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From chath...@apache.org
Subject [38/44] Integrated appCatalog for ssh and gsi modules, commented out old test classes, need to fix this
Date Wed, 05 Nov 2014 18:30:26 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/d94e8c95/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
index ad2731a..f726024 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
@@ -20,11 +20,13 @@
 */
 package org.apache.airavata.gfac.ssh.util;
 
+import org.airavata.appcatalog.cpi.AppCatalog;
+import org.airavata.appcatalog.cpi.AppCatalogException;
+import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.common.utils.StringUtil;
 import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential;
 import org.apache.airavata.gfac.Constants;
@@ -38,21 +40,20 @@ import org.apache.airavata.gfac.ssh.context.SSHAuthWrapper;
 import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
 import org.apache.airavata.gfac.ssh.security.TokenizedSSHAuthInfo;
 import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
 import org.apache.airavata.gsi.ssh.api.ServerInfo;
 import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
 import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
-import org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster;
 import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
 import org.apache.airavata.gsi.ssh.util.CommonUtils;
-import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
+import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol;
 import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
 import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.schemas.gfac.*;
+import org.apache.airavata.schemas.gfac.FileArrayType;
+import org.apache.airavata.schemas.gfac.StringArrayType;
+import org.apache.airavata.schemas.gfac.URIArrayType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -72,77 +73,84 @@ public class GFACSSHUtils {
      * @throws ApplicationSettingsException
      */
     public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
-        HostDescription registeredHost = jobExecutionContext.getApplicationContext().getHostDescription();
-        if (registeredHost.getType() instanceof GlobusHostType || registeredHost.getType() instanceof UnicoreHostType) {
+        JobSubmissionProtocol preferredJobSubmissionProtocol = jobExecutionContext.getPreferredJobSubmissionProtocol();
+        JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
+        if (preferredJobSubmissionProtocol == JobSubmissionProtocol.GLOBUS || preferredJobSubmissionProtocol == JobSubmissionProtocol.UNICORE) {
             logger.error("This is a wrong method to invoke to non ssh host types,please check your gfac-config.xml");
-        } else if (registeredHost.getType() instanceof SSHHostType
-                || registeredHost.getType() instanceof GsisshHostType) {
-            SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
-            String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
-            RequestData requestData = new RequestData(ServerSettings.getDefaultUserGateway());
-            requestData.setTokenId(credentialStoreToken);
-
-            ServerInfo serverInfo = new ServerInfo(null, registeredHost.getType().getHostAddress());
-            Cluster pbsCluster = null;
+        } else if (preferredJobSubmissionProtocol == JobSubmissionProtocol.SSH) {
             try {
-                TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
-                String installedParentPath = ((HpcApplicationDeploymentType)
-                        jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
-                if (installedParentPath == null) {
-                    installedParentPath = "/";
-                }
+                AppCatalog appCatalog = AppCatalogFactory.getAppCatalog();
+                SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(preferredJobSubmissionInterface.getJobSubmissionInterfaceId());
+                if (sshJobSubmission.getSecurityProtocol() == SecurityProtocol.GSI) {
+                    SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+                    String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
+                    RequestData requestData = new RequestData(ServerSettings.getDefaultUserGateway());
+                    requestData.setTokenId(credentialStoreToken);
 
-                SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
-                serverInfo.setUserName(credentials.getPortalUserName());
-                jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
-                // inside the pbsCluser object
+                    ServerInfo serverInfo = new ServerInfo(null, jobExecutionContext.getHostName());
 
-                String key = credentials.getPortalUserName() + registeredHost.getType().getHostAddress() +
-                        serverInfo.getPort();
-                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()) {
-                            pbsCluster = clusters.get(key).get(i);
-                        } else {
-                            clusters.get(key).remove(i);
-                            recreate = true;
+                    Cluster pbsCluster = null;
+                    try {
+                        TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
+                        String installedParentPath = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getExecutablePath();
+                        if (installedParentPath == null) {
+                            installedParentPath = "/";
                         }
-                        if (!recreate) {
-                            try {
-                                pbsCluster.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 pbsCluster to create again if there is any exception druing connection
+
+                        SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
+                        serverInfo.setUserName(credentials.getPortalUserName());
+                        jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
+                        // inside the pbsCluser object
+
+                        String key = credentials.getPortalUserName() + jobExecutionContext.getHostName() + serverInfo.getPort();
+                        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()) {
