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From shame...@apache.org
Subject [4/6] airavata git commit: Removed gsissh module from tools
Date Fri, 05 Jun 2015 05:26:56 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java b/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java
deleted file mode 100644
index 0b91af8..0000000
--- a/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java
+++ /dev/null
@@ -1,247 +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 edu.illinois.ncsa.BCGSS;
-//
-////import edu.illinois.ncsa.bouncycastle.crypto.tls.*;
-////import edu.illinois.ncsa.bouncycastle.asn1.*;
-////import edu.illinois.ncsa.bouncycastle.asn1.x509.*;
-//import org.globus.common.CoGProperties;
-//import org.globus.gsi.CredentialException;
-//import org.globus.gsi.X509Credential;
-//import org.globus.gsi.X509ProxyCertPathParameters;
-//import org.globus.gsi.provider.GlobusProvider;
-//import org.globus.gsi.provider.KeyStoreParametersFactory;
-//import org.globus.gsi.stores.ResourceCertStoreParameters;
-//import org.globus.gsi.stores.ResourceSigningPolicyStore;
-//import org.globus.gsi.stores.ResourceSigningPolicyStoreParameters;
-//import org.globus.gsi.trustmanager.X509ProxyCertPathValidator;
-//import org.globus.gsi.util.CertificateUtil;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//
-//import javax.crypto.Cipher;
-//import java.io.ByteArrayInputStream;
-//import java.io.IOException;
-//import java.io.InputStream;
-//import java.security.KeyStore;
-//import java.security.PrivateKey;
-//import java.security.cert.CertStore;
-//import java.security.cert.CertificateException;
-//import java.security.cert.CertificateFactory;
-//import java.security.cert.X509Certificate;
-//
-//public class GlobusTlsClient extends DefaultTlsClient
-//{
-//    private Certificate clientCert = new Certificate(new X509CertificateStructure[0]);
-//    private PrivateKey clientPrivateKey = null;
-//    private X509Certificate[] peerCerts = null;
-//    private static final Logger logger = LoggerFactory.getLogger(GlobusTlsClient.class);
-//
-//    public X509Certificate[] getPeerCerts() {
-//        return peerCerts;
-//    }
-//
-//    public GlobusTlsClient(X509Credential cred, GlobusTlsCipherFactory factory)
-//            throws IOException, CertificateException, CredentialException {
-//        super(factory);
-//        if (cred == null) {
-//            throw new IllegalArgumentException("'cred' cannot be null");
-//        }
-//
-//        clientCert = new Certificate(
-//                X509CertArrayToStructArray(cred.getCertificateChain()));
-//        clientPrivateKey = cred.getPrivateKey();
-//
-//        if (clientCert.getCerts().length == 0) {
-//            throw new IllegalArgumentException(
-//                    "'cred' contains no certificates");
-//        }
-//
-//        if (clientPrivateKey == null) {
-//            throw new IllegalArgumentException("'clientPrivateKey' cannot be null");
-//        }
-//    }
-//
-//    public TlsAuthentication getAuthentication() throws IOException {
-//        return new GlobusTlsAuth();
-//    }
-//
-//    public int[] getCipherSuites() {
-//        return new int[] {
-//                CipherSuite.TLS_RSA_WITH_AES_256_CBC_SHA,
-//                CipherSuite.TLS_RSA_WITH_AES_128_CBC_SHA,
-//                CipherSuite.TLS_RSA_WITH_3DES_EDE_CBC_SHA,
-//        };
-//    }
-//
-//    public class GlobusTlsAuth implements TlsAuthentication {
-//
-//        /**
-//         * Validates the server's certificate
-//         * @param certificate received from server
-//         * @throws IOException
-//         */
-//        public void notifyServerCertificate(Certificate certificate)
-//                throws IOException {
-//            try {
-//            peerCerts = X509CertStructArrayToCertArray(certificate.getCerts());
-//
-//            String caCertsLocation =
-//                    "file:" + CoGProperties.getDefault().getCaCertLocations();
-//            String crlPattern = caCertsLocation + "/*.r*";
-//            String sigPolPattern = caCertsLocation + "/*.signing_policy";
-//
-//            KeyStore keyStore = KeyStore.getInstance(
-//                    GlobusProvider.KEYSTORE_TYPE, GlobusProvider.PROVIDER_NAME);
-//            CertStore crlStore = CertStore.getInstance(
-//                    GlobusProvider.CERTSTORE_TYPE,
-//                    new ResourceCertStoreParameters(null, crlPattern));
-//            ResourceSigningPolicyStore sigPolStore =
-//                    new ResourceSigningPolicyStore(
-//                            new ResourceSigningPolicyStoreParameters(
-//                                    sigPolPattern));
-//            keyStore.load(
-//                    KeyStoreParametersFactory.createTrustStoreParameters(
-//                            caCertsLocation));
-//            X509ProxyCertPathParameters parameters =
-//                    new X509ProxyCertPathParameters(keyStore, crlStore,
-//                            sigPolStore, false);
-//            X509ProxyCertPathValidator validator =
-//                    new X509ProxyCertPathValidator();
-//            if (validator.engineValidate(CertificateUtil.getCertPath(peerCerts),
-//                    parameters) == null) {
-//                throw new Exception("X509ProxyCertPathValidator did not return a result");
