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From shame...@apache.org
Subject [1/6] airavata git commit: Removed gsissh module from tools
Date Fri, 05 Jun 2015 05:26:53 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 2835d09ef -> 13c2e79e4


http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/util/SSHUtils.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/util/SSHUtils.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/util/SSHUtils.java
deleted file mode 100644
index 35f6a41..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/util/SSHUtils.java
+++ /dev/null
@@ -1,757 +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.ssh.util;
-
-import com.jcraft.jsch.*;
-
-import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo;
-import org.apache.airavata.gfac.ssh.api.SSHApiException;
-import org.apache.airavata.gfac.ssh.api.ServerInfo;
-import org.apache.airavata.gfac.ssh.config.ConfigReader;
-import org.apache.airavata.gfac.ssh.impl.StandardOutReader;
-import org.slf4j.*;
-
-import java.io.*;
-import java.util.Arrays;
-import java.util.List;
-
-/**
- * This class is going to be useful to SCP a file to a remote grid machine using my proxy credentials
- */
-public class SSHUtils {
-    private static final org.slf4j.Logger log = LoggerFactory.getLogger(SSHUtils.class);
-
-    static {
-        JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gfac.ssh.GSSContextX509");
-        JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
-
-    }
-
-    private ServerInfo serverInfo;
-
-    private GSIAuthenticationInfo authenticationInfo;
-
-    private ConfigReader configReader;
-
-    /**
-     * We need to pass certificateLocation when we use SCPTo method standalone
-     *
-     * @param serverInfo
-     * @param authenticationInfo
-     * @param certificateLocation
-     * @param configReader
-     */
-    public SSHUtils(ServerInfo serverInfo, GSIAuthenticationInfo authenticationInfo, String certificateLocation, ConfigReader configReader) {
-        System.setProperty("X509_CERT_DIR", certificateLocation);
-        this.serverInfo = serverInfo;
-        this.authenticationInfo = authenticationInfo;
-        this.configReader = configReader;
-    }
-
-    /**
-     * This can be used when use SCPTo method within SSHAPi because SSHApiFactory already set the system property certificateLocation
-     *
-     * @param serverInfo
-     * @param authenticationInfo
-     * @param configReader
-     */
-    public SSHUtils(ServerInfo serverInfo, GSIAuthenticationInfo authenticationInfo
-            , ConfigReader configReader) {
-        this.serverInfo = serverInfo;
-        this.authenticationInfo = authenticationInfo;
-        this.configReader = configReader;
-    }
-
-    /**
-     * This  method will scp the lFile to the rFile location
-     *
-     * @param rFile remote file Path to use in scp
-     * @param lFile local file path to use in scp
-     * @throws IOException
-     * @throws JSchException
-     * @throws org.apache.airavata.gfac.ssh.api.SSHApiException
-     *
-     */
-    public void scpTo(String rFile, String lFile) throws IOException, JSchException, SSHApiException {
-        FileInputStream fis = null;
-        String prefix = null;
-        if (new File(lFile).isDirectory()) {
-            prefix = lFile + File.separator;
-        }
-        JSch jsch = new JSch();
-
-        log.debug("Connecting to server - " + serverInfo.getHost() + ":" + serverInfo.getPort() + " with user name - "
-                + serverInfo.getUserName());
-
-        Session session = null;
-
-        try {
-            session = jsch.getSession(serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
-        } catch (JSchException e) {
-            throw new SSHApiException("An exception occurred while creating SSH session." +
-                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        java.util.Properties config = this.configReader.getProperties();
-        session.setConfig(config);
-
-        // Not a good way, but we dont have any choice
-        if (session instanceof ExtendedSession) {
-            ((ExtendedSession) session).setAuthenticationInfo(authenticationInfo);
-        }
-
-        try {
-            session.connect();
-        } catch (JSchException e) {
-            throw new SSHApiException("An exception occurred while connecting to server." +
-                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        boolean ptimestamp = true;
-
-        // exec 'scp -t rfile' remotely
-        String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + rFile;
-        Channel channel = session.openChannel("exec");
-
-        StandardOutReader stdOutReader = new StandardOutReader();
-        ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-        ((ChannelExec) channel).setCommand(command);
-
-        // get I/O streams for remote scp
-        OutputStream out = channel.getOutputStream();
-        InputStream in = channel.getInputStream();
-
-        channel.connect();
-
-        if (checkAck(in) != 0) {
-            String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-        }
-
-        File _lfile = new File(lFile);
-
-        if (ptimestamp) {
-            command = "T" + (_lfile.lastModified() / 1000) + " 0";
-            // The access time should be sent here,
-            // but it is not accessible with JavaAPI ;-<
-            command += (" " + (_lfile.lastModified() / 1000) + " 0\n");
-            out.write(command.getBytes());
-            out.flush();
-            if (checkAck(in) != 0) {
-                 String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-            }
-        }
-
-        // send "C0644 filesize filename", where filename should not include '/'
-        long filesize = _lfile.length();
-        command = "C0644 " + filesize + " ";
-        if (lFile.lastIndexOf('/') > 0) {
-            command += lFile.substring(lFile.lastIndexOf('/') + 1);
-        } else {
-            command += lFile;
-        }
-        command += "\n";
-        out.write(command.getBytes());
-        out.flush();
-        if (checkAck(in) != 0) {
-            String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-        }
-
-        // send a content of lFile
-        fis = new FileInputStream(lFile);
-        byte[] buf = new byte[1024];
-        while (true) {
-            int len = fis.read(buf, 0, buf.length);
-            if (len <= 0) break;
-            out.write(buf, 0, len); //out.flush();
-        }
-        fis.close();
-        fis = null;
-        // send '\0'
-        buf[0] = 0;
-        out.write(buf, 0, 1);
-        out.flush();
-        if (checkAck(in) != 0) {
-             String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-        }
-        out.close();
-
-        stdOutReader.onOutput(channel);
-
-
-        if (stdOutReader.getStdErrorString().contains("scp:")) {
-            throw new SSHApiException(stdOutReader.getStdErrorString());
-        }
-        channel.disconnect();
-    }
-
-    /**
-     * This will copy a local file to a remote location
-     *
