            daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        }
-        ThreadedHandler pullMonitorHandler = null;
-        ThreadedHandler pushMonitorHandler = null;
-        MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
-        String jobID = jobExecutionContext.getJobDetails().getJobID();
-        for (ThreadedHandler threadedHandler : daemonHandlers) {
-            if ("org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pullMonitorHandler = threadedHandler;
-                if (monitorMode == null || monitorMode == MonitorMode.POLL_JOB_MANAGER) {
-                    log.info("Job is launched successfully now parsing it to monitoring in pull mode, JobID Returned:  " + jobID);
-                    pullMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PULL" +
-                            " to handle by the GridPullMonitorHandler");
-                }
-            } else if ("org.apache.airavata.gfac.monitor.handlers.GridPushMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pushMonitorHandler = threadedHandler;
-                if (monitorMode == null || monitorMode == MonitorMode.XSEDE_AMQP_SUBSCRIBE) {
-                    log.info("Job is launched successfully now parsing it to monitoring in push mode, JobID Returned:  " + jobID);
-                    pushMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PUSH" +
-                            " to handle by the GridPushMonitorHandler");
-                }
-            }
-            // have to handle the GridPushMonitorHandler logic
-        }
-        if (pullMonitorHandler == null && pushMonitorHandler == null && ExecutionMode.ASYNCHRONOUS.equals(jobExecutionContext.getGFacConfiguration().getExecutionMode())) {
-            log.error("No Daemon handler is configured in gfac-config.xml, either pull or push, so monitoring will not invoked" +
-                    ", execution is configured as asynchronous, so Outhandler will not be invoked");
-
-        }*/
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
deleted file mode 100644
index 85216b4..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
+++ /dev/null
@@ -1,67 +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.gsissh.security;
-
-import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.core.context.AbstractSecurityContext;
-import org.apache.airavata.gfac.core.RequestData;
-import org.apache.airavata.gfac.core.cluster.RemoteCluster;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Handles GRID related security.
- */
-public class GSISecurityContext extends AbstractSecurityContext {
-
-    protected static final Logger log = LoggerFactory.getLogger(GSISecurityContext.class);
-    /*
-     * context name
-     */
-
-    private RemoteCluster remoteCluster = null;
-
-
-    public GSISecurityContext(CredentialReader credentialReader, RequestData requestData, RemoteCluster remoteCluster) {
-        super(credentialReader, requestData);
-        this.remoteCluster = remoteCluster;
-    }
-
-
-    public GSISecurityContext(CredentialReader credentialReader, RequestData requestData) {
-        super(credentialReader, requestData);
-    }
-
-
-    public GSISecurityContext(RemoteCluster remoteCluster) {
-        this.setRemoteCluster(remoteCluster);
-    }
-
-
-
-    public RemoteCluster getRemoteCluster() {
-        return remoteCluster;
-    }
-
-    public void setRemoteCluster(RemoteCluster remoteCluster) {
-        this.remoteCluster = remoteCluster;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/TokenizedMyProxyAuthInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/TokenizedMyProxyAuthInfo.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/TokenizedMyProxyAuthInfo.java
deleted file mode 100644
index 36cb84f..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/TokenizedMyProxyAuthInfo.java
+++ /dev/null
@@ -1,304 +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.gsissh.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.core.GFacConstants;
-import org.apache.airavata.gfac.core.GFacException;
-import org.apache.airavata.gfac.core.RequestData;
-import org.apache.airavata.gfac.core.GFacUtils;
-import org.apache.airavata.gfac.core.authentication.GSIAuthenticationInfo;
-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;
-
-public class TokenizedMyProxyAuthInfo extends GSIAuthenticationInfo {
-    protected static final Logger log = LoggerFactory.getLogger(TokenizedMyProxyAuthInfo.class);
-
-    public static int CREDENTIAL_RENEWING_THRESH_HOLD = 10 * 90;
-
-    private GSSCredential gssCredentials = null;
-
-
-    private CredentialReader credentialReader;
-
-    private RequestData requestData;
-
-    public static final String X509_CERT_DIR = "X509_CERT_DIR";
-
-
-    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(GFacConstants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY, file.getAbsolutePath());
-        }
-    }
-
-    private static void setUpTrustedCertificatePath() throws ApplicationSettingsException {
-
-        String trustedCertificatePath = ServerSettings.getSetting(GFacConstants.TRUSTED_CERT_LOCATION);
-
-        setUpTrustedCertificatePath(trustedCertificatePath);
-    }
-
-    public TokenizedMyProxyAuthInfo(CredentialReader credentialReader, RequestData requestData) {
-        this.credentialReader = credentialReader;
-        this.requestData = requestData;
-        try {
-            properties.setProperty(X509_CERT_DIR, ServerSettings.getSetting(GFacConstants.TRUSTED_CERT_LOCATION));
-        } catch (ApplicationSettingsException e) {
-            log.error("Error while  reading server properties", e);
-        };
-    }
-
-    public TokenizedMyProxyAuthInfo(RequestData requestData) {
-           this.requestData = requestData;
-           try {
-               properties.setProperty(X509_CERT_DIR, ServerSettings.getSetting(GFacConstants.TRUSTED_CERT_LOCATION));
-           } catch (ApplicationSettingsException e) {
-               log.error("Error while  reading server properties", e);
-           };
-       }
-
-    public GSSCredential getCredentials() throws SecurityException {
-
-        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. Provided TokenId:" + requestData.getTokenId(), e);
-            }
-
-            if (gssCredentials == null) {
-                System.out.println("Authenticating with provided token failed, so falling back to authenticate with defaultCredentials");
-                try {
-                    gssCredentials = getDefaultCredentials();
-                } catch (Exception e) {
-                    throw new SecurityException("Error retrieving my proxy using username password");
-                }
-            }
-            // if still null, throw an exception
-            if (gssCredentials == null) {
-                throw new SecurityException("Unable to retrieve my proxy credentials to continue operation.");
-            }
-        } else {
-            try {
-                if (gssCredentials.getRemainingLifetime() < CREDENTIAL_RENEWING_THRESH_HOLD) {
-                    try {
-                        return renewCredentials();
-                    } catch (Exception e) {
-                        throw new SecurityException("Error renewing credentials", e);
-                    }
-                }
-            } catch (GSSException e) {
-                throw new SecurityException("Unable to retrieve remaining life time from credentials.", e);
-            }
-        }
-
-        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) {
-        	credentialReader = GFacUtils.getCredentialReader();
-        	if(credentialReader == 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;
-    }
-
-    /**
-     * 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 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);
-        }
-    }
-
-
-    /**
-     * Gets the default proxy certificate.
