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From lah...@apache.org
Subject [3/4] git commit: moving ssh implementation out of gfac-core
Date Tue, 22 Apr 2014 20:42:22 GMT
moving ssh implementation out of gfac-core


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/5381d599
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/5381d599
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/5381d599

Branch: refs/heads/master
Commit: 5381d5999caf42dc14b7d288cc1817e5ef3236ce
Parents: 56574dd
Author: lahiru <lahiru@apache.org>
Authored: Tue Apr 22 16:40:19 2014 -0400
Committer: lahiru <lahiru@apache.org>
Committed: Tue Apr 22 16:40:19 2014 -0400

----------------------------------------------------------------------
 .../client/samples/CreateLaunchExperiment.java  |   6 +-
 modules/airavata-client/pom.xml                 |  12 +-
 .../context/security/SSHSecurityContext.java    | 120 ---------
 .../gfac/handler/AdvancedSCPInputHandler.java   | 139 ----------
 .../gfac/handler/AdvancedSCPOutputHandler.java  | 115 --------
 .../gfac/handler/SCPDirectorySetupHandler.java  | 100 -------
 .../airavata/gfac/handler/SCPInputHandler.java  | 138 ----------
 .../airavata/gfac/handler/SCPOutputHandler.java | 175 -------------
 .../gfac/provider/impl/SSHProvider.java         | 262 -------------------
 .../services/impl/BigRed2TestWithSSHAuth.java   | 253 ------------------
 .../impl/SSHProviderTestWithSSHAuth.java        | 172 ------------
 .../airavata/job/monitor/AMQPMonitorTest.java   |  18 +-
 modules/gfac/gfac-ssh/pom.xml                   | 132 ++++++++++
 .../context/security/SSHSecurityContext.java    | 120 +++++++++
 .../gfac/handler/AdvancedSCPInputHandler.java   | 139 ++++++++++
 .../gfac/handler/AdvancedSCPOutputHandler.java  | 115 ++++++++
 .../gfac/handler/SCPDirectorySetupHandler.java  | 100 +++++++
 .../airavata/gfac/handler/SCPInputHandler.java  | 138 ++++++++++
 .../airavata/gfac/handler/SCPOutputHandler.java | 175 +++++++++++++
 .../gfac/provider/impl/SSHProvider.java         | 262 +++++++++++++++++++
 .../src/main/resources/errors.properties        | 197 ++++++++++++++
 .../src/main/resources/service.properties       |  58 ++++
 .../services/impl/BigRed2TestWithSSHAuth.java   | 253 ++++++++++++++++++
 .../impl/SSHProviderTestWithSSHAuth.java        | 172 ++++++++++++
 .../src/test/resources/PBSTemplate.xslt         |  73 ++++++
 .../gfac-ssh/src/test/resources/gfac-config.xml |  33 +++
 .../src/test/resources/logging.properties       |  42 +++
 modules/gfac/pom.xml                            |   1 +
 .../airavata/gsi/ssh/config/ConfigReader.java   |   6 +
 .../apache/airavata/job/AMQPMonitorTest.java    |  22 +-
 .../job/QstatMonitorTestWithMyProxyAuth.java    |  10 +-
 31 files changed, 2046 insertions(+), 1512 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index 13a8dae..1a00acb 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@ -60,10 +60,10 @@ public class CreateLaunchExperiment {
             AiravataUtils.setExecutionAsClient();
             final Airavata.Client airavata = AiravataClientFactory.createAiravataClient(THRIFT_SERVER_HOST, THRIFT_SERVER_PORT);
             System.out.println("API version is " + airavata.GetAPIVersion());
-            addDescriptors();
-            final String expId = createExperimentForLocalHost(airavata);
+//            addDescriptors();
 //            final String expId = createExperimentForSSHHost(airavata);
-//            final String expId = createExperimentForTrestles(airavata);
+//            final String expId = createExperimentForSSHHost(airavata);
+            final String expId = createExperimentForTrestles(airavata);
 //            final String expId = createExperimentForStampede(airavata);
             System.out.println("Experiment ID : " + expId);
             launchExperiment(airavata, expId);

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/airavata-client/pom.xml
----------------------------------------------------------------------
diff --git a/modules/airavata-client/pom.xml b/modules/airavata-client/pom.xml
index 40b1b09..4db3993 100644
--- a/modules/airavata-client/pom.xml
+++ b/modules/airavata-client/pom.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<!--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 (theÏ "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 
+<!--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 (theÏ "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. -->
 
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
deleted file mode 100644
index 2d71b7d..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-package org.apache.airavata.gfac.context.security;
-
-import java.io.IOException;
-
-import net.schmizz.sshj.SSHClient;
-import net.schmizz.sshj.connection.channel.direct.Session;
-import net.schmizz.sshj.userauth.keyprovider.KeyProvider;
-
-import org.apache.airavata.gfac.SecurityContext;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Handle SSH security
- */
-public class SSHSecurityContext implements SecurityContext {
-	private static final Logger log = LoggerFactory.getLogger(SSHSecurityContext.class);
-
-	public static final String SSH_SECURITY_CONTEXT = "ssh";
-
-	private String username;
-	private String privateKeyLoc;
-	private String keyPass;
-	private SSHClient sshClient;
-	private Session session;
-
-    private Cluster pbsCluster;
-
-	public String getUsername() {
-		return username;
-	}
-
-	public void setUsername(String username) {
-		this.username = username;
-	}
-
-	public String getPrivateKeyLoc() {
-		return privateKeyLoc;
-	}
-
-	public void setPrivateKeyLoc(String privateKeyLoc) {
-		this.privateKeyLoc = privateKeyLoc;
-	}
-
-	public String getKeyPass() {
-		return keyPass;
-	}
-
-	public void setKeyPass(String keyPass) {
-		this.keyPass = keyPass;