-//            }
-//            } catch (Exception e) {
-//                logger.error(e.getMessage(), e);
-//                throw new TlsFatalAlert(AlertDescription.user_canceled);
-//            }
-//        }
-//
-//        /**
-//         * Returns an object representing the client's credentials
-//         * @param request
-//         * @return the client's credentials
-//         * @throws IOException
-//         */
-//        public TlsCredentials getClientCredentials(CertificateRequest request)
-//                throws IOException {
-//            return new GlobusTlsCred();
-//        }
-//    }
-//
-//    public class GlobusTlsCred implements TlsSignerCredentials {
-//        /**
-//         * Encrypts a hash with the client's private key, producing a signature
-//         * @param md5andsha1 the hash to encrypt
-//         * @return an array of bytes containing the signature
-//         * @throws IOException
-//         */
-//        public byte[] generateCertificateSignature(byte[] md5andsha1)
-//                throws IOException {
-//            // encrypt the input hash with the private key to produce signature
-//            try {
-//                Cipher cipher = Cipher.getInstance(clientPrivateKey.getAlgorithm());
-//                cipher.init(Cipher.ENCRYPT_MODE, clientPrivateKey);
-//                return cipher.doFinal(md5andsha1);
-//            } catch (Exception e) {
-//                logger.error(e.getMessage(), e);
-//                throw new IOException(e);
-//            }
-//        }
-//
-//        public Certificate getCertificate() {
-//            return clientCert;
-//        }
-//    }
-//
-//       /**
-//     *
-//     * @param struct
-//     * @return
-//     * @throws CertificateException
-//     * @throws IOException
-//     */
-//    public static X509Certificate X509CertStructToCert(
-//            X509CertificateStructure struct) throws CertificateException,
-//            IOException {
-//        CertificateFactory cf = CertificateFactory.getInstance("X.509");
-//        InputStream is = new ByteArrayInputStream(struct.getEncoded());
-//        X509Certificate cert = (X509Certificate) cf.generateCertificate(is);
-//        is.close();
-//        return cert;
-//    }
-//
-//    /**
-//     *
-//     * @param structs
-//     * @return
-//     * @throws java.io.IOException
-//     * @throws java.security.cert.CertificateException
-//     */
-//    public static X509Certificate[] X509CertStructArrayToCertArray(
-//            X509CertificateStructure[] structs) throws IOException,
-//            CertificateException {
-//        X509Certificate[] certChain = new X509Certificate[structs.length];
-//
-//        for (int i = 0; i < structs.length; ++i) {
-//            certChain[i] = X509CertStructToCert(structs[i]);
-//        }
-//
-//        return certChain;
-//    }
-//
-//    /**
-//     *
-//     * @param c
-//     * @return
-//     * @throws CertificateException
-//     * @throws IOException
-//     */
-//    public static X509CertificateStructure X509CertToStruct(X509Certificate c)
-//            throws CertificateException, IOException {
-//        ASN1InputStream is = new ASN1InputStream(c.getEncoded());
-//        DERObject o = is.readObject();
-//        return X509CertificateStructure.getInstance(o);
-//    }
-//
-//
-//    /**
-//     *
-//     * @param certs
-//     * @return
-//     * @throws CertificateException
-//     * @throws IOException
-//     */
-//    public static X509CertificateStructure[] X509CertArrayToStructArray(
-//            X509Certificate[] certs) throws CertificateException, IOException {
-//        X509CertificateStructure[] structs =
-//                new X509CertificateStructure[certs.length];
-//
-//        for (int i = 0; i < certs.length; ++i) {
-//            structs[i] = X509CertToStruct(certs[i]);
-//        }
-//
-//        return structs;
-//    }
-//}
-//

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/TlsHandlerUtil.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/TlsHandlerUtil.java b/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/TlsHandlerUtil.java
deleted file mode 100644
index 36eec77..0000000
--- a/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/TlsHandlerUtil.java
+++ /dev/null
@@ -1,282 +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 edu.illinois.ncsa.BCGSS;
-////import edu.illinois.ncsa.bouncycastle.crypto.tls.*;
-//
-//import java.io.*;
-//
-//public class TlsHandlerUtil {
-//    private TlsProtocolHandler tlsHandler;
-//    private TlsClient tlsClient;
-//    private CircularByteBuffer netInStream;
-//    private ByteArrayOutputStream netOutStream;
-//    private boolean connectionThreadStarted = false;
-//    private IOException connectionThreadException = null;
-//
-//    /*
-//    public TlsHandlerUtil(TlsClient client) {
-//        this(client, new TlsProtocolVersion[] {TlsProtocolVersion.TLSv10,
-//                                               TlsProtocolVersion.SSLv3});
-//    }
-//    */
-//
-//    //public TlsHandlerUtil(TlsClient client, TlsProtocolVersion[] protocols) {
-//    public TlsHandlerUtil(TlsClient client) {
-//        this.tlsClient = client;
-//
-//        this.netInStream = new CircularByteBuffer(
-//                CircularByteBuffer.INFINITE_SIZE);
-//
-//        //TODO: set a good initial size of buffer?