-     * @param remoteFile remote location you want to transfer the file, this cannot be a directory, if user pass
-     *                   a dirctory we do copy it to that directory but we simply return the directory name
-     *                   todo handle the directory name as input and return the proper final output file name
-     * @param localFile  Local file to transfer, this can be a directory
-     * @param session
-     * @return returns the final remote file path, so that users can use the new file location
-     * @throws IOException
-     * @throws JSchException
-     * @throws SSHApiException
-     */
-    public static String scpTo(String remoteFile, String localFile, Session session) throws IOException, JSchException, SSHApiException {
-        FileInputStream fis = null;
-        String prefix = null;
-        if (new File(localFile).isDirectory()) {
-            prefix = localFile + File.separator;
-        }
-        boolean ptimestamp = true;
-
-        // exec 'scp -t rfile' remotely
-        String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + remoteFile;
-        Channel channel = session.openChannel("exec");
-
-        StandardOutReader stdOutReader = new StandardOutReader();
-        ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-        ((ChannelExec) channel).setCommand(command);
-
-        // get I/O streams for remote scp
-        OutputStream out = channel.getOutputStream();
-        InputStream in = channel.getInputStream();
-
-        channel.connect();
-
-        if (checkAck(in) != 0) {
-             String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-        }
-
-        File _lfile = new File(localFile);
-
-        if (ptimestamp) {
-            command = "T" + (_lfile.lastModified() / 1000) + " 0";
-            // The access time should be sent here,
-            // but it is not accessible with JavaAPI ;-<
-            command += (" " + (_lfile.lastModified() / 1000) + " 0\n");
-            out.write(command.getBytes());
-            out.flush();
-            if (checkAck(in) != 0) {
-                 String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-            }
-        }
-
-        // send "C0644 filesize filename", where filename should not include '/'
-        long filesize = _lfile.length();
-        command = "C0644 " + filesize + " ";
-        if (localFile.lastIndexOf('/') > 0) {
-            command += localFile.substring(localFile.lastIndexOf('/') + 1);
-        } else {
-            command += localFile;
-        }
-        command += "\n";
-        out.write(command.getBytes());
-        out.flush();
-        if (checkAck(in) != 0) {
-            String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-        }
-
-        // send a content of lFile
-        fis = new FileInputStream(localFile);
-        byte[] buf = new byte[1024];
-        while (true) {
-            int len = fis.read(buf, 0, buf.length);
-            if (len <= 0) break;
-            out.write(buf, 0, len); //out.flush();
-        }
-        fis.close();
-        fis = null;
-        // send '\0'
-        buf[0] = 0;
-        out.write(buf, 0, 1);
-        out.flush();
-        if (checkAck(in) != 0) {
-            String error = "Error Reading input Stream";
-            log.error(error);
-            throw new SSHApiException(error);
-        }
-        out.close();
-        stdOutReader.onOutput(channel);
-
-
-        channel.disconnect();
-        if (stdOutReader.getStdErrorString().contains("scp:")) {
-            throw new SSHApiException(stdOutReader.getStdErrorString());
-        }
-        //since remote file is always a file  we just return the file
-        return remoteFile;
-    }
-
-    /**
-     * This method will copy a remote file to a local directory
-     *
-     * @param remoteFile remote file path, this has to be a full qualified path
-     * @param localFile  This is the local file to copy, this can be a directory too
-     * @param session
-     * @return returns the final local file path of the new file came from the remote resource
-     */
-    public static void scpFrom(String remoteFile, String localFile, Session session) throws IOException, JSchException, SSHApiException {
-        FileOutputStream fos = null;
-        try {
-            String prefix = null;
-            if (new File(localFile).isDirectory()) {
-                prefix = localFile + File.separator;
-            }
-
-            // exec 'scp -f remotefile' remotely
-            String command = "scp -f " + remoteFile;
-            Channel channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-
-            StandardOutReader stdOutReader = new StandardOutReader();
-            ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-            // get I/O streams for remote scp
-            OutputStream out = channel.getOutputStream();
-            InputStream in = channel.getInputStream();
-
-            channel.connect();
-
-            byte[] buf = new byte[1024];
-
-            // send '\0'
-            buf[0] = 0;
-            out.write(buf, 0, 1);
-            out.flush();
-
-            while (true) {
-                int c = checkAck(in);
-                if (c != 'C') {
-                    break;
-                }
-
-                // read '0644 '
-                in.read(buf, 0, 5);
-
-                long filesize = 0L;
-                while (true) {
-                    if (in.read(buf, 0, 1) < 0) {
-                        // error
-                        break;
-                    }
-                    if (buf[0] == ' ') break;
-                    filesize = filesize * 10L + (long) (buf[0] - '0');
-                }
-
-                String file = null;
-                for (int i = 0; ; i++) {
-                    in.read(buf, i, 1);
-                    if (buf[i] == (byte) 0x0a) {
-                        file = new String(buf, 0, i);
-                        break;
-                    }
-                }
-
-                //System.out.println("filesize="+filesize+", file="+file);
-
-                // send '\0'
-                buf[0] = 0;
-                out.write(buf, 0, 1);
-                out.flush();
-
-                // read a content of lfile
-                fos = new FileOutputStream(prefix == null ? localFile : prefix + file);
-                int foo;
-                while (true) {
-                    if (buf.length < filesize) foo = buf.length;
-                    else foo = (int) filesize;
-                    foo = in.read(buf, 0, foo);
-                    if (foo < 0) {
-                        // error
-                        break;
-                    }
-                    fos.write(buf, 0, foo);
-                    filesize -= foo;
-                    if (filesize == 0L) break;
-                }
-                fos.close();
-                fos = null;
-
-                if (checkAck(in) != 0) {
-                    String error = "Error transfering the file content";
-                    log.error(error);
-                    throw new SSHApiException(error);
-                }
-
-                // send '\0'
-                buf[0] = 0;
-                out.write(buf, 0, 1);