-	}
-
-	public void closeSession(Session session) {
-		if (session != null) {
-			try {
-				session.close();
-			} catch (Exception e) {
-				log.warn("Cannot Close SSH Session");
-			}
-		}
-	}
-
-	public Session getSession(String hostAddress) throws IOException {
-		try {
-			if (sshClient == null) {
-				sshClient = new SSHClient();
-			}
-			if (getSSHClient().isConnected())
-				return getSSHClient().startSession();
-
-			KeyProvider pkey = getSSHClient().loadKeys(getPrivateKeyLoc(), getKeyPass());
-
-			getSSHClient().loadKnownHosts();
-
-			getSSHClient().connect(hostAddress);
-			getSSHClient().authPublickey(getUsername(), pkey);
-			session = getSSHClient().startSession();
-			return session;
-
-		} catch (NullPointerException ne) {
-			throw new SecurityException("Cannot load security context for SSH", ne);
-		}
-	}
-
-	public SSHClient getSSHClient() {
-		if (sshClient == null) {
-			sshClient = new SSHClient();
-		}
-		return sshClient;
-	}
-
-    public void setPbsCluster(Cluster pbsCluster) {
-        this.pbsCluster = pbsCluster;
-    }
-
-    public Cluster getPbsCluster() {
-        return this.pbsCluster;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPInputHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPInputHandler.java
deleted file mode 100644
index 361bac7..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPInputHandler.java
+++ /dev/null
@@ -1,139 +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.handler;
-
-import org.apache.airavata.common.utils.StringUtil;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.MessageContext;
-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.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.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.util.*;
-
-/**
- * This handler will copy input data from gateway machine to airavata
- * installed machine, later running handlers can copy the input files to computing resource
- * <Handler class="org.apache.airavata.gfac.handler.AdvancedSCPOutputHandler">
-                            <property name="privateKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa"/>
-                            <property name="publicKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa.pub"/>
-                        <property name="userName" value="airavata"/>
-                        <property name="hostName" value="gw98.iu.xsede.org"/>
-                        <property name="inputPath" value="/home/airavata/outputData"/>
- */
-public class AdvancedSCPInputHandler extends AbstractHandler{
-    private static final Logger log = LoggerFactory.getLogger(AdvancedSCPInputHandler.class);
-
-    private String password = null;
-
-    private String publicKeyPath;
-
-    private String passPhrase;
-
-    private String privateKeyPath;
-
-    private String userName;
-
-    private String hostName;
-
-    private String inputPath;
-
-    public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
-        password = properties.get("password");
-        passPhrase = properties.get("passPhrase");
-        privateKeyPath = properties.get("privateKeyPath");
-        publicKeyPath = properties.get("publicKeyPath");
-        userName = properties.get("userName");
-        hostName = properties.get("hostName");
-        inputPath = properties.get("inputPath");
-    }
-
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException, GFacException {
-        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
-                .getApplicationDeploymentDescription().getType();
-
-        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;
-        MessageContext inputNew = new MessageContext();
-        try {
-            // here doesn't matter what the job manager is because we are only doing some file handling
-            // not really dealing with monitoring or job submission, so we pa
-            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
-            String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
-           (new File(parentPath)).mkdirs();
-            MessageContext input = jobExecutionContext.getInMessageContext();
-            Set<String> parameters = input.getParameters().keySet();
-            for (String paramName : parameters) {
-                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
-                String paramValue = MappingFactory.toString(actualParameter);
-                //TODO: Review this with type
-                if ("URI".equals(actualParameter.getType().getType().toString())) {
-                    ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(pbsCluster, paramValue, parentPath));
-                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
-                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
-                    List<String> newFiles = new ArrayList<String>();
-                    for (String paramValueEach : split) {
-                        String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
-                        newFiles.add(stageInputFiles);
-                    }
-                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
-                }
-                inputNew.getParameters().put(paramName, actualParameter);
-            }
-        } catch (Exception e) {
-            log.error(e.getMessage());
-            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-        }
-        jobExecutionContext.setInMessageContext(inputNew);
-    }
-
-    private String stageInputFiles(Cluster cluster, String paramValue, String parentPath) throws GFacException {
-        try {
-            cluster.scpFrom(paramValue, parentPath);
-            return "file://" + parentPath + File.separator + (new File(paramValue)).getName();
-        } catch (SSHApiException e) {