-     *
-     * @return Default my proxy credentials.
-     * @throws 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);
-        }
-    }
-
-
-    /**
-     * 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 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 = getDefaultCredentials();
-        }
-
-        return gssCredentials;
-    }
-
-    /**
-     * Gets a new proxy certificate given current credentials.
-     *
-     * @return The short lived GSSCredentials
-     * @throws 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);
-        }
-    }
-
-    public void setGssCredentials(GSSCredential gssCredentials) {
-        this.gssCredentials = gssCredentials;
-    }
-
-    public CredentialReader getCredentialReader() {
-        return credentialReader;
-    }
-
-    public void setCredentialReader(CredentialReader credentialReader) {
-        this.credentialReader = credentialReader;
-    }
-
-    public RequestData getRequestData() {
-        return requestData;
-    }
-
-    public void setRequestData(RequestData requestData) {
-        this.requestData = requestData;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
deleted file mode 100644
index 89e3571..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
+++ /dev/null
@@ -1,367 +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.gsissh.util;
-
-import org.apache.airavata.gfac.core.cluster.RemoteCluster;
-import org.apache.airavata.gfac.gsi.ssh.impl.HPCRemoteCluster;
-import org.apache.airavata.registry.cpi.AppCatalog;
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.credential.store.credential.impl.certificate.CertificateCredential;
-import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.core.GFacException;
-import org.apache.airavata.gfac.core.RequestData;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.GFacUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.security.TokenizedMyProxyAuthInfo;
-import org.apache.airavata.gfac.core.cluster.ServerInfo;
-import org.apache.airavata.gfac.core.JobDescriptor;
-import org.apache.airavata.gfac.core.JobManagerConfiguration;
-import org.apache.airavata.gfac.gsi.ssh.impl.GSISSHAbstractCluster;
-import org.apache.airavata.gfac.gsi.ssh.util.CommonUtils;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.appcatalog.computeresource.*;
-import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
-import org.apache.airavata.model.experiment.ComputationalResourceScheduling;
-import org.apache.airavata.model.experiment.TaskDetails;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.util.*;
-
-
-public class GFACGSISSHUtils {
-    private final static Logger logger = LoggerFactory.getLogger(GFACGSISSHUtils.class);
-
-    public static final String PBS_JOB_MANAGER = "pbs";
-    public static final String SLURM_JOB_MANAGER = "slurm";
-    public static final String SUN_GRID_ENGINE_JOB_MANAGER = "UGE";
-    public static final String LSF_JOB_MANAGER = "lsf";
-
-    public static int maxClusterCount = 5;
-    public static Map<String, List<RemoteCluster>> clusters = new HashMap<String, List<RemoteCluster>>();
-
-    public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
-        JobSubmissionInterface jobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
-        JobSubmissionProtocol jobProtocol = jobSubmissionInterface.getJobSubmissionProtocol();
-        try {
-            AppCatalog appCatalog = jobExecutionContext.getAppCatalog();
-            SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(jobSubmissionInterface.getJobSubmissionInterfaceId());
-            if (jobProtocol == JobSubmissionProtocol.GLOBUS || jobProtocol == JobSubmissionProtocol.UNICORE
-                    || jobProtocol == JobSubmissionProtocol.CLOUD || jobProtocol == JobSubmissionProtocol.LOCAL) {
-                logger.error("This is a wrong method to invoke to non ssh host types,please check your gfac-config.xml");
-            } else if (jobProtocol == JobSubmissionProtocol.SSH && sshJobSubmission.getSecurityProtocol() == SecurityProtocol.GSI) {
-                String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
-                RequestData requestData = new RequestData(jobExecutionContext.getGatewayID());
-                requestData.setTokenId(credentialStoreToken);
-                HPCRemoteCluster HPCRemoteCluster = null;
-                GSISecurityContext context = null;
-
-                TokenizedMyProxyAuthInfo tokenizedMyProxyAuthInfo = new TokenizedMyProxyAuthInfo(requestData);
-                CredentialReader credentialReader = GFacUtils.getCredentialReader();
-                if (credentialReader != null) {
-                    CertificateCredential credential = null;
-                    try {
-                        credential = (CertificateCredential) credentialReader.getCredential(jobExecutionContext.getGatewayID(), credentialStoreToken);
-                        requestData.setMyProxyUserName(credential.getCommunityUser().getUserName());
-                    } catch (Exception e) {
-                        logger.error(e.getLocalizedMessage());
-                    }
-                }
-
-                String key = requestData.getMyProxyUserName() + jobExecutionContext.getHostName()+
-                        sshJobSubmission.getSshPort();
-                boolean recreate = false;
-                synchronized (clusters) {
-                    if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
-                        recreate = true;
-                    } else if (clusters.containsKey(key)) {
-                        int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
-                        if (clusters.get(key).get(i).getSession().isConnected()) {