-                out.flush();
-            }
-            stdOutReader.onOutput(channel);
-            if (stdOutReader.getStdErrorString().contains("scp:")) {
-            throw new SSHApiException(stdOutReader.getStdErrorString());
-        }
-
-        } catch (Exception e) {
-            log.error(e.getMessage(), e);
-        } finally {
-            try {
-                if (fos != null) fos.close();
-            } catch (Exception ee) {
-            }
-        }
-    }
-
-    /**
-     * This method will copy a remote file to a local directory
-     *
-     * @param remoteFile remote file path, this has to be a full qualified path
-     * @param localFile  This is the local file to copy, this can be a directory too
-     */
-    public void scpFrom(String remoteFile, String localFile) throws SSHApiException {
-        JSch jsch = new JSch();
-
-        log.debug("Connecting to server - " + serverInfo.getHost() + ":" + serverInfo.getPort() + " with user name - "
-                + serverInfo.getUserName());
-
-        Session session = null;
-
-        try {
-            session = jsch.getSession(serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
-        } catch (JSchException e) {
-            throw new SSHApiException("An exception occurred while creating SSH session." +
-                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        java.util.Properties config = this.configReader.getProperties();
-        session.setConfig(config);
-
-        // Not a good way, but we dont have any choice
-        if (session instanceof ExtendedSession) {
-            ((ExtendedSession) session).setAuthenticationInfo(authenticationInfo);
-        }
-
-        try {
-            session.connect();
-        } catch (JSchException e) {
-            throw new SSHApiException("An exception occurred while connecting to server." +
-                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        FileOutputStream fos = null;
-        try {
-            String prefix = null;
-            if (new File(localFile).isDirectory()) {
-                prefix = localFile + File.separator;
-            }
-
-            // exec 'scp -f remotefile' remotely
-            StandardOutReader stdOutReader = new StandardOutReader();
-            String command = "scp -f " + remoteFile;
-            Channel channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-            ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-            // get I/O streams for remote scp
-            OutputStream out = channel.getOutputStream();
-            InputStream in = channel.getInputStream();
-
-            channel.connect();
-
-            byte[] buf = new byte[1024];
-
-            // send '\0'
-            buf[0] = 0;
-            out.write(buf, 0, 1);
-            out.flush();
-
-            while (true) {
-                int c = checkAck(in);
-                if (c != 'C') {
-                    break;
-                }
-
-                // read '0644 '
-                in.read(buf, 0, 5);
-
-                long filesize = 0L;
-                while (true) {
-                    if (in.read(buf, 0, 1) < 0) {
-                        // error
-                        break;
-                    }
-                    if (buf[0] == ' ') break;
-                    filesize = filesize * 10L + (long) (buf[0] - '0');
-                }
-
-                String file = null;
-                for (int i = 0; ; i++) {
-                    in.read(buf, i, 1);
-                    if (buf[i] == (byte) 0x0a) {
-                        file = new String(buf, 0, i);
-                        break;
-                    }
-                }
-
-                //System.out.println("filesize="+filesize+", file="+file);
-
-                // send '\0'
-                buf[0] = 0;
-                out.write(buf, 0, 1);
-                out.flush();
-
-                // read a content of lfile
-                fos = new FileOutputStream(prefix == null ? localFile : prefix + file);
-                int foo;
-                while (true) {
-                    if (buf.length < filesize) foo = buf.length;
-                    else foo = (int) filesize;
-                    foo = in.read(buf, 0, foo);
-                    if (foo < 0) {
-                        // error
-                        break;
-                    }
-                    fos.write(buf, 0, foo);
-                    filesize -= foo;
-                    if (filesize == 0L) break;
-                }
-                fos.close();
-                fos = null;
-
-                if (checkAck(in) != 0) {
-                    String error = "Error transfering the file content";
-                    log.error(error);
-                    throw new SSHApiException(error);
-                }
-
-                // send '\0'
-                buf[0] = 0;
-                out.write(buf, 0, 1);
-                out.flush();
-            }
-
-//            session.disconnect();
-
-            stdOutReader.onOutput(channel);
-            if (stdOutReader.getStdErrorString().contains("scp:")) {
-                throw new SSHApiException(stdOutReader.getStdErrorString());
-            }
-        } catch (Exception e) {
-            log.error(e.getMessage(), e);
-        } finally {
-            try {
-                if (fos != null) fos.close();
-            } catch (Exception ee) {
-            }
-        }
-    }
-
-    /**
-     * This method will copy a remote file to a local directory
-     *
-     * @param remoteFile remote file path, this has to be a full qualified path
-     * @param localFile  This is the local file to copy, this can be a directory too
-     * @param session
-     * @return returns the final local file path of the new file came from the remote resource
-     */
-    public static void scpThirdParty(String remoteFileSource, String remoteFileTarget, Session session) throws IOException, JSchException, SSHApiException {
-        FileOutputStream fos = null;
-        try {
-            String prefix = null;
-         
-            // exec 'scp -f remotefile' remotely
-            String command = "scp -3 " + remoteFileSource + " " + remoteFileTarget;
-            Channel channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-
-            StandardOutReader stdOutReader = new StandardOutReader();
-            ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-            // get I/O streams for remote scp
-            OutputStream out = channel.getOutputStream();
-            InputStream in = channel.getInputStream();
-
-            channel.connect();
-
-            byte[] buf = new byte[1024];
-
-            // send '\0'
-            buf[0] = 0;
-            out.write(buf, 0, 1);
-            out.flush();
-
-            while (true) {
-                int c = checkAck(in);
-                if (c != 'C') {
-                    break;
-                }
-
-                // read '0644 '
-                in.read(buf, 0, 5);
-
-                long filesize = 0L;
-                while (true) {
-                    if (in.read(buf, 0, 1) < 0) {
-                        // error