-//        this.netOutStream = new ByteArrayOutputStream();
-//
-//        this.tlsHandler = new TlsProtocolHandler(
-//                netInStream.getInputStream(), netOutStream);
-//        //this.tlsHandler.setEnabledProtocols(protocols);
-//    }
-//
-//    /**
-//     *
-//     * @param inNetBuf
-//     * @return
-//     */
-//    public byte[] nextHandshakeToken(byte[] inNetBuf) throws IOException {
-//        return nextHandshakeToken(inNetBuf, 0, inNetBuf.length);
-//    }
-//
-//    /**
-//     *
-//     * @param inNetBuf
-//     * @param off
-//     * @param len
-//     * @return
-//     * @throws java.io.IOException
-//     */
-//    public byte[] nextHandshakeToken(byte[] inNetBuf, int off, int len)
-//            throws IOException {
-//        if (isHandshakeFinished()) {
-//            return null;
-//        }
-//
-//        if (! isConnectionThreadStarted()) {
-//            (new ConnectionThread()).start();
-//        }
-//
-//
-//        if (tlsHandler.getHandshakeBlocking() > 0) {
-//            tlsHandler.decHandshakeBlocking(inNetBuf.length);
-//        }
-//
-//        netInStream.getOutputStream().write(inNetBuf, off, len);
-//
-//        // block until the TlsProtocolHandler's record stream blocks
-//        // or until the handshake is finished.  After either, a handshake
-//        // token may have been produced
-//        while (tlsHandler.getHandshakeBlocking() == 0 &&
-//               ! isHandshakeFinished()) {
-//
-//            IOException e = getConnectionThreadException();
-//            if (e != null) {
-//                throw new IOException("TLS connection thread exception", e);
-//            }
-//
-//            try {
-//                Thread.sleep(25);
-//            } catch (InterruptedException e1) {
-//                throw new IOException("Handshake interrupted while waiting " +
-//                        "for new network data to be processed", e1);
-//            }
-//        }
-//
-//        byte[] token = drainNetOutStream();
-//
-//        if (token.length > 0) {
-//            return token;
-//        }
-//
-//        if (tlsHandler.getHandshakeBlocking() > 0) {
-//            // no token produced; need more data
-//            return null;
-//        }
-//
-//        if (isHandshakeFinished()) {
-//            return null;
-//        } else {
-//            throw new IOException("No handshake data available, but the " +
-//                "record stream is not blocking and wasn't interrupted");
-//        }
-//    }
-//
-//    /**
-//     * 
-//     * @param appData
-//     * @return
-//     * @throws IOException
-//     */
-//    public byte[] wrap(byte[] appData) throws IOException {
-//        return wrap(appData, 0, appData.length);
-//    }
-//
-//    /**
-//     *
-//     * @param appData
-//     * @param off
-//     * @param len
-//     * @return
-//     * @throws IOException
-//     */
-//    public byte[] wrap(byte[] appData, int off, int len) throws IOException {
-//        if (! isHandshakeFinished()) {
-//            return null;
-//        }
-//
-//        tlsHandler.getOutputStream().write(appData, off, len);
-//        return drainNetOutStream();
-//    }
-//
-//    /**
-//     *
-//     * @param netData
-//     * @return
-//     * @throws IOException
-//     */
-//    public byte[] unwrap(byte[] netData) throws IOException {
-//        return unwrap(netData, 0, netData.length);
-//    }
-//
-//    /**
-//     *
-//     * @param netData
-//     * @param off
-//     * @param len
-//     * @return
-//     * @throws IOException
-//     */
-//    public byte[] unwrap(byte[] netData, int off, int len) throws IOException {
-//        if (! isHandshakeFinished()) {
-//            return null;
-//        }
-//
-//        if (netData.length == 0) {
-//            return null;
-//        }
-//
-//        netInStream.getOutputStream().write(netData, off, len);
-//
-//        // Force the record to be processed in order to put an unknown
-//        // amount of data in the application queue.  It's assumed that
-//        // the netData parameter is a full SSL record; if it's not, then
-//        // this method will block indefinitely
-//        byte[] tmp = new byte[1];
-//        tlsHandler.getInputStream().read(tmp, 0, 1);
-//
-//        int avail = tlsHandler.getApplicationDataQueueSize();
-//
-//        if (avail == 0) {
-//            return tmp;
-//        }
-//
-//        byte[] appBuf = new byte[avail + 1];
-//        appBuf[0] = tmp[0];
-//        tlsHandler.getInputStream().read(appBuf, 1, avail);