-                            HPCRemoteCluster = (HPCRemoteCluster) clusters.get(key).get(i);
-                        } else {
-                            clusters.get(key).remove(i);
-                            recreate = true;
-                        }
-                        if (!recreate) {
-                            try {
-                                HPCRemoteCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
-                            } catch (Exception e) {
-                                clusters.get(key).remove(i);
-                                logger.info("Connection found the connection map is expired, so we create from the scratch");
-                                maxClusterCount++;
-                                recreate = true; // we make the HPCRemoteCluster to create again if there is any exception druing connection
-                            }
-                            logger.info("Re-using the same connection used with the connection string:" + key);
-                            context = new GSISecurityContext(tokenizedMyProxyAuthInfo.getCredentialReader(), requestData, HPCRemoteCluster);
-                        }
-                    } else {
-                        recreate = true;
-                    }
-
-                    if (recreate) {
-                        ServerInfo serverInfo = new ServerInfo(requestData.getMyProxyUserName(), jobExecutionContext.getHostName(),
-                                sshJobSubmission.getSshPort());
-
-                        JobManagerConfiguration jConfig = null;
-                        String installedParentPath = sshJobSubmission.getResourceJobManager().getJobManagerBinPath();
-                        String jobManager = sshJobSubmission.getResourceJobManager().getResourceJobManagerType().toString();
-                        if (jobManager == null) {
-                            logger.error("No Job Manager is configured, so we are picking pbs as the default job manager");
-                            jConfig = CommonUtils.getPBSJobManager(installedParentPath);
-                        } else {
-                            if (PBS_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
-                                jConfig = CommonUtils.getPBSJobManager(installedParentPath);
-                            } else if (SLURM_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
-                                jConfig = CommonUtils.getSLURMJobManager(installedParentPath);
-                            } else if (SUN_GRID_ENGINE_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
-                                jConfig = CommonUtils.getUGEJobManager(installedParentPath);
-                            }else if(LSF_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
-                                jConfig = CommonUtils.getLSFJobManager(installedParentPath);
-                            }
-                        }
-                        HPCRemoteCluster = new HPCRemoteCluster(serverInfo, tokenizedMyProxyAuthInfo, jConfig);
-                        context = new GSISecurityContext(tokenizedMyProxyAuthInfo.getCredentialReader(), requestData, HPCRemoteCluster);
-                        List<RemoteCluster> pbsRemoteClusters = null;
-                        if (!(clusters.containsKey(key))) {
-                            pbsRemoteClusters = new ArrayList<RemoteCluster>();
-                        } else {
-                            pbsRemoteClusters = clusters.get(key);
-                        }
-                        pbsRemoteClusters.add(HPCRemoteCluster);
-                        clusters.put(key, pbsRemoteClusters);
-                    }
-                }
-
-                jobExecutionContext.addSecurityContext(jobExecutionContext.getHostName(), context);
-            }
-        } catch (Exception e) {
-            throw new GFacException("An error occurred while creating GSI security context", e);
-        }
-    }
-
-    public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, RemoteCluster remoteCluster) {
-        JobDescriptor jobDescriptor = new JobDescriptor();
-        TaskDetails taskData = jobExecutionContext.getTaskData();
-        ResourceJobManager resourceJobManager = jobExecutionContext.getResourceJobManager();
-        try {
-			if(ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_ENABLE).equalsIgnoreCase("true")){
-				jobDescriptor.setMailOptions(ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_FLAGS));
-				String emailids = ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_EMAILIDS);
-
-				if(jobExecutionContext.getTaskData().isSetEmailAddresses()){
-					List<String> emailList = jobExecutionContext.getTaskData().getEmailAddresses();
-					String elist = GFacUtils.listToCsv(emailList, ',');
-					if(emailids != null && !emailids.isEmpty()){
-						emailids = emailids +"," + elist;
-					}else{
-						emailids = elist;
-					}
-				}
-				if(emailids != null && !emailids.isEmpty()){
-					logger.info("Email list: "+ emailids);
-					jobDescriptor.setMailAddress(emailids);
-				}
-			}
-		} catch (ApplicationSettingsException e) {
-			 logger.error("ApplicationSettingsException : " +e.getLocalizedMessage());
-		}
-        // this is common for any application descriptor
-        jobDescriptor.setCallBackIp(ServerSettings.getIp());
-        jobDescriptor.setCallBackPort(ServerSettings.getSetting(org.apache.airavata.common.utils.Constants.GFAC_SERVER_PORT, "8950"));
-        jobDescriptor.setInputDirectory(jobExecutionContext.getInputDir());
-        jobDescriptor.setOutputDirectory(jobExecutionContext.getOutputDir());
-        jobDescriptor.setExecutablePath(jobExecutionContext.getExecutablePath());