-            log.error("Error tranfering remote file to local file, remote path: " + paramValue);
-            throw new GFacException(e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPOutputHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPOutputHandler.java
deleted file mode 100644
index 080d3c7..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/AdvancedSCPOutputHandler.java
+++ /dev/null
@@ -1,115 +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.handler;
-
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-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.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.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.util.List;
-import java.util.Map;
-
-/**
- * This handler will copy outputs from airavata installed local directory
- * to a remote location, prior to this handler SCPOutputHandler should be invoked
- * Should add following configuration to gfac-config.xml and configure the keys properly
- * <Handler class="org.apache.airavata.gfac.handler.AdvancedSCPOutputHandler">
-                            <property name="privateKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa"/>
-                            <property name="publicKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa.pub"/>
-                        <property name="userName" value="airavata"/>
-                        <property name="hostName" value="gw98.iu.xsede.org"/>
-                        <property name="outputPath" value="/home/airavata/outputData"/>
-                        <property name="passPhrase" value="/home/airavata/outputData"/>
-                        <property name="password" value="/home/airavata/outputData"/>
-
- */
-public class AdvancedSCPOutputHandler extends AbstractHandler {
-    private static final Logger log = LoggerFactory.getLogger(AdvancedSCPOutputHandler.class);
-
-    private String password = null;
-
-    private String publicKeyPath;
-
-    private String passPhrase;
-
-    private String privateKeyPath;
-
-    private String userName;
-
-    private String hostName;
-
-    private String outputPath;
-
-    public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
-        password = properties.get("password");
-        passPhrase = properties.get("passPhrase");
-        privateKeyPath = properties.get("privateKeyPath");
-        publicKeyPath = properties.get("publicKeyPath");
-        userName = properties.get("userName");
-        hostName = properties.get("hostName");
-        outputPath = properties.get("outputPath");
-    }
-
-    @Override
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException, GFacException {
-        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
-                .getApplicationDeploymentDescription().getType();
-        String standardError = app.getStandardError();
-        String standardOutput = app.getStandardOutput();
-        String outputDataDirectory = app.getOutputDataDirectory();
-
-        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);
-        try {
-            Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
-            outputPath = outputPath + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID()
-            + File.separator;
-            pbsCluster.makeDirectory(outputPath);
-            pbsCluster.scpTo(outputPath, standardError);
-            pbsCluster.scpTo(outputPath,standardOutput);
-            for(String files:jobExecutionContext.getOutputFiles()){
-                pbsCluster.scpTo(outputPath,files);
-            }
-        } catch (SSHApiException e) {
-            log.error("Error transfering files to remote host : " + hostName + " with the user: " + userName);
-            log.error(e.getMessage());
-            throw new GFacException(e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
deleted file mode 100644
index a068b77..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
+++ /dev/null
@@ -1,100 +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.handler;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
-import org.apache.airavata.gfac.utils.GFacUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SCPDirectorySetupHandler extends AbstractHandler{
-    private static final Logger log = LoggerFactory.getLogger(SCPDirectorySetupHandler.class);
-
-	public void invoke(JobExecutionContext jobExecutionContext) throws GFacException {
-		log.info("Setup SSH job directorties");
-	    super.invoke(jobExecutionContext);
-		makeDirectory(jobExecutionContext);
-
-	}
-	private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacException {
-		Cluster cluster = null;
-            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
-                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
-            } else {
-                cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
-            }
-            if (cluster == null) {
-                throw new GFacHandlerException("Security context is not set properly");
-            } else { 
-                log.info("Successfully retrieved the Security Context");
-            }
-		ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
-		try {
-            String workingDirectory = app.getScratchWorkingDirectory();
-			cluster.makeDirectory(workingDirectory);
-            cluster.makeDirectory(app.getScratchWorkingDirectory());
-            cluster.makeDirectory(app.getInputDataDirectory());
-            cluster.makeDirectory(app.getOutputDataDirectory());
-            DataTransferDetails detail = new DataTransferDetails();
-            TransferStatus status = new TransferStatus();
-            status.setTransferState(TransferState.DIRECTORY_SETUP);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription("Working directory = " + workingDirectory);
-         