+                                    pbsCluster = clusters.get(key).get(i);
+                                } else {
+                                    clusters.get(key).remove(i);
+                                    recreate = true;
+                                }
+                                if (!recreate) {
+                                    try {
+                                        pbsCluster.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 pbsCluster to create again if there is any exception druing connection
+                                    }
+                                }
+                                logger.info("Re-using the same connection used with the connection string:" + key);
+                            } else {
+                                recreate = true;
+                            }
+                            if (recreate) {
+                                pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,
+                                        CommonUtils.getPBSJobManager(installedParentPath));
+                                List<Cluster> pbsClusters = null;
+                                if (!(clusters.containsKey(key))) {
+                                    pbsClusters = new ArrayList<Cluster>();
+                                } else {
+                                    pbsClusters = clusters.get(key);
+                                }
+                                pbsClusters.add(pbsCluster);
+                                clusters.put(key, pbsClusters);
                             }
                         }
-                        logger.info("Re-using the same connection used with the connection string:" + key);
-                    } else {
-                        recreate = true;
-                    }
-                    if (recreate) {
-                        pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,
-                                    CommonUtils.getPBSJobManager(installedParentPath));
-                        List<Cluster> pbsClusters = null;
-                        if (!(clusters.containsKey(key))) {
-                            pbsClusters = new ArrayList<Cluster>();
-                        } else {
-                            pbsClusters = clusters.get(key);
-                        }
-                        pbsClusters.add(pbsCluster);
-                        clusters.put(key, pbsClusters);
+                    } catch (Exception e) {
+                        throw new GFacException("Error occurred...", e);
                     }
+                    sshSecurityContext.setPbsCluster(pbsCluster);
+                    jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT, sshSecurityContext);
                 }
-            } catch (Exception e) {
-                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+            } catch (AppCatalogException e) {
+                throw new GFacException("Error while getting SSH Submission object from app catalog", e);
             }
-            sshSecurityContext.setPbsCluster(pbsCluster);
-            jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT+"-"+registeredHost.getType().getHostAddress(), sshSecurityContext);
         }
     }
 
@@ -154,76 +162,75 @@ public class GFACSSHUtils {
      * @throws ApplicationSettingsException
      */
     public static void addSecurityContext(JobExecutionContext jobExecutionContext,SSHAuthWrapper sshAuth) throws GFacException, ApplicationSettingsException {
-            try {
-                if(sshAuth== null) {
-                    throw new GFacException("Error adding security Context, because sshAuthWrapper is null");
-                }
-                SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
-                Cluster pbsCluster = null;
-                String key=sshAuth.getKey();
-                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()) {
-                            pbsCluster = clusters.get(key).get(i);
-                        } else {
-                            clusters.get(key).remove(i);
-                            recreate = true;
-                        }
-                        if (!recreate) {
-                            try {
-                                pbsCluster.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 pbsCluster to create again if there is any exception druing connection
-                            }
-                        }
-                        logger.info("Re-using the same connection used with the connection string:" + key);
+        try {
+            if(sshAuth== null) {
+                throw new GFacException("Error adding security Context, because sshAuthWrapper is null");
+            }
+            SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+            Cluster pbsCluster = null;
+            String key=sshAuth.getKey();
+            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()) {
+                        pbsCluster = clusters.get(key).get(i);
                     } else {
+                        clusters.get(key).remove(i);
                         recreate = true;
                     }
-                    if (recreate) {
-                        pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),null);
-                        key = sshAuth.getKey();
-                        List<Cluster> pbsClusters = null;
-                        if (!(clusters.containsKey(key))) {
-                            pbsClusters = new ArrayList<Cluster>();
-                        } else {
-                            pbsClusters = clusters.get(key);
+                    if (!recreate) {
+                        try {
+                            pbsCluster.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 pbsCluster to create again if there is any exception druing connection
                         }
-                        pbsClusters.add(pbsCluster);
-                        clusters.put(key, pbsClusters);
                     }
+                    logger.info("Re-using the same connection used with the connection string:" + key);
+                } else {
+                    recreate = true;
+                }
+                if (recreate) {
+                    pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),null);
+                    key = sshAuth.getKey();