-        jobDescriptor.setStandardOutFile(jobExecutionContext.getStandardOutput());
-        jobDescriptor.setStandardErrorFile(jobExecutionContext.getStandardError());
-        String computationalProjectAccount = taskData.getTaskScheduling().getComputationalProjectAccount();
-        taskData.getEmailAddresses();
-        if (computationalProjectAccount == null){
-            ComputeResourcePreference computeResourcePreference = jobExecutionContext.getApplicationContext().getComputeResourcePreference();
-            if (computeResourcePreference != null) {
-                computationalProjectAccount = computeResourcePreference.getAllocationProjectNumber();
-            }
-        }
-        if (computationalProjectAccount != null) {
-            jobDescriptor.setAcountString(computationalProjectAccount);
-        }
-
-        Random random = new Random();
-        int i = random.nextInt(Integer.MAX_VALUE); // We always set the job name
-        jobDescriptor.setJobName("A" + String.valueOf(i+99999999));
-        jobDescriptor.setWorkingDirectory(jobExecutionContext.getWorkingDir());
-
-        List<String> inputValues = new ArrayList<String>();
-        MessageContext input = jobExecutionContext.getInMessageContext();
-        // sort the inputs first and then build the command List
-        Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>() {
-            @Override
-            public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType t1) {
-                return inputDataObjectType.getInputOrder() - t1.getInputOrder();
-            }
-        };
-        Set<InputDataObjectType> sortedInputSet = new TreeSet<InputDataObjectType>(inputOrderComparator);
-        for (Object object : input.getParameters().values()) {
-            if (object instanceof InputDataObjectType) {
-                InputDataObjectType inputDOT = (InputDataObjectType) object;
-                sortedInputSet.add(inputDOT);
-            }
-        }
-        for (InputDataObjectType inputDataObjectType : sortedInputSet) {
-            if (!inputDataObjectType.isRequiredToAddedToCommandLine()) {
-                continue;
-            }
-            if (inputDataObjectType.getApplicationArgument() != null
-                    && !inputDataObjectType.getApplicationArgument().equals("")) {
-                inputValues.add(inputDataObjectType.getApplicationArgument());
-            }
-
-            if (inputDataObjectType.getValue() != null
-                    && !inputDataObjectType.getValue().equals("")) {
-                if (inputDataObjectType.getType() == DataType.URI) {
-                    // set only the relative path
-                    String filePath = inputDataObjectType.getValue();
-                    filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar) + 1, filePath.length());
-                    inputValues.add(filePath);
-                }else {
-                    inputValues.add(inputDataObjectType.getValue());
-                }
-
-            }
-        }
-
-        Map<String, Object> outputParams = jobExecutionContext.getOutMessageContext().getParameters();
-        for (Object outputParam : outputParams.values()) {
-            if (outputParam instanceof OutputDataObjectType) {
-                OutputDataObjectType output = (OutputDataObjectType) outputParam;
-                if (output.getApplicationArgument() != null
-                        && !output.getApplicationArgument().equals("")) {
-                    inputValues.add(output.getApplicationArgument());
-                }
-                if (output.getValue() != null && !output.getValue().equals("") && output.isRequiredToAddedToCommandLine()) {
-                    if (output.getType() == DataType.URI){
-                        String filePath = output.getValue();
-                        filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar) + 1, filePath.length());
-                        inputValues.add(filePath);
-                    }
-                }
-            }
-        }
-        jobDescriptor.setInputValues(inputValues);
-
-        jobDescriptor.setUserName(((GSISSHAbstractCluster) remoteCluster).getServerInfo().getUserName());
-        jobDescriptor.setShellName("/bin/bash");
-        jobDescriptor.setAllEnvExport(true);
-        jobDescriptor.setOwner(((HPCRemoteCluster) remoteCluster).getServerInfo().getUserName());
-
-        ComputationalResourceScheduling taskScheduling = taskData.getTaskScheduling();
-        if (taskScheduling != null) {
-            int totalNodeCount = taskScheduling.getNodeCount();
-            int totalCPUCount = taskScheduling.getTotalCPUCount();
-
-//        jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
-            if (taskScheduling.getComputationalProjectAccount() != null) {
-                jobDescriptor.setAcountString(taskScheduling.getComputationalProjectAccount());
-            }
-            if (taskScheduling.getQueueName() != null) {
-                jobDescriptor.setQueueName(taskScheduling.getQueueName());
-            }
-
-            if (totalNodeCount > 0) {
-                jobDescriptor.setNodes(totalNodeCount);
-            }
-            if (taskScheduling.getComputationalProjectAccount() != null) {
-                jobDescriptor.setAcountString(taskScheduling.getComputationalProjectAccount());
-            }
-            if (taskScheduling.getQueueName() != null) {
-                jobDescriptor.setQueueName(taskScheduling.getQueueName());
-            }
-            if (totalCPUCount > 0) {
-                int ppn = totalCPUCount / totalNodeCount;
-                jobDescriptor.setProcessesPerNode(ppn);
-                jobDescriptor.setCPUCount(totalCPUCount);