-                        break;
-                    }
-                    if (buf[0] == ' ') break;
-                    filesize = filesize * 10L + (long) (buf[0] - '0');
-                }
-                int foo;
-                while (true) {
-                	   if (buf.length < filesize) foo = buf.length;
-                       else foo = (int) filesize;
-                    
-                    int len = in.read(buf, 0, foo);
-                    if (len <= 0) break;
-                    out.write(buf, 0, len); 
-                }
-             // send '\0'
-                buf[0] = 0;
-                out.write(buf, 0, 1);
-                out.flush();
-                if (checkAck(in) != 0) {
-                    String error = "Error transfering the file content";
-                    log.error(error);
-                    throw new SSHApiException(error);
-                }
-
-            }
-            out.close();
-
-            stdOutReader.onOutput(channel);
-            if (stdOutReader.getStdErrorString().contains("scp:")) {
-            throw new SSHApiException(stdOutReader.getStdErrorString());
-        }
-
-        } catch (Exception e) {
-            log.error(e.getMessage(), e);
-        } finally {
-            try {
-                if (fos != null) fos.close();
-            } catch (Exception ee) {
-            }
-        }
-    }
-
-    public static void makeDirectory(String path, Session session) throws IOException, JSchException, SSHApiException {
-
-        // exec 'scp -t rfile' remotely
-        String command = "mkdir -p " + path;
-        Channel channel = session.openChannel("exec");
-        StandardOutReader stdOutReader = new StandardOutReader();
-
-        ((ChannelExec) channel).setCommand(command);
-
-
-        ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-        try {
-            channel.connect();
-        } catch (JSchException e) {
-
-            channel.disconnect();
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to retrieve command output. Command - " + command +
-                    " on server - " + session.getHost() + ":" + session.getPort() +
-                    " connecting user name - "
-                    + session.getUserName(), e);
-        }
-        stdOutReader.onOutput(channel);
-        if (stdOutReader.getStdErrorString().contains("mkdir:")) {
-            throw new SSHApiException(stdOutReader.getStdErrorString());
-        }
-
-        channel.disconnect();
-    }
-
-    public static List<String> listDirectory(String path, Session session) throws IOException, JSchException, SSHApiException {
-
-        // exec 'scp -t rfile' remotely
-        String command = "ls " + path;
-        Channel channel = session.openChannel("exec");
-        StandardOutReader stdOutReader = new StandardOutReader();
-
-        ((ChannelExec) channel).setCommand(command);
-
-
-        ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
-        try {
-            channel.connect();
-        } catch (JSchException e) {
-
-            channel.disconnect();
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to retrieve command output. Command - " + command +
-                    " on server - " + session.getHost() + ":" + session.getPort() +
-                    " connecting user name - "
-                    + session.getUserName(), e);
-        }
-        stdOutReader.onOutput(channel);
-        stdOutReader.getStdOutputString();
-        if (stdOutReader.getStdErrorString().contains("ls:")) {
-            throw new SSHApiException(stdOutReader.getStdErrorString());
-        }
-        channel.disconnect();
-        return Arrays.asList(stdOutReader.getStdOutputString().split("\n"));
-    }
-
-    static int checkAck(InputStream in) throws IOException {
-        int b = in.read();
-        if (b == 0) return b;
-        if (b == -1) return b;
-
-        if (b == 1 || b == 2) {
-            StringBuffer sb = new StringBuffer();
-            int c;
-            do {
-                c = in.read();
-                sb.append((char) c);
-            }
-            while (c != '\n');
-            if (b == 1) { // error
-                System.out.print(sb.toString());
-            }
-            if (b == 2) { // fatal error
-                System.out.print(sb.toString());
-            }
-        }
-        return b;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/resources/LSFTemplate.xslt
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/LSFTemplate.xslt b/tools/gsissh/src/main/resources/LSFTemplate.xslt
deleted file mode 100644
index c548d8e..0000000
--- a/tools/gsissh/src/main/resources/LSFTemplate.xslt
+++ /dev/null
@@ -1,93 +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 (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. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"  xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-    <xsl:output method="text" />
-    <xsl:template match="/ns:JobDescriptor">
-        <xsl:param name="quote">"</xsl:param>
-#! /bin/bash
-# LSF batch job submission script generated by Apache Airavata
-#
-        <xsl:choose>
-            <xsl:when test="ns:shellName">
-#BSUB -L <xsl:value-of select="ns:shellName"/>
-            </xsl:when></xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:queueName">
-#BSUB -q <xsl:value-of select="ns:queueName"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:nodes">
-#BSUB -n <xsl:value-of select="ns:nodes"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:mailAddress">
-#BSUB -u <xsl:value-of select="ns:mailAddress"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:jobName">
-#BSUB -J <xsl:value-of select="ns:jobName"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:acountString">
-#BSUB -P <xsl:value-of select="ns:acountString"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:maxWallTime">
-#BSUB -W <xsl:value-of select="ns:maxWallTime"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:standardOutFile">
-#BSUB -o "<xsl:value-of select="ns:standardOutFile"/>"
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:standardOutFile">
-#BSUB -e "<xsl:value-of select="ns:standardErrorFile"/>"
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:chassisName">
-#BSUB -m c<xsl:value-of select="ns:chassisName"/>
-            </xsl:when>
-        </xsl:choose>
-        <xsl:choose>
-            <xsl:when test="ns:usedMem">
-#BSUB -R rusage[mem=<xsl:value-of select="ns:usedMem"/>]
-            </xsl:when>
-        </xsl:choose>
-
-        <xsl:text>&#xa;</xsl:text>
-
-        <xsl:text>&#xa;</xsl:text>
-        <xsl:for-each select="ns:moduleLoadCommands/ns:command">
-            <xsl:text>&#xa;</xsl:text>
-            <xsl:value-of select="."/><xsl:text>   </xsl:text>
-        </xsl:for-each>
-        <xsl:text>&#xa;</xsl:text>
-cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
-        <xsl:for-each select="ns:preJobCommands/ns:command">
-            <xsl:value-of select="."/><xsl:text>   </xsl:text>
-            <xsl:text>&#xa;</xsl:text>
-        </xsl:for-each>
-        <xsl:text>&#xa;</xsl:text>
-        <xsl:choose><xsl:when test="ns:jobSubmitterCommand != ''">