-//
-//        return appBuf;
-//    }
-//
-//    /**
-//     *
-//     * @return
-//     * @throws java.io.IOException
-//     */
-//    public byte[] close() throws IOException {
-//        tlsHandler.close();
-//        return drainNetOutStream();
-//    }
-//
-//    /**
-//     *
-//     * @return
-//     */
-//    public boolean isHandshakeFinished() {
-//        return this.tlsHandler.isHandshakeFinished();
-//    }
-//
-//    /**
-//     *
-//     * @return
-//     */
-//    private byte[] drainNetOutStream() {
-//        byte[] rval = netOutStream.toByteArray();
-//        netOutStream.reset();
-//        return rval;
-//    }
-//
-//    /**
-//     *
-//     * @param b
-//     */
-//    private synchronized void setConnectionThreadStarted(boolean b) {
-//        connectionThreadStarted = b;
-//    }
-//
-//    /**
-//     *
-//     * @return
-//     */
-//    private synchronized boolean isConnectionThreadStarted() {
-//        return connectionThreadStarted;
-//    }
-//
-//    /**
-//     *
-//     * @return
-//     */
-//    private IOException getConnectionThreadException() {
-//        return connectionThreadException;
-//    }
-//
-//    /**
-//     *
-//     * @param e
-//     */
-//    private void setConnectionThreadException(IOException e) {
-//        this.connectionThreadException = e;
-//    }
-//
-//    /**
-//     *
-//     */
-//    private class ConnectionThread extends Thread {
-//        /**
-//         *
-//         */
-//        public void run() {
-//            setConnectionThreadStarted(true);
-//            try {
-//                tlsHandler.connect(tlsClient);
-//            } catch (IOException e) {
-//                setConnectionThreadException(e);
-//            }
-//            //System.out.println("TLS connection thread done");
-//        }
-//    }
-//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
deleted file mode 100644
index 1c07a39..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
+++ /dev/null
@@ -1,210 +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;
-
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-
-import org.globus.common.CoGProperties;
-import org.globus.gsi.gssapi.auth.HostAuthorization;
-import org.gridforum.jgss.ExtendedGSSCredential;
-import org.gridforum.jgss.ExtendedGSSManager;
-import org.ietf.jgss.GSSContext;
-import org.ietf.jgss.GSSCredential;
-import org.ietf.jgss.GSSException;
-import org.ietf.jgss.GSSName;
-import org.ietf.jgss.MessageProp;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.jcraft.jsch.JSchException;
-
-/**
- * This class is based on GSSContextKrb5; it substitutes the globus
- * ExtendedGSSManager and uses the SecurityUtils method to get the credential if
- * one is not passed in from memory.
- *
- */
-public class GSSContextX509 implements com.jcraft.jsch.GSSContext {
-
-    private GSSContext context = null;
-    private GSSCredential credential;
-    private static final Logger logger = LoggerFactory.getLogger(GSSContextX509.class);
-
-    public void create(String user, String host) throws JSchException {
-        try {
-//			ExtendedGSSManager manager = (ExtendedGSSManager) ExtendedGSSManager.getInstance();
-
-            if (credential == null) {
-                try {
-                    credential = getCredential();
-                } catch (SecurityException t) {
-                    System.out.printf("Could not get proxy: %s: %s\n", t.getClass().getSimpleName(), t.getMessage());
-                    throw new JSchException(t.toString());
-                }
-            }
-
-            String cname = host;
-
-            try {
-                cname = InetAddress.getByName(cname).getCanonicalHostName();
-            } catch (UnknownHostException e) {
-            }
-
-            GSSName name = HostAuthorization.getInstance().getExpectedName(credential, cname);
-
-//			context = manager.createContext(name, null, credential, GSSContext.DEFAULT_LIFETIME);
-//
-//			// RFC4462 3.4. GSS-API Session
-//			//
-//			// When calling GSS_Init_sec_context(), the client MUST set
-//			// integ_req_flag to "true" to request that per-message integrity
-//			// protection be supported for this context. In addition,
-//			// deleg_req_flag MAY be set to "true" to request access delegation,
-//			// if
-//			// requested by the user.
-//			//
-//			// Since the user authentication process by its nature authenticates
-//			// only the client, the setting of mutual_req_flag is not needed for
-//			// this process. This flag SHOULD be set to "false".