-            }
-            if (taskScheduling.getWallTimeLimit() > 0) {
-                jobDescriptor.setMaxWallTime(String.valueOf(taskScheduling.getWallTimeLimit()));
-                if(resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)){
-                    jobDescriptor.setMaxWallTimeForLSF(String.valueOf(taskScheduling.getWallTimeLimit()));
-                }
-            }
-
-            if (taskScheduling.getTotalPhysicalMemory() > 0) {
-                jobDescriptor.setUsedMemory(taskScheduling.getTotalPhysicalMemory() + "");
-            }
-        } else {
-            logger.error("Task scheduling cannot be null at this point..");
-        }
-
-        ApplicationDeploymentDescription appDepDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
-        List<String> moduleCmds = appDepDescription.getModuleLoadCmds();
-        if (moduleCmds != null) {
-            for (String moduleCmd : moduleCmds) {
-                jobDescriptor.addModuleLoadCommands(moduleCmd);
-            }
-        }
-        List<String> preJobCommands = appDepDescription.getPreJobCommands();
-        if (preJobCommands != null) {
-            for (String preJobCommand : preJobCommands) {
-                jobDescriptor.addPreJobCommand(parseCommand(preJobCommand, jobExecutionContext));
-            }
-        }
-
-        List<String> postJobCommands = appDepDescription.getPostJobCommands();
-        if (postJobCommands != null) {
-            for (String postJobCommand : postJobCommands) {
-                jobDescriptor.addPostJobCommand(parseCommand(postJobCommand, jobExecutionContext));
-            }
-        }
-
-        ApplicationParallelismType parallelism = appDepDescription.getParallelism();
-        if (parallelism != null){
-            if (parallelism == ApplicationParallelismType.MPI || parallelism == ApplicationParallelismType.OPENMP || parallelism == ApplicationParallelismType.OPENMP_MPI){
-                Map<JobManagerCommand, String> jobManagerCommands = resourceJobManager.getJobManagerCommands();
-                if (jobManagerCommands != null && !jobManagerCommands.isEmpty()) {
-                    for (JobManagerCommand command : jobManagerCommands.keySet()) {
-                        if (command == JobManagerCommand.SUBMISSION) {
-                            String commandVal = jobManagerCommands.get(command);
-                            jobDescriptor.setJobSubmitter(commandVal);
-                        }
-                    }
-                }
-            }
-        }
-        return jobDescriptor;
-    }
-
-    private static String parseCommand(String value, JobExecutionContext jobExecutionContext) {
-        String parsedValue = value.replaceAll("\\$workingDir", jobExecutionContext.getWorkingDir());
-        parsedValue = parsedValue.replaceAll("\\$inputDir", jobExecutionContext.getInputDir());
-        parsedValue = parsedValue.replaceAll("\\$outputDir", jobExecutionContext.getOutputDir());
-        return parsedValue;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
index 5ab2e96..a0d3a9b 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
@@ -21,13 +21,27 @@
 package org.apache.airavata.gfac.impl;
 
 import com.google.common.eventbus.EventBus;
+import org.apache.airavata.common.exception.AiravataException;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.LocalEventPublisher;
 import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.gfac.core.GFacEngine;
 import org.apache.airavata.gfac.core.GFacException;
+import org.apache.airavata.gfac.core.JobManagerConfiguration;
 import org.apache.airavata.gfac.core.cluster.RemoteCluster;
 import org.apache.airavata.gfac.core.cluster.ServerInfo;
+import org.apache.airavata.gfac.core.monitor.JobMonitor;
+import org.apache.airavata.gfac.impl.job.LSFJobConfiguration;
+import org.apache.airavata.gfac.impl.job.LSFOutputParser;
+import org.apache.airavata.gfac.impl.job.PBSJobConfiguration;
+import org.apache.airavata.gfac.impl.job.PBSOutputParser;
+import org.apache.airavata.gfac.impl.job.SlurmJobConfiguration;
+import org.apache.airavata.gfac.impl.job.SlurmOutputParser;
+import org.apache.airavata.gfac.impl.job.UGEJobConfiguration;
+import org.apache.airavata.gfac.impl.job.UGEOutputParser;
+import org.apache.airavata.gfac.monitor.email.EmailBasedMonitor;
+import org.apache.airavata.gfac.monitor.email.EmailMonitorFactory;
+import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManagerType;
 import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory;
 import org.apache.airavata.registry.cpi.AppCatalog;
 import org.apache.airavata.registry.cpi.AppCatalogException;
@@ -38,6 +52,10 @@ import org.apache.curator.framework.CuratorFramework;
 import org.apache.curator.framework.CuratorFrameworkFactory;
 import org.apache.curator.retry.ExponentialBackoffRetry;
 
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
 import java.util.Map;
 
 public abstract class Factory {
@@ -46,6 +64,8 @@ public abstract class Factory {
 	private static Map<String, RemoteCluster> remoteClusterMap;
 	private static LocalEventPublisher localEventPublisher;
 	private static CuratorFramework curatorClient;
+	private static EmailBasedMonitor emailBasedMonitor;
+	private static Date startMonitorDate = Calendar.getInstance().getTime();
 
 	public static GFacEngine getGFacEngine() throws GFacException {
 		if (engine == null) {
@@ -93,4 +113,37 @@ public abstract class Factory {
 		}
 		return curatorClient;
 	}
+
+	public static JobMonitor getJobMonitor(ResourceJobManagerType resourceJobManagerType) throws AiravataException {
+		if (resourceJobManagerType == ResourceJobManagerType.FORK) {
+			return null; // TODO write a job monitor for this.