+                    List<Cluster> pbsClusters = null;
+                    if (!(clusters.containsKey(key))) {
+                        pbsClusters = new ArrayList<Cluster>();
+                    } else {
+                        pbsClusters = clusters.get(key);
+                    }
+                    pbsClusters.add(pbsCluster);
+                    clusters.put(key, pbsClusters);
                 }
-                sshSecurityContext.setPbsCluster(pbsCluster);
-                jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT+key, sshSecurityContext);
-            } catch (Exception e) {
-                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
             }
+            sshSecurityContext.setPbsCluster(pbsCluster);
+            jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT+key, sshSecurityContext);
+        } catch (Exception e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+        }
     }
 
-    public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext,
-                                                    ApplicationDeploymentDescriptionType app, Cluster cluster) {
+
+    public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, Cluster cluster) {
         JobDescriptor jobDescriptor = new JobDescriptor();
         // 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(app.getInputDataDirectory());
-        jobDescriptor.setOutputDirectory(app.getOutputDataDirectory());
-        jobDescriptor.setExecutablePath(app.getExecutableLocation());
-        jobDescriptor.setStandardOutFile(app.getStandardOutput());
-        jobDescriptor.setStandardErrorFile(app.getStandardError());
+        jobDescriptor.setInputDirectory(jobExecutionContext.getInputDir());
+        jobDescriptor.setOutputDirectory(jobExecutionContext.getOutputDir());
+        jobDescriptor.setExecutablePath(jobExecutionContext.getApplicationContext()
+                .getApplicationDeploymentDescription().getExecutablePath());
+        jobDescriptor.setStandardOutFile(jobExecutionContext.getStandardOutput());
+        jobDescriptor.setStandardErrorFile(jobExecutionContext.getStandardError());
         Random random = new Random();
         int i = random.nextInt(Integer.MAX_VALUE);
         jobDescriptor.setJobName(String.valueOf(i + 99999999));
-        jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());
-
-
+        jobDescriptor.setWorkingDirectory(jobExecutionContext.getWorkingDir());
         List<String> inputValues = new ArrayList<String>();
         MessageContext input = jobExecutionContext.getInMessageContext();
         Map<String, Object> inputs = input.getParameters();
@@ -249,51 +256,6 @@ public class GFACSSHUtils {
         }
         jobDescriptor.setInputValues(inputValues);
 
-        // this part will fill out the hpcApplicationDescriptor
-        if (app instanceof HpcApplicationDeploymentType) {
-            HpcApplicationDeploymentType applicationDeploymentType
-                    = (HpcApplicationDeploymentType) app;
-            jobDescriptor.setUserName(((GSISSHAbstractCluster) cluster).getServerInfo().getUserName());
-            jobDescriptor.setShellName("/bin/bash");
-            jobDescriptor.setAllEnvExport(true);
-            jobDescriptor.setMailOptions("n");
-            jobDescriptor.setNodes(applicationDeploymentType.getNodeCount());
-            jobDescriptor.setProcessesPerNode(applicationDeploymentType.getProcessorsPerNode());
-            jobDescriptor.setMaxWallTime(String.valueOf(applicationDeploymentType.getMaxWallTime()));
-            jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
-            jobDescriptor.setCPUCount(applicationDeploymentType.getCpuCount());
-            if (applicationDeploymentType.getProjectAccount() != null) {
-                if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
-                    jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
-                }
-            }
-            if (applicationDeploymentType.getQueue() != null) {
-                if (applicationDeploymentType.getQueue().getQueueName() != null) {
-                    jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
-                }
-            }
-            jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
-            TaskDetails taskData = jobExecutionContext.getTaskData();
-            if (taskData != null && taskData.isSetTaskScheduling()) {
-                ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
-                if (computionnalResource.getNodeCount() > 0) {
-                    jobDescriptor.setNodes(computionnalResource.getNodeCount());
-                }
-                if (computionnalResource.getComputationalProjectAccount() != null) {
-                    jobDescriptor.setAcountString(computionnalResource.getComputationalProjectAccount());
-                }
-                if (computionnalResource.getQueueName() != null) {
-                    jobDescriptor.setQueueName(computionnalResource.getQueueName());
-                }
-                if (computionnalResource.getTotalCPUCount() > 0) {
-                    jobDescriptor.setProcessesPerNode(computionnalResource.getTotalCPUCount());
-                }
-                if (computionnalResource.getWallTimeLimit() > 0) {
-                    jobDescriptor.setMaxWallTime(String.valueOf(computionnalResource.getWallTimeLimit()));
-                }
-            }
-
-        }
         return jobDescriptor;
     }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/d94e8c95/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
index e84848c..c65f386 100644
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
+++ b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
@@ -1,252 +1,252 @@
-/*
- *
- * 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.core.gfac.services.impl;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.commons.gfac.type.HostDescription;
-import org.apache.airavata.commons.gfac.type.ServiceDescription;
-import org.apache.airavata.gfac.GFacConfiguration;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.SecurityContext;
-import org.apache.airavata.gfac.core.context.ApplicationContext;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
-import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.ServerInfo;
-import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
-import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