-//
-//			// TODO: OpenSSH's sshd does accept 'false' for mutual_req_flag
-//			// context.requestMutualAuth(false);
-//			context.requestMutualAuth(true);
-//			context.requestConf(true);
-//			context.requestInteg(true); // for MIC
-//			context.requestCredDeleg(true);
-//			context.requestAnonymity(false);
-
-//            context = new BCGSSContextImpl(name, (GlobusGSSCredentialImpl) credential);
-//            context.requestLifetime(GSSCredential.DEFAULT_LIFETIME);
-//            context.requestCredDeleg(true);
-//            context.requestMutualAuth(true);
-//            context.requestReplayDet(true);
-//            context.requestSequenceDet(true);
-//            context.requestConf(false);
-//            context.requestInteg(true);
-//            ((ExtendedGSSContext)context).setOption(GSSConstants.DELEGATION_TYPE, GSIConstants.DELEGATION_TYPE_FULL);
-
-            return;
-        } catch (GSSException ex) {
-            throw new JSchException(ex.toString());
-        }
-    }
-
-    private static GSSCredential getProxy() {
-        return getProxy(null, GSSCredential.DEFAULT_LIFETIME);
-    }
-
-    /**
-     * @param x509_USER_PROXY
-     *            path to the proxy.
-     * @param credentialLifetime
-     *            in seconds.
-     * @return valid credential.
-     *             if proxy task throws exception (or if proxy cannot be found).
-     */
-    private static GSSCredential getProxy(String x509_USER_PROXY, int credentialLifetime) throws SecurityException {
-        if (x509_USER_PROXY == null)
-            x509_USER_PROXY = System.getProperty("x509.user.proxy");
-
-//		if (x509_USER_PROXY == null) {
-//			SystemUtils.envToProperties();
-//			x509_USER_PROXY = System.getProperty("x509.user.proxy");
-//		}
-
-        if (x509_USER_PROXY == null || "".equals(x509_USER_PROXY))
-            x509_USER_PROXY = CoGProperties.getDefault().getProxyFile();
-
-        if (x509_USER_PROXY == null)
-            throw new SecurityException("could not get credential; no location defined");
-
-        ExtendedGSSManager manager = (ExtendedGSSManager) ExtendedGSSManager.getInstance();
-
-        // file...load file into a buffer
-        try {
-            File f = new File(x509_USER_PROXY);
-            byte[] data = new byte[(int) f.length()];
-            FileInputStream in = new FileInputStream(f);
-            // read in the credential data
-            in.read(data);
-            in.close();
-            return manager.createCredential(data, ExtendedGSSCredential.IMPEXP_OPAQUE, credentialLifetime, null, // use
-                    // default
-                    // mechanism
-                    // -
-                    // GSI
-                    GSSCredential.INITIATE_AND_ACCEPT);
-        } catch (Throwable t) {
-            throw new SecurityException("could not get credential from " + x509_USER_PROXY, t);
-        }
-    }
-
-    public boolean isEstablished() {
-        // this must check to see if the call returned GSS_S_COMPLETE
-        if (context != null){
-            return context.isEstablished();
-        }
-        return false;
-    }
-
-    public byte[] init(byte[] token, int s, int l) throws JSchException {
-        try {
-            if (context != null){
-                return context.initSecContext(token, s, l);
-            }else {
-                throw new JSchException("Context is null..");
-            }
-        } catch (GSSException ex) {
-            throw new JSchException(ex.toString());
-        }
-    }
-
-    public byte[] getMIC(byte[] message, int s, int l) {
-        try {
-            MessageProp prop = new MessageProp(0, false);
-            return context.getMIC(message, s, l, prop);
-        } catch (GSSException ex) {
-            logger.error(ex.getMessage(), ex);
-            return null;
-        }
-    }
-
-    public void dispose() {
-        try {
-            context.dispose();
-        } catch (GSSException ex) {
-        }
-    }
-
-    public void setCredential(GSSCredential credential) {
-        this.credential = credential;
-    }
-
-    public GSSCredential getCredential() {
-        return credential;
-    }
-}
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
deleted file mode 100644
index beb5b37..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
+++ /dev/null
@@ -1,162 +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.api;
-
-import java.util.List;
-import java.util.Map;
-
-import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gfac.ssh.impl.JobStatus;
-
-import com.jcraft.jsch.Session;
-
-/**
- * This interface represents a Cluster machine
- * End users of the API can implement this and come up with their own
- * implementations, but mostly this interface is for internal usage.
- */
-public interface Cluster {
-
-    /**
-     * This will submit a job to the cluster with a given pbs file and some parameters
-     *
-     * @param pbsFilePath  path of the pbs file
-     * @param workingDirectory working directory where pbs should has to copy
-     * @return jobId after successful job submission
-     * @throws SSHApiException throws exception during error
-     */
-    public String submitBatchJobWithScript(String pbsFilePath, String workingDirectory) throws SSHApiException;
-
-    /**
-     * This will submit the given job and not performing any monitoring
-     *
-     * @param jobDescriptor  job descriptor to submit to cluster, this contains all the parameter
-     * @return jobID after successful job submission.