+		} else {
+			if (emailBasedMonitor == null) {
+				synchronized (EmailMonitorFactory.class){
+					if (emailBasedMonitor == null) {
+						emailBasedMonitor = new EmailBasedMonitor(resourceJobManagerType);
+						emailBasedMonitor.setDate(startMonitorDate);
+						new Thread(emailBasedMonitor).start();
+					}
+				}
+			}
+			return emailBasedMonitor;
+		}
+	}
+
+	public static JobManagerConfiguration getPBSJobManager(String installedPath) {
+		return new PBSJobConfiguration("PBSTemplate.xslt",".pbs", installedPath, new PBSOutputParser());
+	}
+
+	public static JobManagerConfiguration getSLURMJobManager(String installedPath) {
+		return new SlurmJobConfiguration("SLURMTemplate.xslt", ".slurm", installedPath, new SlurmOutputParser());
+	}
+
+	public static JobManagerConfiguration getUGEJobManager(String installedPath) {
+		return new UGEJobConfiguration("UGETemplate.xslt", ".pbs", installedPath, new UGEOutputParser());
+	}
+
+	public static JobManagerConfiguration getLSFJobManager(String installedPath) {
+		return new LSFJobConfiguration("LSFTemplate.xslt", ".lsf", installedPath, new LSFOutputParser());
+	}
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/HPCRemoteCluster.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/HPCRemoteCluster.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/HPCRemoteCluster.java
new file mode 100644
index 0000000..645cb30
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/HPCRemoteCluster.java
@@ -0,0 +1,332 @@
+/*
+ *
+ * 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.impl;
+
+import com.jcraft.jsch.ChannelExec;
+import com.jcraft.jsch.JSch;
+import com.jcraft.jsch.JSchException;
+import com.jcraft.jsch.Session;
+import com.jcraft.jsch.UserInfo;
+import org.apache.airavata.common.exception.AiravataException;
+import org.apache.airavata.gfac.core.authentication.AuthenticationInfo;
+import org.apache.airavata.gfac.core.SSHApiException;
+import org.apache.airavata.gfac.core.authentication.SSHKeyAuthentication;
+import org.apache.airavata.gfac.core.cluster.CommandInfo;
+import org.apache.airavata.gfac.core.cluster.CommandOutput;
+import org.apache.airavata.gfac.core.cluster.OutputParser;
+import org.apache.airavata.gfac.core.cluster.RawCommandInfo;
+import org.apache.airavata.gfac.core.cluster.RemoteCluster;
+import org.apache.airavata.gfac.core.cluster.ServerInfo;
+import org.apache.airavata.gfac.core.JobManagerConfiguration;
+import org.apache.airavata.model.status.JobStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * One Remote cluster instance for each compute resource.
+ */
+public class HPCRemoteCluster implements RemoteCluster{
+    private static final Logger log = LoggerFactory.getLogger(HPCRemoteCluster.class);
+	private final SSHKeyAuthentication authentication;
+	private final ServerInfo serverInfo;
+	private final JobManagerConfiguration jobManagerConfiguration;
+	private final JSch jSch;
+	private Session session;
+	private OutputParser outputParser;
+
+	public HPCRemoteCluster(ServerInfo serverInfo, JobManagerConfiguration jobManagerConfiguration, AuthenticationInfo
+			authenticationInfo, OutputParser outputParser) throws AiravataException {
+		try {
+			this.serverInfo = serverInfo;
+			this.jobManagerConfiguration = jobManagerConfiguration;
+			if (authenticationInfo instanceof SSHKeyAuthentication) {
+				authentication = (SSHKeyAuthentication) authenticationInfo;
+			} else {
+				throw new AiravataException("Support ssh key authentication only");
+			}
+			this.outputParser = outputParser;
+			jSch = new JSch();
+			jSch.addIdentity(authentication.getPrivateKeyFilePath(), authentication.getPublicKeyFilePath(), authentication
+					.getPassphrase().getBytes());
+			session = jSch.getSession(serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
+			session.setUserInfo(new DefaultUserInfo(serverInfo.getUserName(), null, authentication.getPassphrase()));
+			session.connect(); // 0 connection timeout
+		} catch (JSchException e) {
+			throw new AiravataException("JSch initialization error ", e);
+		}
+	}
+
+	@Override
+	public String submitBatchJob(String jobScriptFilePath, String workingDirectory) throws SSHApiException {
+		scpTo(jobScriptFilePath, workingDirectory); // scp script file to working directory
+		RawCommandInfo submitCommand = jobManagerConfiguration.getSubmitCommand(workingDirectory, jobScriptFilePath);
+
+		StandardOutReader reader = new StandardOutReader();
+		executeCommand(submitCommand, reader);
+		throwExceptionOnError(reader, submitCommand);
+		return outputParser.parseJobSubmission(reader.getStdOutputString());
+	}
+
+	@Override
+	public void scpTo(String localFile, String remoteFile) throws SSHApiException {
+		int retry = 3;
+		while (retry > 0) {
+			try {
+				if (!session.isConnected()) {
+					session.connect();
+				}
+				log.info("Transferring localhost:" + localFile  + " to " + serverInfo.getHost() + ":" + remoteFile);
+				SSHUtils.scpTo(localFile, remoteFile, session);
+				retry = 0;
+			} catch (Exception e) {