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-          
-		} catch (SSHApiException e) {
-            throw new GFacHandlerException("Error executing the Handler: " + SCPDirectorySetupHandler.class,e);  
-        }catch (Exception e){
-            DataTransferDetails detail = new DataTransferDetails();
-            TransferStatus status = new TransferStatus();
-            status.setTransferState(TransferState.FAILED);
-            detail.setTransferStatus(status);
-            try {
-				registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-				GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE,  jobExecutionContext.getTaskData().getTaskID());
-	        } catch (Exception e1) {
-			    throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
-		   }
-            throw new GFacHandlerException("Error executing the Handler: " + SCPDirectorySetupHandler.class,e); 
-        }
-	}
-
-    public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
deleted file mode 100644
index 4bf352b..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
+++ /dev/null
@@ -1,138 +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.handler;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.airavata.common.utils.StringUtil;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.MessageContext;
-import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
-import org.apache.airavata.gfac.utils.GFacUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.ErrorDetails;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SCPInputHandler extends AbstractHandler {
-
-    private static final Logger log = LoggerFactory.getLogger(SCPInputHandler.class);
-
-
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException, GFacException {
-
-        log.info("Invoking SCPInputHandler");
-        super.invoke(jobExecutionContext);
-       
-        DataTransferDetails detail = new DataTransferDetails();
-        TransferStatus status = new TransferStatus();
-    
-        MessageContext inputNew = new MessageContext();
-        try {
-            MessageContext input = jobExecutionContext.getInMessageContext();
-            Set<String> parameters = input.getParameters().keySet();
-            for (String paramName : parameters) {
-                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
-                String paramValue = MappingFactory.toString(actualParameter);
-                //TODO: Review this with type
-                if ("URI".equals(actualParameter.getType().getType().toString())) {
-                    ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(jobExecutionContext, paramValue));
-                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
-                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
-                    List<String> newFiles = new ArrayList<String>();
-                    for (String paramValueEach : split) {
-                        String stageInputFiles = stageInputFiles(jobExecutionContext, paramValueEach);
-                        status.setTransferState(TransferState.UPLOAD);
-                        detail.setTransferStatus(status);
-                        detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
-                        registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-                   	newFiles.add(stageInputFiles);
-                    }
-                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
-                }
-                inputNew.getParameters().put(paramName, actualParameter);
-            }
-        } catch (Exception e) {
-            log.error(e.getMessage());
-            status.setTransferState(TransferState.FAILED);
-            detail.setTransferStatus(status);
-            try {
-    			GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE,  jobExecutionContext.getTaskData().getTaskID());
-    			registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-			} catch (Exception e1) {
-			    throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
-		   }
-            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-        }
-        jobExecutionContext.setInMessageContext(inputNew);
-    }
-
-    private static String stageInputFiles(JobExecutionContext jobExecutionContext, String paramValue) throws IOException, GFacException {
-        Cluster cluster = null;
-        if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
-            cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
-        } else {
-            cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
-        }
-        if (cluster == null) {
-            throw new GFacException("Security context is not set properly");
-        } else {
-            log.info("Successfully retrieved the Security Context");
-        }
-        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
-        int i = paramValue.lastIndexOf(File.separator);
-        String substring = paramValue.substring(i + 1);
-        try {
-            String targetFile = app.getInputDataDirectory() + File.separator + substring;
-            if(paramValue.startsWith("file")){
-                paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
-            }
-            cluster.scpTo(targetFile, paramValue);
-            return targetFile;
-        } catch (SSHApiException e) {
-            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-        }
-    }
-
-    public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPOutputHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPOutputHandler.java
deleted file mode 100644
index 10287a5..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPOutputHandler.java
+++ /dev/null
@@ -1,175 +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.handler;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import net.schmizz.sshj.connection.ConnectionException;