-     * @throws SSHApiException  throws exception during error
-     */
-    public String submitBatchJob(JobDescriptor jobDescriptor) throws SSHApiException;
-
-    /**
-     * This will copy the localFile to remoteFile location in configured cluster
-     *
-     * @param remoteFile remote file location, this can be a directory too
-     * @param localFile local file path of the file which needs to copy to remote location
-     * @throws SSHApiException throws exception during error
-     */
-    public void scpTo(String remoteFile, String localFile) throws SSHApiException;
-
-    /**
-     * This will copy a remote file in path rFile to local file lFile
-     * @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
-     * @throws SSHApiException
-     */
-    public void scpFrom(String remoteFile, String localFile) throws SSHApiException;
-
-    /**
-     * This will copy a remote file in path rFile to local file lFile
-     * @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
-     * @throws SSHApiException
-     */
-    public void scpThirdParty(String remoteFileSorce, String remoteFileTarget) throws SSHApiException;
-    
-    /**
-     * This will create directories in computing resources
-     * @param directoryPath the full qualified path for the directory user wants to create
-     * @throws SSHApiException throws during error
-     */
-    public void makeDirectory(String directoryPath) throws SSHApiException;
-
-
-    /**
-     * This will get the job description of a job which is there in the cluster
-     * if jbo is not available with the given ID it returns
-     * @param jobID jobId has to pass
-     * @return Returns full job description of the job which submitted successfully
-     * @throws SSHApiException throws exception during error
-     */
-    public JobDescriptor getJobDescriptorById(String jobID) throws SSHApiException;
-
-    /**
-     * This will delete the given job from the queue
-     *
-     * @param jobID  jobId of the job which user wants to delete
-     * @return return the description of the deleted job
-     * @throws SSHApiException throws exception during error
-     */
-    public JobDescriptor cancelJob(String jobID) throws SSHApiException;
-
-    /**
-     * This will get the job status of the the job associated with this jobId
-     *
-     * @param jobID jobId of the job user want to get the status
-     * @return job status of the given jobID
-     * @throws SSHApiException throws exception during error
-     */
-    public JobStatus getJobStatus(String jobID) throws SSHApiException;
-    /**
-     * This will get the job status of the the job associated with this jobId
-     *
-     * @param jobName jobName of the job user want to get the status
-     * @return jobId of the given jobName
-     * @throws SSHApiException throws exception during error
-     */
-    public String getJobIdByJobName(String jobName, String userName) throws SSHApiException;
-
-    /**
-     * This method can be used to poll the jobstatuses based on the given
-     * user but we should pass the jobID list otherwise we will get unwanted
-     * job statuses which submitted by different middleware outside apache
-     * airavata with the same uername which we are not considering
-     * @param userName userName of the jobs which required to get the status
-     * @param jobIDs precises set of jobIDs
-     * @return
-     */
-    public void getJobStatuses(String userName,Map<String,JobStatus> jobIDs)throws SSHApiException;
-    /**
-     * This will list directories in computing resources
-     * @param directoryPath the full qualified path for the directory user wants to create
-     * @throws SSHApiException throws during error
-     */
-    public List<String> listDirectory(String directoryPath) throws SSHApiException;
-
-    /**
-     * This method can be used to get created ssh session
-     * to reuse the created session.
-     * @throws SSHApiException
-     */
-    public Session getSession() throws SSHApiException;
-    
-    /**
-     * This method can be used to close the connections initialized
-     * to handle graceful shutdown of the system
-     * @throws SSHApiException
-     */
-    public void disconnect() throws SSHApiException;
-
-    /**
-     * This gives the server Info
-     * @return
-     */
-    public ServerInfo getServerInfo();
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
deleted file mode 100644
index 024c53d..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
+++ /dev/null
@@ -1,278 +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.api;
-
-import com.jcraft.jsch.*;
-import org.apache.airavata.gfac.ssh.api.authentication.*;
-import org.apache.airavata.gfac.ssh.config.ConfigReader;
-import org.apache.airavata.gfac.ssh.jsch.ExtendedJSch;
-import org.apache.airavata.gfac.ssh.util.SSHAPIUIKeyboardInteractive;
-import org.apache.airavata.gfac.ssh.util.SSHKeyPasswordHandler;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This is a generic class which take care of command execution
- * in a shell, this is used through out the other places of the API.
- */
-public class CommandExecutor {
-    static {
-        JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gfac.ssh.GSSContextX509");
-        JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
-        JSch jSch = new JSch();
-    }
-
-    private static final Logger log = LoggerFactory.getLogger(CommandExecutor.class);
-    public static final String X509_CERT_DIR = "X509_CERT_DIR";
-
-    /**
-     * This will execute the given command with given session and session is not closed at the end.