-            <xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text>
-        </xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text>   </xsl:text>
-        <xsl:for-each select="ns:inputs/ns:input">
-            <xsl:value-of select="."/><xsl:text>   </xsl:text>
-        </xsl:for-each>
-        <xsl:text>&#xa;</xsl:text>
-    </xsl:template>
-
-</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/resources/PBSTemplate.xslt
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/PBSTemplate.xslt b/tools/gsissh/src/main/resources/PBSTemplate.xslt
deleted file mode 100644
index 73c5eb6..0000000
--- a/tools/gsissh/src/main/resources/PBSTemplate.xslt
+++ /dev/null
@@ -1,82 +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 (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. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-<xsl:output method="text" />
-<xsl:template match="/ns:JobDescriptor">
-#! /bin/sh
-#   <xsl:choose>
-    <xsl:when test="ns:shellName">
-##PBS -S <xsl:value-of select="ns:shellName"/>
-    </xsl:when></xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:queueName">
-#PBS -q <xsl:value-of select="ns:queueName"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:mailOptions">
-#PBS -m <xsl:value-of select="ns:mailOptions"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-<xsl:when test="ns:acountString">
-#PBS -A <xsl:value-of select="ns:acountString"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:maxWallTime">
-#PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:jobName">
-#PBS -N <xsl:value-of select="ns:jobName"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#PBS -o <xsl:value-of select="ns:standardOutFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#PBS -e <xsl:value-of select="ns:standardErrorFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:usedMem">
-#PBS -l mem=<xsl:value-of select="ns:usedMem"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
-#PBS -l nodes=<xsl:value-of select="ns:nodes"/>:ppn=<xsl:value-of select="ns:processesPerNode"/>
-<xsl:text>&#xa;</xsl:text>
-    </xsl:when>
-    </xsl:choose>
-<xsl:for-each select="ns:exports/ns:name">
-<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>&#xa;</xsl:text>
-export<xsl:text>   </xsl:text><xsl:value-of select="."/>
-<xsl:text>&#xa;</xsl:text>
-</xsl:for-each>
-<xsl:for-each select="ns:preJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
-    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text>   </xsl:text>
-<xsl:for-each select="ns:inputs/ns:input">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-<xsl:for-each select="ns:postJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-</xsl:for-each>
-
-</xsl:template>
-
-</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/resources/SLURMTemplate.xslt
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/SLURMTemplate.xslt b/tools/gsissh/src/main/resources/SLURMTemplate.xslt
deleted file mode 100644
index 4a62722..0000000
--- a/tools/gsissh/src/main/resources/SLURMTemplate.xslt
+++ /dev/null
@@ -1,78 +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 (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. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-<xsl:output method="text" />
-<xsl:template match="/ns:JobDescriptor">
-<xsl:choose>
-<xsl:when test="ns:shellName">
-#!<xsl:value-of select="ns:shellName"/>
-    </xsl:when>
-    </xsl:choose>
-<xsl:choose>
-    <xsl:when test="ns:queueName">
-#SBATCH -p <xsl:value-of select="ns:queueName"/>
-    </xsl:when>
-    </xsl:choose>
-<xsl:choose>
-    <xsl:when test="ns:nodes">
-#SBATCH -N <xsl:value-of select="ns:nodes"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:cpuCount">
-#SBATCH -n <xsl:value-of select="ns:cpuCount"/>
-        </xsl:when>
-        </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:mailAddress">
-#SBATCH -mail-user=<xsl:value-of select="ns:mailAddress"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:mailType">
-#SBATCH -mail-type=<xsl:value-of select="ns:mailType"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-<xsl:when test="ns:acountString">
-#SBATCH -A <xsl:value-of select="ns:acountString"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:maxWallTime">
-#SBATCH -t <xsl:value-of select="ns:maxWallTime"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:jobName">
-#SBATCH -J <xsl:value-of select="ns:jobName"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#SBATCH -o <xsl:value-of select="ns:standardOutFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#SBATCH -e <xsl:value-of select="ns:standardErrorFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:for-each select="ns:preJobCommands/ns:command">
-        <xsl:text>&#xa;</xsl:text>
-        <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
-    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text>   </xsl:text>
-<xsl:for-each select="ns:inputs/ns:input">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-</xsl:template>
-
-</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/resources/UGETemplate.xslt
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/UGETemplate.xslt b/tools/gsissh/src/main/resources/UGETemplate.xslt
deleted file mode 100644
index 5b57265..0000000
--- a/tools/gsissh/src/main/resources/UGETemplate.xslt
+++ /dev/null
@@ -1,74 +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 (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. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-<xsl:output method="text" />
-<xsl:template match="/ns:JobDescriptor">
-#! /bin/bash
-# Grid Engine batch job script built by Apache Airavata
-#   <xsl:choose>
-    <xsl:when test="ns:shellName">
-#$ -S <xsl:value-of select="ns:shellName"/>
-    </xsl:when></xsl:choose>
-#$ -V
-    <xsl:choose>
-    <xsl:when test="ns:queueName">
-#$ -q <xsl:value-of select="ns:queueName"/>
-    </xsl:when>
-    </xsl:choose>
-#$ -m beas <xsl:choose>
-<xsl:when test="ns:acountString">
-#$ -A <xsl:value-of select="ns:acountString"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:maxWallTime">
-#$ -l h_rt=<xsl:value-of select="ns:maxWallTime"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:jobName">
-#$ -N <xsl:value-of select="ns:jobName"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#$ -o <xsl:value-of select="ns:standardOutFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#$ -e <xsl:value-of select="ns:standardErrorFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
-#$ -pe <xsl:value-of select="ns:processesPerNode"/>way <xsl:value-of select="12 * ns:nodes"/>
-<xsl:text>&#xa;</xsl:text>
-    </xsl:when>
-    </xsl:choose>
-<xsl:for-each select="ns:exports/ns:name">
-<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>&#xa;</xsl:text>
-export<xsl:text>   </xsl:text><xsl:value-of select="."/>
-<xsl:text>&#xa;</xsl:text>
-</xsl:for-each>
-<xsl:for-each select="ns:preJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
-    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text>   </xsl:text>
-<xsl:for-each select="ns:inputs/ns:input">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-<xsl:for-each select="ns:postJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-</xsl:for-each>