-import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
-import org.apache.airavata.gsi.ssh.util.CommonUtils;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
-import org.apache.airavata.schemas.gfac.*;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-public class BigRed2TestWithSSHAuth {
-    private JobExecutionContext jobExecutionContext;
-
-    private String userName;
-    private String password;
-    private String passPhrase;
-    private String hostName;
-    private String workingDirectory;
-    private String privateKeyPath;
-    private String publicKeyPath;
-
-    @BeforeClass
-    public void setUp() throws Exception {
-
-        System.out.println("Test case name " + this.getClass().getName());
-//        System.setProperty("ssh.host","bigred2.uits.iu.edu");        //default ssh host
-//        System.setProperty("ssh.user", "lginnali");
-//        System.setProperty("ssh.private.key.path", "/Users/lahirugunathilake/.ssh/id_dsa");
-//        System.setProperty("ssh.public.key.path", "/Users/lahirugunathilake/.ssh/id_dsa.pub");
-//        System.setProperty("ssh.working.directory", "/tmp");
-
-        this.hostName = "bigred2.uits.iu.edu";
-        this.hostName = System.getProperty("ssh.host");
-        this.userName = System.getProperty("ssh.username");
-        this.password = System.getProperty("ssh.password");
-        this.privateKeyPath = System.getProperty("private.ssh.key");
-        this.publicKeyPath = System.getProperty("public.ssh.key");
-        this.passPhrase = System.getProperty("ssh.keypass");
-        this.workingDirectory = System.getProperty("ssh.working.directory");
-
-
-         if (this.userName == null
-                || (this.password==null && (this.publicKeyPath == null || this.privateKeyPath == null)) || this.workingDirectory == null) {
-            System.out.println("########### In order to test you have to either username password or private,public keys");
-            System.out.println("Use -Dssh.username=xxx -Dssh.password=yyy -Dssh.keypass=zzz " +
-                    "-Dprivate.ssh.key -Dpublic.ssh.key -Dssh.working.directory ");
-        }
-        URL resource = BigRed2TestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
-        assert resource != null;
-        System.out.println(resource.getFile());
-        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null);
-
-//        gFacConfiguration.setMyProxyLifeCycle(3600);
-//        gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
-//        gFacConfiguration.setMyProxyUser("*****");
-//        gFacConfiguration.setMyProxyPassphrase("*****");
-//        gFacConfiguration.setTrustedCertLocation("./certificates");
-//        //have to set InFlwo Handlers and outFlowHandlers
-//        gFacConfiguration.setInHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
-//        gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
-
-        /*
-        * Host
-        */
-        HostDescription host = new HostDescription(SSHHostType.type);
-        host.getType().setHostAddress(hostName);
-        host.getType().setHostName(hostName);
-        ((SSHHostType)host.getType()).setHpcResource(true);
-        /*
-        * App
-        */
-        ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
-        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
-        ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
-        name.setStringValue("EchoLocal");
-        app.setApplicationName(name);
-
-        app.setCpuCount(1);
-        app.setJobType(JobTypeType.SERIAL);
-        app.setNodeCount(1);
-        app.setProcessorsPerNode(1);
-
-        /*
-        * Use bat file if it is compiled on Windows
-        */
-        app.setExecutableLocation("/bin/echo");
-
-        /*
-        * Default tmp location
-        */
-        String tempDir = "/tmp";
-        String date = (new Date()).toString();
-        date = date.replaceAll(" ", "_");
-        date = date.replaceAll(":", "_");
-
-        tempDir = tempDir + File.separator
-                + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
-
-        System.out.println(tempDir);
-        app.setScratchWorkingDirectory(tempDir);
-        app.setStaticWorkingDirectory(tempDir);
-        app.setInputDataDirectory(tempDir + File.separator + "inputData");
-        app.setOutputDataDirectory(tempDir + File.separator + "outputData");
-        app.setStandardOutput(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stdout");
-        app.setStandardError(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stderr");
-        app.setMaxWallTime(5);
-        app.setJobSubmitterCommand("aprun -n 1");
-        app.setInstalledParentPath("/opt/torque/torque-4.2.3.1/bin/");
-
-        /*
-        * Service
-        */
-        ServiceDescription serv = new ServiceDescription();
-        serv.getType().setName("SimpleEcho");
-
-        List<InputParameterType> inputList = new ArrayList<InputParameterType>();
-
-        InputParameterType input = InputParameterType.Factory.newInstance();
-        input.setParameterName("echo_input");
-        input.setParameterType(StringParameterType.Factory.newInstance());
-        inputList.add(input);
-
-        InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
-
-                .size()]);
-        List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
-        OutputParameterType output = OutputParameterType.Factory.newInstance();
-        output.setParameterName("echo_output");
-        output.setParameterType(StringParameterType.Factory.newInstance());
-        outputList.add(output);
-
-        OutputParameterType[] outputParamList = outputList
-                .toArray(new OutputParameterType[outputList.size()]);
-
-        serv.getType().setInputParametersArray(inputParamList);
-        serv.getType().setOutputParametersArray(outputParamList);
-
-        jobExecutionContext = new JobExecutionContext(gFacConfiguration, serv.getType().getName());
-        // Adding security context
-        jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext(app));
-        ApplicationContext applicationContext = new ApplicationContext();
-        jobExecutionContext.setApplicationContext(applicationContext);
-        applicationContext.setServiceDescription(serv);
-        applicationContext.setApplicationDeploymentDescription(appDesc);
-        applicationContext.setHostDescription(host);