-     *
-     * @param commandInfo
-     * @param session
-     * @param commandOutput
-     * @throws SSHApiException
-     */
-    public static Session executeCommand(CommandInfo commandInfo, Session session,
-                                         CommandOutput commandOutput) throws SSHApiException {
-
-        String command = commandInfo.getCommand();
-
-        Channel channel = null;
-        try {
-            if (!session.isConnected()) {
-                session.connect();
-            }
-            channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-        } catch (JSchException e) {
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to execute command - ", e);
-        }
-
-        channel.setInputStream(null);
-        ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
-        try {
-            channel.connect();
-        } catch (JSchException e) {
-
-            channel.disconnect();
-//            session.disconnect();
-            throw new SSHApiException("Unable to retrieve command output. Command - " + command, e);
-        }
-
-
-        commandOutput.onOutput(channel);
-        //Only disconnecting the channel, session can be reused
-        channel.disconnect();
-        return session;
-    }
-
-    /**
-     * This will not reuse any session, it will create the session and close it at the end
-     *
-     * @param commandInfo        Encapsulated information about command. E.g :- executable name
-     *                           parameters etc ...
-     * @param serverInfo         The SSHing server information.
-     * @param authenticationInfo Security data needs to be communicated with remote server.
-     * @param commandOutput      The output of the command.
-     * @param configReader       configuration required for ssh/gshissh connection
-     * @throws SSHApiException   throw exception when error occurs
-     */
-    public static void executeCommand(CommandInfo commandInfo, ServerInfo serverInfo,
-                                      AuthenticationInfo authenticationInfo,
-                                      CommandOutput commandOutput, ConfigReader configReader) throws SSHApiException {
-
-        if (authenticationInfo instanceof GSIAuthenticationInfo) {
-            System.setProperty(X509_CERT_DIR, (String) ((GSIAuthenticationInfo)authenticationInfo).getProperties().
-                    get("X509_CERT_DIR"));
-        }
-
-
-        JSch jsch = new ExtendedJSch();
-
-        log.debug("Connecting to server - " + serverInfo.getHost() + ":" + serverInfo.getPort() + " with user name - "
-                + serverInfo.getUserName());
-
-        Session session;
-
-        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 = configReader.getProperties();
-        session.setConfig(config);
-
-        //=============================================================
-        // Handling vanilla SSH pieces
-        //=============================================================
-        if (authenticationInfo instanceof SSHPasswordAuthentication) {
-            String password = ((SSHPasswordAuthentication) authenticationInfo).
-                    getPassword(serverInfo.getUserName(), serverInfo.getHost());
-
-            session.setUserInfo(new SSHAPIUIKeyboardInteractive(password));
-
-            // TODO figure out why we need to set password to session
-            session.setPassword(password);
-
-        } else if (authenticationInfo instanceof SSHPublicKeyFileAuthentication) {
-            SSHPublicKeyFileAuthentication sshPublicKeyFileAuthentication
-                    = (SSHPublicKeyFileAuthentication)authenticationInfo;
-
-            String privateKeyFile = sshPublicKeyFileAuthentication.
-                    getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
-
-            logDebug("The private key file for vanilla SSH " + privateKeyFile);
-
-            String publicKeyFile = sshPublicKeyFileAuthentication.
-                    getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
-
-            logDebug("The public key file for vanilla SSH " + publicKeyFile);
-
-            Identity identityFile;
-
-            try {
-                identityFile = GSISSHIdentityFile.newInstance(privateKeyFile, null, jsch);
-            } catch (JSchException e) {
-                throw new SSHApiException("An exception occurred while initializing keys using files. " +
-                        "(private key and public key)." +
-                        "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                        " connecting user name - "
-                        + serverInfo.getUserName() + " private key file - " + privateKeyFile + ", public key file - " +
-                        publicKeyFile, e);
-            }
-
-            // Add identity to identity repository
-            GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(jsch);
-            identityRepository.add(identityFile);
-
-            // Set repository to session
-            session.setIdentityRepository(identityRepository);
-
-            // Set the user info
-            SSHKeyPasswordHandler sshKeyPasswordHandler
-                    = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
-
-            session.setUserInfo(sshKeyPasswordHandler);
-
-        } else if (authenticationInfo instanceof SSHPublicKeyAuthentication) {
-
-            SSHPublicKeyAuthentication sshPublicKeyAuthentication
-                    = (SSHPublicKeyAuthentication)authenticationInfo;
-
-            Identity identityFile;
-
-            try {
-                String name = serverInfo.getUserName() + "_" + serverInfo.getHost();
-                identityFile = GSISSHIdentityFile.newInstance(name,
-                        sshPublicKeyAuthentication.getPrivateKey(serverInfo.getUserName(), serverInfo.getHost()),
-                        sshPublicKeyAuthentication.getPublicKey(serverInfo.getUserName(), serverInfo.getHost()), jsch);
-            } catch (JSchException e) {
-                throw new SSHApiException("An exception occurred while initializing keys using byte arrays. " +
-                        "(private key and public key)." +
-                        "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                        " connecting user name - "
-                        + serverInfo.getUserName(), e);
-            }
-
-            // Add identity to identity repository
-            GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(jsch);
-            identityRepository.add(identityFile);
-
-            // Set repository to session
-            session.setIdentityRepository(identityRepository);
-
-            // Set the user info
-            SSHKeyPasswordHandler sshKeyPasswordHandler
-                    = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
-
-            session.setUserInfo(sshKeyPasswordHandler);
-
-        }
-
-        // Not a good way, but we dont have any choice
-        if (session instanceof ExtendedSession) {
-            if (authenticationInfo instanceof GSIAuthenticationInfo) {
-                ((ExtendedSession) session).setAuthenticationInfo((GSIAuthenticationInfo)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);
-        }
-
-        String command = commandInfo.getCommand();
-
-        Channel channel;
-        try {
-            channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-        } catch (JSchException e) {
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to execute command - " + command +
-                    " on server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-
-        channel.setInputStream(null);
-        ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
-
-        try {
-            channel.connect();
-        } catch (JSchException e) {
-
-            channel.disconnect();
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to retrieve command output. Command - " + command +
-                    " on server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        commandOutput.onOutput(channel);
-
-        channel.disconnect();
-//        session.disconnect();
-    }
-
-    private static void logDebug(String message) {
-        if (log.isDebugEnabled()) {
-            log.debug(message);
-        }
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
deleted file mode 100644
index e6797ce..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.apache.airavata.gfac.ssh.api;/*
- *
- * 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.