-import net.schmizz.sshj.transport.TransportException;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
-import org.apache.airavata.gfac.provider.GFacProviderException;
-import org.apache.airavata.gfac.utils.GFacUtils;
-import org.apache.airavata.gfac.utils.OutputUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.util.SSHUtils;
-import org.apache.airavata.model.workspace.experiment.*;
-import org.apache.airavata.persistance.registry.jpa.model.DataTransferDetail;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.apache.xmlbeans.XmlException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SCPOutputHandler extends AbstractHandler{
-    private static final Logger log = LoggerFactory.getLogger(SCPOutputHandler.class);
-
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException, GFacException {
-
-    	super.invoke(jobExecutionContext);
-        DataTransferDetails detail = new DataTransferDetails();
-        TransferStatus status = new TransferStatus();
-
-    	ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
-                .getApplicationDeploymentDescription().getType();
-        try {
-            Cluster cluster = null;
-            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
-                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
-            } else {
-                cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
-            }
-            if (cluster == null) {
-                throw new GFacProviderException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-
-            // Get the Stdouts and StdErrs
-            String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());
-
-            TaskDetails taskData = jobExecutionContext.getTaskData();
-            String outputDataDir = null;
-            File localStdOutFile;
-            File localStdErrFile;
-
-            if (taskData.getAdvancedOutputDataHandling() != null) {
-                outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
-            }
-            if(outputDataDir == null) {
-                outputDataDir = File.separator + "tmp";
-            }
-            outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" +jobExecutionContext.getTaskData().getTaskID();
-            (new File(outputDataDir)).mkdirs();
-
-
-            localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
-            localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
-//            cluster.makeDirectory(outputDataDir);
-            cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
-            Thread.sleep(1000);
-            cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
-            Thread.sleep(1000);
-
-            String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
-            String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
-            status.setTransferState(TransferState.COMPLETE);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription("STDOUT:" + stdOutStr);
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-
-            status.setTransferState(TransferState.COMPLETE);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription("STDERR:" + stdErrStr);
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-
-
-            Map<String, ActualParameter> stringMap = new HashMap<String, ActualParameter>();
-            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
-            Set<String> keys = output.keySet();
-            for (String paramName : keys) {
-            ActualParameter actualParameter = (ActualParameter) output.get(paramName);
-            if ("URI".equals(actualParameter.getType().getType().toString())) {
-
-                List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
-                if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
-                    stringMap = OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr);
-                } else {
-					String valueList = outputList.get(0);
-                    cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
-                    jobExecutionContext.addOutputFile(outputDataDir + File.separator + valueList);
-					((URIParameterType) actualParameter.getType()).setValue(valueList);
-					stringMap = new HashMap<String, ActualParameter>();
-					stringMap.put(paramName, actualParameter);
-				}
-			}else{
-				 stringMap = OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr);
-			}
-            }
-            if (stringMap == null || stringMap.isEmpty()) {
-                throw new GFacHandlerException(
-                        "Empty Output returned from the Application, Double check the application"
-                                + "and ApplicationDescriptor output Parameter Names");
-            }
-            status.setTransferState(TransferState.DOWNLOAD);
-            detail.setTransferStatus(status);
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
-
-            app.setStandardError(localStdErrFile.getAbsolutePath());
-            app.setStandardOutput(localStdOutFile.getAbsolutePath());
-            app.setOutputDataDirectory(outputDataDir);
-        } catch (XmlException e) {
-            throw new GFacHandlerException("Cannot read output:" + e.getMessage(), e);
-        } catch (ConnectionException e) {
-            throw new GFacHandlerException(e.getMessage(), e);
-        } catch (TransportException e) {
-            throw new GFacHandlerException(e.getMessage(), e);
-        } catch (IOException e) {
-            throw new GFacHandlerException(e.getMessage(), e);
-        } catch (Exception e) {
-        	 try {
-         	    status.setTransferState(TransferState.FAILED);
- 				detail.setTransferStatus(status);