+				retry--;
+				if (!session.isConnected()) {
+					try {
+						session.connect();
+					} catch (JSchException e1) {
+						throw new SSHApiException("JSch Session connection failed");
+					}
+				}
+				if (retry == 0) {
+					throw new SSHApiException("Failed to scp localhost:" + localFile + " to " + serverInfo.getHost() +
+							":" + remoteFile, e);
+				} else {
+					log.info("Retry transfer localhost:" + localFile + " to " + serverInfo.getHost() + ":" +
+							remoteFile);
+				}
+			}
+		}
+	}
+
+	@Override
+	public void scpFrom(String remoteFile, String localFile) throws SSHApiException {
+		int retry = 3;
+		while(retry>0) {
+			try {
+				if (!session.isConnected()) {
+					session.connect();
+				}
+				log.info("Transferring " + serverInfo.getHost() + ":" + remoteFile + " To localhost:" + localFile);
+				SSHUtils.scpFrom(remoteFile, localFile, session);
+				retry=0;
+			} catch (Exception e) {
+				retry--;
+				if (!session.isConnected()) {
+					try {
+						session.connect();
+					} catch (JSchException e1) {
+						throw new SSHApiException("JSch Session connection failed");
+					}
+				}
+				if (retry == 0) {
+					throw new SSHApiException("Failed to scp " + serverInfo.getHost() + ":" + remoteFile + " to " +
+							"localhost:" + localFile, e);
+				} else {
+					log.info("Retry transfer " + serverInfo.getHost() + ":" + remoteFile + "  to localhost:" + localFile);
+				}
+			}
+		}
+	}
+
+	@Override
+	public void scpThirdParty(String remoteFileSource, String remoteFileTarget) throws SSHApiException {
+		try {
+			if(!session.isConnected()){
+				session.connect();
+			}
+			log.info("Transferring from:" + remoteFileSource + " To: " + remoteFileTarget);
+			SSHUtils.scpThirdParty(remoteFileSource, remoteFileTarget, session);
+		} catch (IOException | JSchException e) {
+			throw new SSHApiException("Failed scp file:" + remoteFileSource + " to remote file "
+					+remoteFileTarget , e);
+		}
+	}
+
+	@Override
+	public void makeDirectory(String directoryPath) throws SSHApiException {
+		try {
+			if (!session.isConnected()) {
+				session.connect();
+			}
+			log.info("Creating directory: " + serverInfo.getHost() + ":" + directoryPath);
+			SSHUtils.makeDirectory(directoryPath, session);
+		} catch (JSchException | IOException e) {
+			throw new SSHApiException("Failed to create directory " + serverInfo.getHost() + ":" + directoryPath);
+		}
+	}
+
+	@Override
+	public boolean cancelJob(String jobId) throws SSHApiException {
+		RawCommandInfo cancelCommand = jobManagerConfiguration.getCancelCommand(jobId);
+		StandardOutReader reader = new StandardOutReader();
+		executeCommand(cancelCommand, reader);
+		throwExceptionOnError(reader, cancelCommand);
+		return true;
+	}
+
+	@Override
+	public JobStatus getJobStatus(String jobId) throws SSHApiException {
+		RawCommandInfo monitorCommand = jobManagerConfiguration.getMonitorCommand(jobId);
+		StandardOutReader reader = new StandardOutReader();
+		executeCommand(monitorCommand, reader);
+		throwExceptionOnError(reader, monitorCommand);
+		return outputParser.parseJobStatus(jobId, reader.getStdOutputString());
+	}
+
+	@Override
+	public String getJobIdByJobName(String jobName, String userName) throws SSHApiException {
+		RawCommandInfo jobIdMonitorCommand = jobManagerConfiguration.getJobIdMonitorCommand(jobName, userName);
+		StandardOutReader reader = new StandardOutReader();
+		executeCommand(jobIdMonitorCommand, reader);
+		throwExceptionOnError(reader, jobIdMonitorCommand);
+		return outputParser.parseJobId(jobName, reader.getStdOutputString());
+	}
+
+	@Override
+	public void getJobStatuses(String userName, Map<String, JobStatus> jobStatusMap) throws SSHApiException {
+		RawCommandInfo userBasedMonitorCommand = jobManagerConfiguration.getUserBasedMonitorCommand(userName);
+		StandardOutReader reader = new StandardOutReader();
+		executeCommand(userBasedMonitorCommand, reader);
+		throwExceptionOnError(reader, userBasedMonitorCommand);
+		outputParser.parseJobStatuses(userName, jobStatusMap, reader.getStdOutputString());
+	}
+
+	@Override
+	public List<String> listDirectory(String directoryPath) throws SSHApiException {
+		try {
+			if (!session.isConnected()) {
+				session.connect();
+			}
+			log.info("Creating directory: " + serverInfo.getHost() + ":" + directoryPath);
+			return SSHUtils.listDirectory(directoryPath, session);
+		} catch (JSchException | IOException e) {
+			throw new SSHApiException("Failed to list directory " + serverInfo.getHost() + ":" + directoryPath);
+		}
+	}
+
+	@Override
+	public Session getSession() throws SSHApiException {
+		return session;
+	}
+
+	@Override
+	public void disconnect() throws SSHApiException {
+		session.disconnect();
+	}
+
+	/**
+	 * This method return <code>true</code> if there is an error in standard output. If not return <code>false</code>
+	 * @param reader - command output reader
+	 * @param submitCommand - command which executed in remote machine.
+	 * @return command has return error or not.