-
-        MessageContext inMessage = new MessageContext();
-        ActualParameter echo_input = new ActualParameter();
-        ((StringParameterType) echo_input.getType()).setValue("echo_output=hello");
-        inMessage.addParameter("echo_input", echo_input);
-
-
-        jobExecutionContext.setInMessageContext(inMessage);
-
-        MessageContext outMessage = new MessageContext();
-        ActualParameter echo_out = new ActualParameter();
-//		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
-        outMessage.addParameter("echo_output", echo_out);
-        jobExecutionContext.setRegistry(RegistryFactory.getLoggingRegistry());
-        jobExecutionContext.setTaskData(new TaskDetails("11323"));
-        jobExecutionContext.setOutMessageContext(outMessage);
-
-    }
-
-
-    private SecurityContext getSecurityContext(HpcApplicationDeploymentType app) {
-         try {
-
-        AuthenticationInfo authenticationInfo = null;
-        if (password != null) {
-            authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
-        } else {
-            authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
-                    this.passPhrase);
-        }
-        // Server info
-        ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
-
-        Cluster pbsCluster = null;
-        SSHSecurityContext sshSecurityContext = null;
-
-            JobManagerConfiguration pbsJobManager = CommonUtils.getPBSJobManager(app.getInstalledParentPath());
-            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, pbsJobManager);
-
-
-            sshSecurityContext = new SSHSecurityContext();
-            sshSecurityContext.setPbsCluster(pbsCluster);
-            sshSecurityContext.setUsername(userName);
-            sshSecurityContext.setKeyPass(passPhrase);
-            sshSecurityContext.setPrivateKeyLoc(privateKeyPath);
-             return sshSecurityContext;
-        } catch (SSHApiException e) {
-            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-        }
-        return null;
-    }
-
-    @Test
-    public void testSSHProvider() throws GFacException {
-        BetterGfacImpl gFacAPI = new BetterGfacImpl();
-        gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
-        org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobDescription());
-        org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobID());
-    }
-
-}
+///*
+// *
+// * 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.core.gfac.services.impl;
+//
+//import org.apache.airavata.commons.gfac.type.ActualParameter;
+//import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+//import org.apache.airavata.commons.gfac.type.HostDescription;
+//import org.apache.airavata.commons.gfac.type.ServiceDescription;
+//import org.apache.airavata.gfac.GFacConfiguration;
+//import org.apache.airavata.gfac.GFacException;
+//import org.apache.airavata.gfac.SecurityContext;
+//import org.apache.airavata.gfac.core.context.ApplicationContext;
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.context.MessageContext;
+//import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
+//import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
+//import org.apache.airavata.gsi.ssh.api.Cluster;
+//import org.apache.airavata.gsi.ssh.api.SSHApiException;
+//import org.apache.airavata.gsi.ssh.api.ServerInfo;
+//import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
+//import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
+//import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+//import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+//import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
+//import org.apache.airavata.gsi.ssh.util.CommonUtils;
+//import org.apache.airavata.model.workspace.experiment.TaskDetails;
+//import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
+//import org.apache.airavata.schemas.gfac.*;
+//import org.testng.annotations.BeforeClass;
+//import org.testng.annotations.Test;
+//
+//import java.io.File;
+//import java.net.URL;
+//import java.util.ArrayList;
+//import java.util.Date;
+//import java.util.List;
+//import java.util.UUID;
+//
+//public class BigRed2TestWithSSHAuth {
+//    private JobExecutionContext jobExecutionContext;
+//
+//    private String userName;
+//    private String password;
+//    private String passPhrase;
+//    private String hostName;
+//    private String workingDirectory;
+//    private String privateKeyPath;
+//    private String publicKeyPath;
+//
+//    @BeforeClass
+//    public void setUp() throws Exception {
+//
+//        System.out.println("Test case name " + this.getClass().getName());
+////        System.setProperty("ssh.host","bigred2.uits.iu.edu");        //default ssh host
+////        System.setProperty("ssh.user", "lginnali");
+////        System.setProperty("ssh.private.key.path", "/Users/lahirugunathilake/.ssh/id_dsa");
+////        System.setProperty("ssh.public.key.path", "/Users/lahirugunathilake/.ssh/id_dsa.pub");
+////        System.setProperty("ssh.working.directory", "/tmp");
+//
+//        this.hostName = "bigred2.uits.iu.edu";
+//        this.hostName = System.getProperty("ssh.host");
+//        this.userName = System.getProperty("ssh.username");
+//        this.password = System.getProperty("ssh.password");
+//        this.privateKeyPath = System.getProperty("private.ssh.key");
+//        this.publicKeyPath = System.getProperty("public.ssh.key");
+//        this.passPhrase = System.getProperty("ssh.keypass");
+//        this.workingDirectory = System.getProperty("ssh.working.directory");
+//
+//
+//         if (this.userName == null
+//                || (this.password==null && (this.publicKeyPath == null || this.privateKeyPath == null)) || this.workingDirectory == null) {
+//            System.out.println("########### In order to test you have to either username password or private,public keys");
+//            System.out.println("Use -Dssh.username=xxx -Dssh.password=yyy -Dssh.keypass=zzz " +
+//                    "-Dprivate.ssh.key -Dpublic.ssh.key -Dssh.working.directory ");
+//        }
+//        URL resource = BigRed2TestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+//        assert resource != null;
+//        System.out.println(resource.getFile());
+//        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null);
+//
+////        gFacConfiguration.setMyProxyLifeCycle(3600);