- 				registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
- 				GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE,  jobExecutionContext.getTaskData().getTaskID());
-  			} catch (Exception e1) {
-  			    throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
-  		   }
-            throw new GFacHandlerException("Error in retrieving results", e);
-        }
-
-    }
-
-    public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
deleted file mode 100644
index 5914dd3..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
+++ /dev/null
@@ -1,262 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.provider.impl;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.Calendar;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Random;
-import java.util.Set;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.gfac.Constants;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.MessageContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
-import org.apache.airavata.gfac.provider.GFacProvider;
-import org.apache.airavata.gfac.provider.GFacProviderException;
-import org.apache.airavata.gfac.utils.GFacUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.CommandExecutor;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
-import org.apache.airavata.gsi.ssh.impl.StandardOutReader;
-import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.NameValuePairType;
-import org.apache.airavata.schemas.gfac.SSHHostType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
-
-/**
- * Execute application using remote SSH
- */
-public class SSHProvider extends AbstractProvider implements GFacProvider{
-    private static final Logger log = LoggerFactory.getLogger(SSHProvider.class);
-    private Cluster cluster;
-    private String jobID = null;
-    private String taskID = null;
-    // we keep gsisshprovider to support qsub submission incase of hpc scenario with ssh
-    private GSISSHProvider gsiSshProvider = null;
-
-    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-    	super.initialize(jobExecutionContext);
-    	taskID = jobExecutionContext.getTaskData().getTaskID();
-		if (!((SSHHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getHpcResource()) {
-            jobID = "SSH_" + jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress() + "_" + Calendar.getInstance().getTimeInMillis();
-            cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
-            
-            ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
-            String remoteFile = app.getStaticWorkingDirectory() + File.separatorChar + Constants.EXECUTABLE_NAME;
-            details.setJobID(taskID);
-            details.setJobDescription(remoteFile);
-            jobExecutionContext.setJobDetails(details);
-            JobDescriptor jobDescriptor = GFacUtils.createJobDescriptor(jobExecutionContext, app, null);
-            details.setJobDescription(jobDescriptor.toXML());
-         
-            GFacUtils.saveJobStatus(details, JobState.SETUP, taskID);
-            log.info(remoteFile);
-            try {
-            	File runscript = createShellScript(jobExecutionContext);
-                cluster.scpTo(remoteFile, runscript.getAbsolutePath());
-            } catch (Exception e) {
-                throw new GFacProviderException(e.getLocalizedMessage(), e);
-            }
-        }else{
-           gsiSshProvider = new GSISSHProvider();
-        }
-    }
-
-
-    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        if (gsiSshProvider == null) {
-            ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
-            try {
-                /*
-                 * Execute
-                 */
-                String execuable = app.getStaticWorkingDirectory() + File.separatorChar + Constants.EXECUTABLE_NAME;
-                details.setJobDescription(execuable);
-
-//                GFacUtils.updateJobStatus(details, JobState.SUBMITTED);
-                RawCommandInfo rawCommandInfo = new RawCommandInfo("/bin/chmod 755 " + execuable + "; " + execuable);
-
-                StandardOutReader jobIDReaderCommandOutput = new StandardOutReader();
-                
-                CommandExecutor.executeCommand(rawCommandInfo, cluster.getSession(), jobIDReaderCommandOutput);
-                String stdOutputString = getOutputifAvailable(jobIDReaderCommandOutput, "Error submitting job to resource");
-
-                log.info("stdout=" + stdOutputString);
-             
-//                GFacUtils.updateJobStatus(details, JobState.COMPLETE);
-            } catch (Exception e) {
-                throw new GFacProviderException(e.getMessage(), e);
-            } finally {
-                if (cluster != null) {
-                	try {
-						cluster.disconnect();
-					} catch (SSHApiException e) {
-						throw new GFacProviderException(e.getMessage(), e);
-					}
-                }
-            }
-        } else {
-            try {
-                gsiSshProvider.execute(jobExecutionContext);
-            } catch (GFacException e) {
-                throw new GFacProviderException(e.getMessage(), e);
-            }
-        }
-    }
-
-    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        if (gsiSshProvider != null){
-            try {
-                gsiSshProvider.dispose(jobExecutionContext);
-            } catch (GFacException e) {
-                throw new GFacProviderException(e.getMessage(),e);
-            }
-        }
-    }
-
-
-    public void cancelJob(String jobId, JobExecutionContext jobExecutionContext) throws GFacException {
-        throw new NotImplementedException();
-    }
-
-
-    private File createShellScript(JobExecutionContext context) throws IOException {
-        ApplicationDeploymentDescriptionType app = context.getApplicationContext()