-
-</xsl:template>
-
-</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd b/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd
deleted file mode 100644
index d5c5992..0000000
--- a/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd
+++ /dev/null
@@ -1,114 +0,0 @@
-<?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. -->
-
-<schema targetNamespace="http://airavata.apache.org/gsi/ssh/2012/12" xmlns:gsissh="http://airavata.apache.org/gsi/ssh/2012/12"
-	xmlns="http://www.w3.org/2001/XMLSchema" xmlns:xsd="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified">
-
-	<element name="JobDescriptor" type="gsissh:pbsParams" />
-
-	<complexType name="pbsParams">
-		<sequence>
-            <element name="jobID" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="userName" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-			<element name="shellName" type="xsd:string" minOccurs="0" maxOccurs="1" default="/bin/bash"/>
-            <element name="queueName" type="xsd:string" minOccurs="0" maxOccurs="1" default="normal"/>
-            <element name="jobName" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="allEnvExport" type="xsd:boolean" minOccurs="0 " maxOccurs="1" default="true"/>
-			<element name="mailOptions" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="mailAddress" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="partition" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="mailType" type="xsd:string" minOccurs="0" maxOccurs="1" />
-			<element name="acountString" type="xsd:string" minOccurs="0" maxOccurs="1" />
-			<element name="maxWallTime" type="xsd:string" minOccurs="0" maxOccurs="1" default="1:00:00"/>
-            <element name="standardOutFile" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="standardErrorFile" type="xsd:string" minOccurs="0" maxOccurs="1" />
-			<element name="outputDirectory" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="inputDirectory" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="nodes" type="xsd:int" minOccurs="0" maxOccurs="1" default="1"/>
-            <element name="processesPerNode" type="xsd:int" minOccurs="0" maxOccurs="1" default="1" />
-            <element name="cpuCount" type="xsd:int" minOccurs="0" maxOccurs="1" default="1" />
-            <element name="nodeList" type="xsd:string" minOccurs="0" maxOccurs="1" default="1" />
-            <element name="workingDirectory" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="executablePath" type="xsd:string" minOccurs="0" maxOccurs="1" />
-            <element name="inputs" type="gsissh:inputList" minOccurs="1" maxOccurs="1"/>
-            <element name="exports" type="gsissh:exportProperties" minOccurs="1" maxOccurs="1"/>
-            <element name="status" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="afterAny" type="gsissh:afterAnyList" minOccurs="0" maxOccurs="1"/>
-            <element name="afterOKList" type="gsissh:afterOKList" minOccurs="0" maxOccurs="1"/>
-            <element name="cTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="qTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="mTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="sTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="compTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="owner" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="executeNode" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="ellapsedTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="usedCPUTime" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="usedMem" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="submitArgs" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="variableList" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="preJobCommands" type="gsissh:preJobCommands" minOccurs="0" maxOccurs="1"/>
-            <element name="moduleLoadCommands" type="gsissh:moduleLoadCommands" minOccurs="0" maxOccurs="1"/>
-            <element name="postJobCommands" type="gsissh:postJobCommands" minOccurs="0" maxOccurs="1"/>
-            <element name="jobSubmitterCommand" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="callBackIp" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="callBackPort" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-            <element name="chassisName" type="xsd:string" minOccurs="0" maxOccurs="1"/>
-        </sequence>
-	</complexType>
-
-    <complexType name="moduleLoadCommands">
-        <sequence>
-			<element name="command" type="xsd:string" minOccurs="0" maxOccurs="unbounded" />
-		</sequence>
-    </complexType>
-    <complexType name="preJobCommands">
-        <sequence>
-			<element name="command" type="xsd:string" minOccurs="0" maxOccurs="unbounded" />
-		</sequence>
-    </complexType>
-
-    <complexType name="postJobCommands">
-        <sequence>
-			<element name="command" type="xsd:string" minOccurs="0" maxOccurs="unbounded" />
-		</sequence>
-    </complexType>
-    <complexType name="inputList">
-        <sequence>
-			<element name="input" type="xsd:string" minOccurs="0" maxOccurs="unbounded" />
-		</sequence>
-    </complexType>
-    <complexType name="afterAnyList">
-        <sequence>
-			<element name="afterAny" type="xsd:string" minOccurs="0" maxOccurs="unbounded" />
-		</sequence>
-    </complexType>
-
-    <complexType name="afterOKList">
-        <sequence>
-			<element name="afterOKList" type="xsd:string" minOccurs="0" maxOccurs="unbounded" />
-		</sequence>
-    </complexType>
-
-    <complexType name="exportProperties">
-		<sequence>
-
-			<element name="name" minOccurs="1" maxOccurs="unbounded">
-				<complexType>
-					<simpleContent>
-						<extension base="xsd:string">
-							<attribute name="value" type="xsd:string" use="required" />
-						</extension>
-					</simpleContent>
-				</complexType>
-			</element>
-
-		</sequence>
-	</complexType>
-</schema>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/resources/schemas/gsissh-schemas.xsdconfig
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/schemas/gsissh-schemas.xsdconfig b/tools/gsissh/src/main/resources/schemas/gsissh-schemas.xsdconfig
deleted file mode 100644
index a46cadc..0000000
--- a/tools/gsissh/src/main/resources/schemas/gsissh-schemas.xsdconfig
+++ /dev/null
@@ -1,14 +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 (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. -->
-
-<xb:config  xmlns:xb="http://www.bea.com/2002/09/xbean/config">
-
-    <xb:namespace uri="http://airavata.apache.org/schemas/gsi/ssh/2012/12">
-        <xb:package>org.apache.airavata.gfac.ssh</xb:package>
-    </xb:namespace>
-</xb:config>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/config/ConfigReaderTest.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/config/ConfigReaderTest.java b/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/config/ConfigReaderTest.java
deleted file mode 100644
index a90dcba..0000000
--- a/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/config/ConfigReaderTest.java
+++ /dev/null
@@ -1,37 +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.ssh.config;
-