+	 */
+	private void throwExceptionOnError(StandardOutReader reader, RawCommandInfo submitCommand) throws SSHApiException{
+		String stdErrorString = reader.getStdErrorString();
+		String command = submitCommand.getCommand().substring(submitCommand.getCommand().lastIndexOf(File.separator)
+				+ 1);
+		if (stdErrorString == null) {
+			// noting to do
+		}else if ((stdErrorString.contains(command.trim()) && !stdErrorString.contains("Warning")) || stdErrorString
+				.contains("error")) {
+			log.error("Command {} , Standard Error output {}", command, stdErrorString);
+			throw new SSHApiException("Error running command " + command + "  on remote cluster. StandardError: " +
+					stdErrorString);
+		}
+	}
+
+	private void executeCommand(CommandInfo commandInfo, CommandOutput commandOutput) throws SSHApiException {
+		String command = commandInfo.getCommand();
+		ChannelExec channelExec = null;
+		try {
+			if (!session.isConnected()) {
+				session.connect();
+			}
+			channelExec = ((ChannelExec) session.openChannel("exec"));
+			channelExec.setCommand(command);
+		    channelExec.setInputStream(null);
+			channelExec.setErrStream(commandOutput.getStandardError());
+			log.info("Executing command {}", commandInfo.getCommand());
+			channelExec.connect();
+			commandOutput.onOutput(channelExec);
+		} catch (JSchException e) {
+			throw new SSHApiException("Unable to execute command - ", e);
+		}finally {
+			//Only disconnecting the channel, session can be reused
+			if (channelExec != null) {
+				channelExec.disconnect();
+			}
+		}
+	}
+
+	@Override
+	public ServerInfo getServerInfo() {
+		return this.serverInfo;
+	}
+
+	private class DefaultUserInfo implements UserInfo {
+
+		private String userName;
+		private String password;
+		private String passphrase;
+
+		public DefaultUserInfo(String userName, String password, String passphrase) {
+			this.userName = userName;
+			this.password = password;
+			this.passphrase = passphrase;
+		}
+
+		@Override
+		public String getPassphrase() {
+			return null;
+		}
+
+		@Override
+		public String getPassword() {
+			return null;
+		}
+
+		@Override
+		public boolean promptPassword(String s) {
+			return false;
+		}
+
+		@Override
+		public boolean promptPassphrase(String s) {
+			return false;
+		}
+
+		@Override
+		public boolean promptYesNo(String s) {
+			return false;
+		}
+
+		@Override
+		public void showMessage(String s) {
+
+		}
+	}
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
index eef6cf3..6a100a9 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
@@ -25,7 +25,6 @@ import com.jcraft.jsch.ChannelExec;
 import com.jcraft.jsch.JSchException;
 import com.jcraft.jsch.Session;
 import org.apache.airavata.gfac.core.SSHApiException;
-import org.apache.airavata.gfac.gsi.ssh.impl.StandardOutReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/StandardOutReader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/StandardOutReader.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/StandardOutReader.java
new file mode 100644
index 0000000..e34858b
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/StandardOutReader.java
@@ -0,0 +1,79 @@
+/*
+ *
+ * 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.impl;
+
+import com.jcraft.jsch.Channel;
+
+import org.apache.airavata.gfac.core.cluster.CommandOutput;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+public class StandardOutReader implements CommandOutput {
+
+    private static final Logger logger = LoggerFactory.getLogger(StandardOutReader.class);
+    String stdOutputString = null;
+    ByteArrayOutputStream errorStream = new ByteArrayOutputStream();
+    public void onOutput(Channel channel) {
+        try {
+            StringBuffer pbsOutput = new StringBuffer("");
+            InputStream inputStream =  channel.getInputStream();
+            byte[] tmp = new byte[1024];
+            do {
+                while (inputStream.available() > 0) {
+                    int i = inputStream.read(tmp, 0, 1024);
+                    if (i < 0) break;
+                    pbsOutput.append(new String(tmp, 0, i));
+                }
+            } while (!channel.isClosed()) ;
+            String output = pbsOutput.toString();
+            this.setStdOutputString(output);
+        } catch (IOException e) {
+            logger.error(e.getMessage(), e);
+        }
+
+    }
+
+
+    public void exitCode(int code) {
+        System.out.println("Program exit code - " + code);
+    }
+
+    public String getStdOutputString() {
+        return stdOutputString;
+    }
+
+    public void setStdOutputString(String stdOutputString) {
+        this.stdOutputString = stdOutputString;
+    }
+
+    public String getStdErrorString() {
+        return errorStream.toString();
+    }
+
+    public OutputStream getStandardError() {
+        return errorStream;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/job/LSFJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/job/LSFJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/job/LSFJobConfiguration.java
new file mode 100644
index 0000000..b84b8ff
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/job/LSFJobConfiguration.java
@@ -0,0 +1,123 @@
+/*
+ *
+ * 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.impl.job;
+
+import org.apache.airavata.gfac.core.JobManagerConfiguration;
+import org.apache.airavata.gfac.core.cluster.OutputParser;
+import org.apache.airavata.gfac.core.cluster.RawCommandInfo;
+import org.apache.commons.io.FilenameUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+
+public class LSFJobConfiguration implements JobManagerConfiguration {
+    private final static Logger logger = LoggerFactory.getLogger(LSFJobConfiguration.class);
+
+    private String jobDescriptionTemplateName;
+
+    private String scriptExtension;
+
+    private String installedPath;
+
+    private OutputParser parser;
+
+    public LSFJobConfiguration(){
+        // this can be used to construct and use setter methods to set all the params in order
+    }
+    public LSFJobConfiguration(String jobDescriptionTemplateName,
+                                 String scriptExtension,String installedPath,OutputParser parser) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+        this.scriptExtension = scriptExtension;
+        this.parser = parser;
+        if (installedPath.endsWith("/") || installedPath.isEmpty()) {
+            this.installedPath = installedPath;
+        } else {
+            this.installedPath = installedPath + "/";
+        }
+    }
+
+    @Override
+    public RawCommandInfo getCancelCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + "bkill " + jobID);
+    }
+
+    @Override
+    public String getJobDescriptionTemplateName() {
+        return jobDescriptionTemplateName;
+    }
+
+    @Override
+    public RawCommandInfo getMonitorCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + "bjobs " + jobID);
+    }
+
+    @Override
+    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+        return new RawCommandInfo(this.installedPath + "bjobs -u " + userName);
+    }
+
+    @Override
+    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+        return new RawCommandInfo(this.installedPath + "bjobs -J " + jobName);
+    }
+
+    @Override
+    public String getScriptExtension() {
+        return scriptExtension;
+    }
+
+    @Override
+    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
+        return new RawCommandInfo(this.installedPath + "bsub < " +
+                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+    }
+
+    @Override
+    public OutputParser getParser() {
+        return parser;
+    }
+
+    public void setParser(OutputParser parser) {
+        this.parser = parser;
+    }
+
+    @Override
+    public String getInstalledPath() {
+        return installedPath;
+    }
+
+
+    @Override
+    public String getBaseCancelCommand() {
+        return "bkill";
+    }
+
+    @Override
+    public String getBaseMonitorCommand() {
+        return "bjobs";
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return "bsub";
+    }
+}


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