-                .getApplicationDeploymentDescription().getType();
-        String uniqueDir = app.getApplicationName().getStringValue() + System.currentTimeMillis()
-                + new Random().nextLong();
-
-        File shellScript = File.createTempFile(uniqueDir, "sh");
-        OutputStream out = new FileOutputStream(shellScript);
-
-        out.write("#!/bin/bash\n".getBytes());
-        out.write(("cd " + app.getStaticWorkingDirectory() + "\n").getBytes());
-        out.write(("export " + Constants.INPUT_DATA_DIR_VAR_NAME + "=" + app.getInputDataDirectory() + "\n").getBytes());
-        out.write(("export " + Constants.OUTPUT_DATA_DIR_VAR_NAME + "=" + app.getOutputDataDirectory() + "\n")
-                .getBytes());
-        // get the env of the host and the application
-        NameValuePairType[] env = app.getApplicationEnvironmentArray();
-
-        Map<String, String> nv = new HashMap<String, String>();
-        if (env != null) {
-            for (int i = 0; i < env.length; i++) {
-                String key = env[i].getName();
-                String value = env[i].getValue();
-                nv.put(key, value);
-            }
-        }
-        for (Entry<String, String> entry : nv.entrySet()) {
-            log.debug("Env[" + entry.getKey() + "] = " + entry.getValue());
-            out.write(("export " + entry.getKey() + "=" + entry.getValue() + "\n").getBytes());
-
-        }
-
-        // prepare the command
-        final String SPACE = " ";
-        StringBuffer cmd = new StringBuffer();
-        cmd.append(app.getExecutableLocation());
-        cmd.append(SPACE);
-
-        MessageContext input = context.getInMessageContext();
-        ;
-        Map<String, Object> inputs = input.getParameters();
-        Set<String> keys = inputs.keySet();
-        for (String paramName : keys) {
-            ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
-            if ("URIArray".equals(actualParameter.getType().getType().toString())) {
-                String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
-                for (String value : values) {
-                    cmd.append(value);
-                    cmd.append(SPACE);
-                }
-            } else {
-                String paramValue = MappingFactory.toString(actualParameter);
-                cmd.append(paramValue);
-                cmd.append(SPACE);
-            }
-        }
-        // We redirect the error and stdout to remote files, they will be read
-        // in later
-        cmd.append(SPACE);
-        cmd.append("1>");
-        cmd.append(SPACE);
-        cmd.append(app.getStandardOutput());
-        cmd.append(SPACE);
-        cmd.append("2>");
-        cmd.append(SPACE);
-        cmd.append(app.getStandardError());
-
-        String cmdStr = cmd.toString();
-        log.info("Command = " + cmdStr);
-        out.write((cmdStr + "\n").getBytes());
-        String message = "\"execuationSuceeded\"";
-        out.write(("echo " + message + "\n").getBytes());
-        out.close();
-
-        return shellScript;
-    }
-
-    public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
-         if (gsiSshProvider != null){
-            try {
-               initProperties(properties);
-            } catch (GFacException e) {
-                throw new GFacProviderException(e.getMessage(),e);
-            }
-        }
-    }
-    /**
-     * This method will read standard output and if there's any it will be parsed
-     * @param jobIDReaderCommandOutput
-     * @param errorMsg
-     * @return
-     * @throws SSHApiException
-     */
-    private String getOutputifAvailable(StandardOutReader jobIDReaderCommandOutput, String errorMsg) throws SSHApiException {
-        String stdOutputString = jobIDReaderCommandOutput.getStdOutputString();
-        String stdErrorString = jobIDReaderCommandOutput.getStdErrorString();
-
-        if(stdOutputString == null || stdOutputString.isEmpty() || (stdErrorString != null && !stdErrorString.isEmpty())){
-            log.error("Standard Error output : " + stdErrorString);
-            throw new SSHApiException(errorMsg + stdErrorString);
-        }
-        return stdOutputString;
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
deleted file mode 100644
index de8e1b4..0000000
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
+++ /dev/null
@@ -1,253 +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.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.context.ApplicationContext;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.MessageContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
-import org.apache.airavata.gfac.cpi.GFacImpl;
-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.AfterClass;
-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 = GramProviderTestWithMyProxyAuth.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, 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 {
-        GFacImpl gFacAPI = new GFacImpl();
-        gFacAPI.submitJob(jobExecutionContext);
-        org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobDescription());
-        org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobID());
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
deleted file mode 100644
index cd5611c..0000000
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
+++ /dev/null
@@ -1,172 +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.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.context.ApplicationContext;
-import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.gfac.context.MessageContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
-import org.apache.airavata.gfac.cpi.GFacImpl;
-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 = GramProviderTestWithMyProxyAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