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-public class ConfigReaderTest {
-
-    @Test
-    public void testGetConfiguration() throws Exception {
-
-        System.out.println("Test case name " + this.getClass().getName());
-        ConfigReader configReader = new ConfigReader();
-        Assert.assertEquals(configReader.getConfiguration("StrictHostKeyChecking"), "no");
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
deleted file mode 100644
index 61a7437..0000000
--- a/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
+++ /dev/null
@@ -1,77 +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.ssh.impl;
-
-import org.apache.airavata.gfac.ssh.api.*;
-import org.apache.airavata.gfac.ssh.config.ConfigReader;
-import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPublicKeyAuthentication;
-import org.apache.commons.io.IOUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.*;
-
-public class DefaultSSHApiTestWithMyProxyAuth {
-    private static final Logger log = LoggerFactory.getLogger(PBSCluster.class);
-
-
-
-    public void tearDown() throws Exception {
-    }
-
-
-    public static void main(String[]ars) throws IOException {
-         String myProxyUserName = "lg11w";
-
-//        DefaultPasswordAuthenticationInfo authenticationInfo
-//                = new DefaultPasswordAuthenticationInfo("");
-        byte[] privateKey = IOUtils.toByteArray(new BufferedInputStream(new FileInputStream("/Users/lginnali/.ssh/id_dsa")));
-        byte[] publicKey = IOUtils.toByteArray(new BufferedInputStream(new FileInputStream("/Users/lginnali/.ssh/id_dsa.pub")));
-        DefaultPublicKeyAuthentication authenticationInfo = new DefaultPublicKeyAuthentication(privateKey,publicKey,"");
-
-        // Create command
-        CommandInfo commandInfo = new RawCommandInfo("source /etc/bashrc; bsub </home/lg11w/mywork/sshEchoExperiment_9d267072-ca65-4ca8-847a-cd3d130f6050/366787899.lsf");
-
-        // Server info
-        //Stampede
-//        ServerInfo serverInfo = new ServerInfo(myProxyUserName, "stampede.tacc.utexas.edu", 2222);
-        //Trestles
-//        ServerInfo serverInfo = new ServerInfo(myProxyUserName, "trestles.sdsc.xsede.org", 22);
-        
-        //Lonestar
-         ServerInfo serverInfo = new ServerInfo(myProxyUserName, "ghpcc06.umassrc.org", 22);
-        // Output
-        CommandOutput commandOutput = new SystemCommandOutput();
-
-        // Execute command
-        try {
-            CommandExecutor.executeCommand(commandInfo, serverInfo, authenticationInfo, commandOutput, new ConfigReader());
-        } catch (SSHApiException e) {
-            log.error(e.getMessage(), e);
-        } catch (IOException e) {
-            log.error(e.getMessage(), e);
-        }
-    }
-
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java
deleted file mode 100644
index 6f2840f..0000000
--- a/tools/gsissh/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.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.ssh.impl;
-
-import org.apache.airavata.gfac.ssh.api.*;
-import org.apache.airavata.gfac.ssh.api.authentication.AuthenticationInfo;
-import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
-import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
-import org.apache.airavata.gfac.ssh.util.CommonUtils;
-import org.testng.AssertJUnit;
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-public class VanilaTestWithSSHAuth {
-
-    private String userName;
-    private String password;
-    private String passPhrase;
-    private String hostName;
-    private String workingDirectory;
-    private String privateKeyPath;
-    private String publicKeyPath;
-    private String path;
-
-    @BeforeTest
-    public void setUp() throws Exception {
-        System.out.println("Test case name " + this.getClass().getName());
-        //Trestles
-        this.hostName = "trestles.sdsc.xsede.org";      
-        this.userName = "ogce";
-        this.path="/opt/torque/bin/";
-        //Stampede:
-//        this.hostName = "stampede.tacc.xsede.org";        
-//        this.userName = "ogce";
-//        this.path="/usr/bin";
-        //Lonestar:
-//         this.hostName = "lonestar.tacc.utexas.edu";        
-//         this.userName = "us3";
-//        this.path="/opt/sge6.2/bin/lx24-amd64";
-        //Alamo:
-//        this.hostName = "alamo.uthscsa.edu";        
-//        this.userName = "raminder";
-//        this.path="/opt/torque/bin/";
-        //Bigred:
-//        this.hostName = "bigred2.uits.iu.edu";        
-//        this.userName = "cgateway";
-//        this.path="/opt/torque/torque-5.0.1/bin/";
-        
-        System.setProperty("ssh.host",hostName);
-        System.setProperty("ssh.username", userName);
-        System.setProperty("private.ssh.key", "/home/lginnali/.ssh/id_dsa");
-        System.setProperty("public.ssh.key", "/home/lginnali/.ssh/id_dsa.pub");
-        System.setProperty("ssh.working.directory", "/tmp");
-
-        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");
-        
-        System.setProperty("ssh.keypass", "");
-        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.user=xxx -Dssh.password=yyy -Dssh.private.key.passphrase=zzz " +
-                    "-Dssh.private.key.path -Dssh.public.key.path -Dssh.working.directory ");
-        }
-    }
-
-
-    @Test
-    public void testSimplePBSJob() throws Exception {
-
-        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 = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));
-
-        String date = new Date().toString();
-        date = date.replaceAll(" ", "_");
-        date = date.replaceAll(":", "_");
-
-        String pomFile =  new File("").getAbsolutePath() + File.separator + "pom.xml";
-
-        workingDirectory = workingDirectory + File.separator
-                + date + "_" + UUID.randomUUID();
-        pbsCluster.makeDirectory(workingDirectory);
-        Thread.sleep(1000);
-        pbsCluster.makeDirectory(workingDirectory + File.separator + "inputs");
-        Thread.sleep(1000);
-        pbsCluster.makeDirectory(workingDirectory + File.separator + "outputs");
-
-
-        // doing file transfer to the remote resource
-        String remoteLocation = workingDirectory + File.separator + "inputs";
-        pbsCluster.scpTo(remoteLocation, pomFile);
-
-        int i = pomFile.lastIndexOf(File.separator);
-        String fileName = pomFile.substring(i + 1);
-        // constructing the job object
-        JobDescriptor jobDescriptor = new JobDescriptor();
-        jobDescriptor.setWorkingDirectory(workingDirectory);
-        jobDescriptor.setShellName("/bin/bash");
-        jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
-        jobDescriptor.setExecutablePath("/bin/echo");
-        jobDescriptor.setAllEnvExport(true);
-        jobDescriptor.setMailOptions("n");
-        jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
-        jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
-        jobDescriptor.setNodes(1);
-        jobDescriptor.setProcessesPerNode(1);
-        jobDescriptor.setQueueName("normal");
-        jobDescriptor.setMaxWallTime("5");
-        //jobDescriptor.setJobSubmitter("aprun -n 1");