+////        gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+////        gFacConfiguration.setMyProxyUser("*****");
+////        gFacConfiguration.setMyProxyPassphrase("*****");
+////        gFacConfiguration.setTrustedCertLocation("./certificates");
+////        //have to set InFlwo Handlers and outFlowHandlers
+////        gFacConfiguration.setInHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
+////        gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
+//
+//        /*
+//        * Host
+//        */
+//        HostDescription host = new HostDescription(SSHHostType.type);
+//        host.getType().setHostAddress(hostName);
+//        host.getType().setHostName(hostName);
+//        ((SSHHostType)host.getType()).setHpcResource(true);
+//        /*
+//        * App
+//        */
+//        ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
+//        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
+//        ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+//        name.setStringValue("EchoLocal");
+//        app.setApplicationName(name);
+//
+//        app.setCpuCount(1);
+//        app.setJobType(JobTypeType.SERIAL);
+//        app.setNodeCount(1);
+//        app.setProcessorsPerNode(1);
+//
+//        /*
+//        * Use bat file if it is compiled on Windows
+//        */
+//        app.setExecutableLocation("/bin/echo");
+//
+//        /*
+//        * Default tmp location
+//        */
+//        String tempDir = "/tmp";
+//        String date = (new Date()).toString();
+//        date = date.replaceAll(" ", "_");
+//        date = date.replaceAll(":", "_");
+//
+//        tempDir = tempDir + File.separator
+//                + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
+//
+//        System.out.println(tempDir);
+//        app.setScratchWorkingDirectory(tempDir);
+//        app.setStaticWorkingDirectory(tempDir);
+//        app.setInputDataDirectory(tempDir + File.separator + "inputData");
+//        app.setOutputDataDirectory(tempDir + File.separator + "outputData");
+//        app.setStandardOutput(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stdout");
+//        app.setStandardError(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stderr");
+//        app.setMaxWallTime(5);
+//        app.setJobSubmitterCommand("aprun -n 1");
+//        app.setInstalledParentPath("/opt/torque/torque-4.2.3.1/bin/");
+//
+//        /*
+//        * Service
+//        */
+//        ServiceDescription serv = new ServiceDescription();
+//        serv.getType().setName("SimpleEcho");
+//
+//        List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+//
+//        InputParameterType input = InputParameterType.Factory.newInstance();
+//        input.setParameterName("echo_input");
+//        input.setParameterType(StringParameterType.Factory.newInstance());
+//        inputList.add(input);
+//
+//        InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+//
+//                .size()]);
+//        List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+//        OutputParameterType output = OutputParameterType.Factory.newInstance();
+//        output.setParameterName("echo_output");
+//        output.setParameterType(StringParameterType.Factory.newInstance());
+//        outputList.add(output);
+//
+//        OutputParameterType[] outputParamList = outputList
+//                .toArray(new OutputParameterType[outputList.size()]);
+//
+//        serv.getType().setInputParametersArray(inputParamList);
+//        serv.getType().setOutputParametersArray(outputParamList);
+//
+//        jobExecutionContext = new JobExecutionContext(gFacConfiguration, serv.getType().getName());
+//        // Adding security context
+//        jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext(app));
+//        ApplicationContext applicationContext = new ApplicationContext();
+//        jobExecutionContext.setApplicationContext(applicationContext);
+//        applicationContext.setServiceDescription(serv);
+//        applicationContext.setApplicationDeploymentDescription(appDesc);
+//        applicationContext.setHostDescription(host);
+//
+//        MessageContext inMessage = new MessageContext();
+//        ActualParameter echo_input = new ActualParameter();
+//        ((StringParameterType) echo_input.getType()).setValue("echo_output=hello");
+//        inMessage.addParameter("echo_input", echo_input);
+//
+//
+//        jobExecutionContext.setInMessageContext(inMessage);
+//
+//        MessageContext outMessage = new MessageContext();
+//        ActualParameter echo_out = new ActualParameter();
+////		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+//        outMessage.addParameter("echo_output", echo_out);
+//        jobExecutionContext.setRegistry(RegistryFactory.getLoggingRegistry());
+//        jobExecutionContext.setTaskData(new TaskDetails("11323"));
+//        jobExecutionContext.setOutMessageContext(outMessage);
+//
+//    }
+//
+//
+//    private SecurityContext getSecurityContext(HpcApplicationDeploymentType app) {
+//         try {
+//
+//        AuthenticationInfo authenticationInfo = null;
+//        if (password != null) {
+//            authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+//        } else {
+//            authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
+//                    this.passPhrase);
+//        }
+//        // Server info
+//        ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+//
+//        Cluster pbsCluster = null;
+//        SSHSecurityContext sshSecurityContext = null;
+//
+//            JobManagerConfiguration pbsJobManager = CommonUtils.getPBSJobManager(app.getInstalledParentPath());
+//            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, pbsJobManager);
+//
+//
+//            sshSecurityContext = new SSHSecurityContext();
+//            sshSecurityContext.setPbsCluster(pbsCluster);
+//            sshSecurityContext.setUsername(userName);
+//            sshSecurityContext.setKeyPass(passPhrase);
+//            sshSecurityContext.setPrivateKeyLoc(privateKeyPath);
+//             return sshSecurityContext;
+//        } catch (SSHApiException e) {
+//            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+//        }
+//        return null;
+//    }
+//
+//    @Test
+//    public void testSSHProvider() throws GFacException {