-        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null,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();
-//		((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 {
-        GFacImpl gFacAPI = new GFacImpl();
-        gFacAPI.submitJob(jobExecutionContext);
-        MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
-        Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")), "hello");
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/monitor/AMQPMonitorTest.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/monitor/AMQPMonitorTest.java b/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/monitor/AMQPMonitorTest.java
index 65ab8d0..1515310 100644
--- a/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/monitor/AMQPMonitorTest.java
+++ b/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/monitor/AMQPMonitorTest.java
@@ -54,11 +54,11 @@ public class AMQPMonitorTest {
 
     @Before
     public void setUp() throws Exception {
-//        System.setProperty("myproxy.username", "ogce");
-//        System.setProperty("myproxy.password", "");
-//        System.setProperty("basedir", "/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
-//        System.setProperty("gsi.working.directory", "/home/ogce");
-//        System.setProperty("trusted.cert.location", "/Users/lahirugunathilake/Downloads/certificates");
+        System.setProperty("myproxy.username", "ogce");
+        System.setProperty("myproxy.password", "OpenGwy14");
+        System.setProperty("basedir", "/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
+        System.setProperty("gsi.working.directory", "/home/ogce");
+        System.setProperty("trusted.cert.location", "/Users/lahirugunathilake/Downloads/certificates");
         myProxyUserName = System.getProperty("myproxy.username");
         myProxyPassword = System.getProperty("myproxy.password");
         workingDirectory = System.getProperty("gsi.working.directory");
@@ -140,13 +140,5 @@ public class AMQPMonitorTest {
         } catch (InterruptedException e) {
             e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
         }
-        try {
-            Thread.sleep(5000);
-            Iterator<MonitorID> iterator = monitorManager.getPushQueue().iterator();
-            MonitorID next = iterator.next();
-            org.junit.Assert.assertNotNull(next.getStatus());
-        } catch (InterruptedException e) {
-            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-        }
     }
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/5381d599/modules/gfac/gfac-ssh/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/pom.xml b/modules/gfac/gfac-ssh/pom.xml
new file mode 100644
index 0000000..ab8afc2
--- /dev/null
+++ b/modules/gfac/gfac-ssh/pom.xml
@@ -0,0 +1,132 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--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 (theÏ "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. -->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <groupId>org.apache.airavata</groupId>
+        <artifactId>gfac</artifactId>
+        <version>0.12-SNAPSHOT</version>
+        <relativePath>../pom.xml</relativePath>
+    </parent>
+
+    <modelVersion>4.0.0</modelVersion>
+    <artifactId>airavata-gfac-ssh</artifactId>
+    <name>Airavata GFac SSH providers and handler implementation</name>
+    <description>This is the extension of </description>
+    <url>http://airavata.apache.org/</url>
+
+    <dependencies>
+        <!-- Logging -->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+
+        <!-- GFAC schemas -->
+        <dependency>
+            <groupId>org.apache.airavata</groupId>
+            <artifactId>airavata-gfac-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <!-- Credential Store -->
+        <dependency>
+            <groupId>org.apache.airavata</groupId>
+            <artifactId>airavata-credential-store</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.airavata</groupId>
+            <artifactId>airavata-server-configuration</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.airavata</groupId>
+            <artifactId>airavata-client-configuration</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+
+        <!-- Test -->
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.1.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>jcl-over-slf4j</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-log4j12</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <!-- gsi-ssh api dependencies -->
+        <dependency>
+            <groupId>org.apache.airavata</groupId>
+            <artifactId>gsissh</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.airavata</groupId>
+            <artifactId>airavata-data-models</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.jcraft</groupId>
+            <artifactId>jsch</artifactId>
+            <version>0.1.50</version>
+        </dependency>
+        <dependency>
+            <groupId>org.ogce</groupId>
+            <artifactId>bcgss</artifactId>
+            <version>146</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.xmlbeans</groupId>
+            <artifactId>xmlbeans</artifactId>
+            <version>${xmlbeans.version}</version>
+        </dependency>
+
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>copy-dependencies</id>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>copy-dependencies</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>target/lib</outputDirectory>
+                            <overWriteReleases>false</overWriteReleases>
+                            <overWriteSnapshots>true</overWriteSnapshots>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>


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