-        List<String> inputs = new ArrayList<String>();
-        inputs.add(remoteLocation + File.separator + fileName);
-        jobDescriptor.setInputValues(inputs);
-        //finished construction of job object
-        System.out.println(jobDescriptor.toXML());
-        if(hostName.contains("trestles")){
-        String jobID = pbsCluster.submitBatchJob(jobDescriptor);
-        System.out.println("JobID returned : " + jobID);
-
-//        Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
-        Thread.sleep(1000);
-        JobDescriptor jobById = pbsCluster.getJobDescriptorById(jobID);
-
-        //printing job data got from previous call
-        AssertJUnit.assertEquals(jobById.getJobId(), jobID);
-        System.out.println(jobById.getAcountString());
-        System.out.println(jobById.getAllEnvExport());
-        System.out.println(jobById.getCompTime());
-        System.out.println(jobById.getExecutablePath());
-        System.out.println(jobById.getEllapsedTime());
-        System.out.println(jobById.getQueueName());
-        System.out.println(jobById.getExecuteNode());
-        System.out.println(jobById.getJobName());
-        System.out.println(jobById.getCTime());
-        System.out.println(jobById.getSTime());
-        System.out.println(jobById.getMTime());
-        System.out.println(jobById.getCompTime());
-        System.out.println(jobById.getOwner());
-        System.out.println(jobById.getQTime());
-        System.out.println(jobById.getUsedCPUTime());
-        System.out.println(jobById.getUsedMemory());
-        System.out.println(jobById.getVariableList());
-        }
-    }
-
-    @Test
-    public void testSimpleLSFJob() throws Exception {
-
-        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);
-
-
-        // constructing the job object
-        JobDescriptor jobDescriptor = new JobDescriptor();
-        jobDescriptor.setWorkingDirectory(workingDirectory);
-        jobDescriptor.setShellName("/bin/bash");
-        jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
-        jobDescriptor.setExecutablePath("/bin/echo");
-        jobDescriptor.setAllEnvExport(true);
-        jobDescriptor.setMailOptions("n");
-        jobDescriptor.setMailAddress("test@gmail.com");
-        jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
-        jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
-        jobDescriptor.setNodes(1);
-        jobDescriptor.setProcessesPerNode(1);
-        jobDescriptor.setQueueName("long");
-        jobDescriptor.setMaxWallTimeForLSF("5");
-        jobDescriptor.setJobSubmitter("mpiexec");
-        jobDescriptor.setModuleLoadCommands(new String[]{"module load openmpi/1.6.5"});
-        jobDescriptor.setUsedMemory("1000");
-        jobDescriptor.setChassisName("01");
-
-        //jobDescriptor.setJobSubmitter("aprun -n 1");
-        List<String> inputs = new ArrayList<String>();
-        jobDescriptor.setInputValues(inputs);
-        //finished construction of job object
-        System.out.println(jobDescriptor.toXML());
-        Cluster pbsCluster = new PBSCluster(CommonUtils.getLSFJobManager(""));
-        ((PBSCluster) pbsCluster).generateJobScript(jobDescriptor);
-    }
-
-    @Test
-    public void testSCPFromAndSCPTo() throws Exception {
-
-        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 = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));
-        new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));;
-
-        String date = new Date().toString();
-        date = date.replaceAll(" ", "_");
-        date = date.replaceAll(":", "_");
-
-        String pomFile = (new File(".")).getAbsolutePath() + File.separator + "pom.xml";
-        File file = new File(pomFile);
-        if(!file.exists()){
-            file.createNewFile();
-        }
-        // Constructing theworking directory for demonstration and creating directories in the remote
-        // resource
-        workingDirectory = workingDirectory + File.separator
-                + date + "_" + UUID.randomUUID();
-        pbsCluster.makeDirectory(workingDirectory);
-        pbsCluster.scpTo(workingDirectory, pomFile);
-        Thread.sleep(1000);
-        pbsCluster.scpFrom(workingDirectory + File.separator + "pom.xml", (new File(".")).getAbsolutePath());
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/resources/gsissh.properties
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/resources/gsissh.properties b/tools/gsissh/src/test/resources/gsissh.properties
deleted file mode 100644
index 3fdf76d..0000000
--- a/tools/gsissh/src/test/resources/gsissh.properties
+++ /dev/null
@@ -1,26 +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.
-#
-
-###########################################################################
-# Specifies system level configurations as a key/value pairs.
-###########################################################################
-
-StrictHostKeyChecking=no
-ssh.session.timeout=360000

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/resources/log4j.properties
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/resources/log4j.properties b/tools/gsissh/src/test/resources/log4j.properties
deleted file mode 100644
index 257802c..0000000
--- a/tools/gsissh/src/test/resources/log4j.properties
+++ /dev/null
@@ -1,34 +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.
-#
-
-# Set root category priority to INFO and its only appender to CONSOLE.
-log4j.rootCategory=ALL, CONSOLE,LOGFILE
-log4j.rootLogger=ALL, CONSOLE, LOGFILE
-
-
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=[%p] %m%n
-
-# LOGFILE is set to be a File appender using a PatternLayout.
-log4j.appender.LOGFILE=org.apache.log4j.FileAppender
-log4j.appender.LOGFILE.File=./target/integration-tests.log
-log4j.appender.LOGFILE.Append=true
-log4j.appender.LOGFILE.layout=org.apache.log4j.PatternLayout
-log4j.appender.LOGFILE.layout.ConversionPattern=%d [%t] %-5p %c %x - %m%n

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/resources/sleep.pbs
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/resources/sleep.pbs b/tools/gsissh/src/test/resources/sleep.pbs
deleted file mode 100644
index 126e045..0000000
--- a/tools/gsissh/src/test/resources/sleep.pbs
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/bash
-#
-#
-# 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.
-#
-
-#$ -S /bin/bash
-#$ -V
-#$ -pe 1way 32
-#$ -m n
-#$ -q normal
-#$ -A
-#$ -l h_rt=0:60:00
-#$ -o application.stdout
-#$ -e application.stderr
-#PBS -N GSI_SSH_SLEEP_JOB
-/bin/sleep 60

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/test/resources/test.pbs
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/resources/test.pbs b/tools/gsissh/src/test/resources/test.pbs
deleted file mode 100644
index d18269b..0000000
--- a/tools/gsissh/src/test/resources/test.pbs
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/bash
-#
-#
-# 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.
-#
-
-#PBS -q normal
-#PBS -A sds128
-#PBS -l nodes=1:ppn=1
-#PBS -l walltime=00:00:01
-#PBS -o job_output
-#PBS -N GSI_SSH_JOB
-#PBS -V
-
-/bin/date


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