+//        BetterGfacImpl gFacAPI = new BetterGfacImpl();
+//        gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
+//        org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobDescription());
+//        org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobID());
+//    }
+//
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d94e8c95/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
index 5cb1200..b115b6c 100644
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
+++ b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
@@ -1,172 +1,172 @@
-/*
- *
- * 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.core.gfac.services.impl;
-
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.commons.gfac.type.HostDescription;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.commons.gfac.type.ServiceDescription;
-import org.apache.airavata.gfac.GFacConfiguration;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.core.context.ApplicationContext;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
-import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.InputParameterType;
-import org.apache.airavata.schemas.gfac.OutputParameterType;
-import org.apache.airavata.schemas.gfac.SSHHostType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.commons.lang.SystemUtils;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SSHProviderTestWithSSHAuth {
-	private JobExecutionContext jobExecutionContext;
-    @Before
-    public void setUp() throws Exception {
-
-    	URL resource = SSHProviderTestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
-        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null);
-//        gFacConfiguration.s
-        //have to set InFlwo Handlers and outFlowHandlers
-        ApplicationContext applicationContext = new ApplicationContext();
-        HostDescription host = new HostDescription(SSHHostType.type);
-        host.getType().setHostName("bigred");
-        host.getType().setHostAddress("bigred2.uits.iu.edu");
-        applicationContext.setHostDescription(host);
-        /*
-           * App
-           */
-        ApplicationDescription appDesc = new ApplicationDescription();
-        ApplicationDeploymentDescriptionType app = appDesc.getType();
-        ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
-        name.setStringValue("EchoSSH");
-        app.setApplicationName(name);
-
-        /*
-           * Use bat file if it is compiled on Windows
-           */
-        if (SystemUtils.IS_OS_WINDOWS) {
-            URL url = this.getClass().getClassLoader().getResource("echo.bat");
-            app.setExecutableLocation(url.getFile());
-        } else {
-            //for unix and Mac
-            app.setExecutableLocation("/bin/echo");
-        }
-
-        /*
-         * Job location
-        */
-        String tempDir = "/tmp";
-        String date = (new Date()).toString();
-        date = date.replaceAll(" ", "_");
-        date = date.replaceAll(":", "_");
-
-        tempDir = tempDir + File.separator
-                + "EchoSSH" + "_" + date + "_" + UUID.randomUUID();
-
-        app.setScratchWorkingDirectory(tempDir);
-        app.setStaticWorkingDirectory(tempDir);
-        app.setInputDataDirectory(tempDir + File.separator + "input");
-        app.setOutputDataDirectory(tempDir + File.separator + "output");
-        app.setStandardOutput(tempDir + File.separator + "echo.stdout");
-        app.setStandardError(tempDir + File.separator + "echo.stderr");
-
-        applicationContext.setApplicationDeploymentDescription(appDesc);
-
-        /*
-           * Service
-           */
-        ServiceDescription serv = new ServiceDescription();
-        serv.getType().setName("EchoSSH");
-
-        List<InputParameterType> inputList = new ArrayList<InputParameterType>();
-        InputParameterType input = InputParameterType.Factory.newInstance();
-        input.setParameterName("echo_input");
-        input.setParameterType(StringParameterType.Factory.newInstance());
-        inputList.add(input);
-        InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
-                .size()]);
-
-        List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
-        OutputParameterType output = OutputParameterType.Factory.newInstance();
-        output.setParameterName("echo_output");
-        output.setParameterType(StringParameterType.Factory.newInstance());
-        outputList.add(output);
-        OutputParameterType[] outputParamList = outputList
-                .toArray(new OutputParameterType[outputList.size()]);
-
-        serv.getType().setInputParametersArray(inputParamList);
-        serv.getType().setOutputParametersArray(outputParamList);
-
-        jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
-        jobExecutionContext.setApplicationContext(applicationContext);
-
-        // Add security context
-        jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext());
-        /*
-        * Host
-        */
-        applicationContext.setServiceDescription(serv);
-
-        MessageContext inMessage = new MessageContext();
-        ActualParameter echo_input = new ActualParameter();
-		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
-        inMessage.addParameter("echo_input", echo_input);
-
-        jobExecutionContext.setInMessageContext(inMessage);
-
-        MessageContext outMessage = new MessageContext();
-        ActualParameter echo_out = new ActualParameter();
+///*
+// *
+// * 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.core.gfac.services.impl;
+//
+//import java.io.File;
+//import java.net.URL;
+//import java.util.ArrayList;
+//import java.util.Date;
+//import java.util.List;
+//import java.util.UUID;
+//
+//import org.apache.airavata.commons.gfac.type.ActualParameter;
+//import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+//import org.apache.airavata.commons.gfac.type.HostDescription;
+//import org.apache.airavata.commons.gfac.type.MappingFactory;
+//import org.apache.airavata.commons.gfac.type.ServiceDescription;
+//import org.apache.airavata.gfac.GFacConfiguration;
+//import org.apache.airavata.gfac.GFacException;
+//import org.apache.airavata.gfac.core.context.ApplicationContext;
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.context.MessageContext;
+//import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
+//import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
+//import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+//import org.apache.airavata.schemas.gfac.InputParameterType;
+//import org.apache.airavata.schemas.gfac.OutputParameterType;
+//import org.apache.airavata.schemas.gfac.SSHHostType;
+//import org.apache.airavata.schemas.gfac.StringParameterType;
+//import org.apache.commons.lang.SystemUtils;
+//import org.junit.Assert;
+//import org.junit.Before;
+//import org.junit.Test;
+//
+//public class SSHProviderTestWithSSHAuth {
+//	private JobExecutionContext jobExecutionContext;
+//    @Before
+//    public void setUp() throws Exception {
+//
+//    	URL resource = SSHProviderTestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+//        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null);
+////        gFacConfiguration.s
+//        //have to set InFlwo Handlers and outFlowHandlers
+//        ApplicationContext applicationContext = new ApplicationContext();
+//        HostDescription host = new HostDescription(SSHHostType.type);
+//        host.getType().setHostName("bigred");
+//        host.getType().setHostAddress("bigred2.uits.iu.edu");
+//        applicationContext.setHostDescription(host);
+//        /*
+//           * App
+//           */
+//        ApplicationDescription appDesc = new ApplicationDescription();
+//        ApplicationDeploymentDescriptionType app = appDesc.getType();
+//        ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+//        name.setStringValue("EchoSSH");
+//        app.setApplicationName(name);
+//
+//        /*
+//           * Use bat file if it is compiled on Windows
+//           */
+//        if (SystemUtils.IS_OS_WINDOWS) {
+//            URL url = this.getClass().getClassLoader().getResource("echo.bat");
+//            app.setExecutableLocation(url.getFile());
+//        } else {
+//            //for unix and Mac
+//            app.setExecutableLocation("/bin/echo");
+//        }
+//
+//        /*
+//         * Job location
+//        */
+//        String tempDir = "/tmp";
+//        String date = (new Date()).toString();
+//        date = date.replaceAll(" ", "_");
+//        date = date.replaceAll(":", "_");
+//
+//        tempDir = tempDir + File.separator
+//                + "EchoSSH" + "_" + date + "_" + UUID.randomUUID();
+//
+//        app.setScratchWorkingDirectory(tempDir);
+//        app.setStaticWorkingDirectory(tempDir);
+//        app.setInputDataDirectory(tempDir + File.separator + "input");
+//        app.setOutputDataDirectory(tempDir + File.separator + "output");
+//        app.setStandardOutput(tempDir + File.separator + "echo.stdout");
+//        app.setStandardError(tempDir + File.separator + "echo.stderr");
+//
+//        applicationContext.setApplicationDeploymentDescription(appDesc);
+//
+//        /*
+//           * Service
+//           */
+//        ServiceDescription serv = new ServiceDescription();
+//        serv.getType().setName("EchoSSH");
+//
+//        List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+//        InputParameterType input = InputParameterType.Factory.newInstance();
+//        input.setParameterName("echo_input");
+//        input.setParameterType(StringParameterType.Factory.newInstance());
+//        inputList.add(input);
+//        InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+//                .size()]);
+//
+//        List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+//        OutputParameterType output = OutputParameterType.Factory.newInstance();
+//        output.setParameterName("echo_output");
+//        output.setParameterType(StringParameterType.Factory.newInstance());
+//        outputList.add(output);
+//        OutputParameterType[] outputParamList = outputList
+//                .toArray(new OutputParameterType[outputList.size()]);
+//
+//        serv.getType().setInputParametersArray(inputParamList);
+//        serv.getType().setOutputParametersArray(outputParamList);
+//
+//        jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
+//        jobExecutionContext.setApplicationContext(applicationContext);
+//
+//        // Add security context
+//        jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext());
+//        /*
+//        * Host
+//        */
+//        applicationContext.setServiceDescription(serv);
+//
+//        MessageContext inMessage = new MessageContext();
+//        ActualParameter echo_input = new ActualParameter();
 //		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
-        outMessage.addParameter("echo_output", echo_out);
-
-        jobExecutionContext.setOutMessageContext(outMessage);
-
-    }
-
-	private SSHSecurityContext getSecurityContext() {
-		SSHSecurityContext context = new SSHSecurityContext();
-        context.setUsername("lginnali");
-        context.setPrivateKeyLoc("~/.ssh/id_dsa");
-        context.setKeyPass("i want to be free");
-		return context;
-	}
-
-    @Test
-    public void testLocalProvider() throws GFacException {
-        BetterGfacImpl gFacAPI = new BetterGfacImpl();
-        gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
-        MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
-        Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")), "hello");
-    }
-}
+//        inMessage.addParameter("echo_input", echo_input);
+//
+//        jobExecutionContext.setInMessageContext(inMessage);
+//
+//        MessageContext outMessage = new MessageContext();
+//        ActualParameter echo_out = new ActualParameter();
+////		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+//        outMessage.addParameter("echo_output", echo_out);
+//
+//        jobExecutionContext.setOutMessageContext(outMessage);
+//
+//    }
+//
+//	private SSHSecurityContext getSecurityContext() {
+//		SSHSecurityContext context = new SSHSecurityContext();
+//        context.setUsername("lginnali");
+//        context.setPrivateKeyLoc("~/.ssh/id_dsa");
+//        context.setKeyPass("i want to be free");
+//		return context;
+//	}
+//
+//    @Test
+//    public void testLocalProvider() throws GFacException {
+//        BetterGfacImpl gFacAPI = new BetterGfacImpl();
+//        gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
+//        MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
+//        Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")), "hello");
+//    }
+//}


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