- *
- */
-
-/**
- * Encapsulates information about
- */
-public interface CommandInfo {
-
-    /**
-     * Gets the executable command as a string.
-     * @return String encoded command. Should be able to execute
-     * directly on remote shell. Should includes appropriate parameters.
-     */
-    String getCommand();
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
deleted file mode 100644
index f275ff0..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.apache.airavata.gfac.ssh.api;/*
- *
- * 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.
- *
- */
-
-
-import com.jcraft.jsch.Channel;
-
-import java.io.OutputStream;
-
-/**
- * Output of a certain command. TODO rethink
- */
-public interface CommandOutput {
-
-    /**
-     * Gets the output of the command as a stream.
-     * @param  channel Command output as a stream.
-     */
-    void onOutput(Channel channel);
-
-    /**
-     * Gets standard error as a output stream.
-     * @return Command error as a stream.
-     */
-    OutputStream getStandardError();
-
-    /**
-     * The command exit code.
-     * @param code The program exit code
-     */
-    void exitCode(int code);
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
deleted file mode 100644
index 67dd043..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
+++ /dev/null
@@ -1,59 +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.api;
-
-import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
-
-/**
- * This represents a CPU core of a machine in the cluster
- */
-public class Core {
-    private JobDescriptor job;
-    private String id;
-
-    public Core(String id) {
-        this.id = id;
-        this.job = null;
-    }
-
-    /**
-     * @return core's id
-     */
-    public String getId() {
-        return id;
-    }
-
-    public void setId(String id) {
-        this.id = id;
-    }
-
-    /**
-     * @return job running on the core
-     */
-    public JobDescriptor getJob() {
-        return job;
-    }
-
-    public void setJob(JobDescriptor job) {
-        this.job = job;
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
deleted file mode 100644
index 1515f39..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
+++ /dev/null
@@ -1,104 +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.api;
-
-import java.util.HashMap;
-
-public class Node {
-    private String Name;
-    private Core[] Cores;
-    private String state;
-    private HashMap<String, String> status;
-    private String np;
-    private String ntype;
-
-    /**
-     * @return the machine's name
-     */
-    public String getName() {
-        return Name;
-    }
-
-    public void setName(String Name) {
-        this.Name = Name;
-    }
-
-    /**
-     * @return machine cores as an array
-     */
-    public Core[] getCores() {
-        return Cores;
-    }
-
-    public void setCores(Core[] Cores) {
-        this.Cores = Cores;
-    }
-
-
-    /**
-     * @return the machine state
-     */
-    public String getState() {
-        return state;
-    }
-
-    public void setState(String state) {
-        this.state = state;
-    }
-
-    /**
-     * @return the status
-     */
-    public HashMap<String, String> getStatus() {
-        return status;
-    }
-
-    public void setStatus(HashMap<String, String> status) {
-        this.setStatus(status);
-    }
-
-
-    /**
-     * @return the number of cores in the machine
-     */
-    public String getNp() {
-        return np;
-    }
-
-
-    public void setNp(String np) {
-        this.np = np;
-    }
-
-    /**
-     * @return the ntype of the machine
-     */
-    public String getNtype() {
-        return ntype;
-    }
-
-
-    public void setNtype(String ntype) {
-        this.ntype = ntype;
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
deleted file mode 100644
index f78825b..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
+++ /dev/null
@@ -1,36 +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.api;
-
-/**
- * An exception class to wrap SSH command execution related errors.
- */
-public class SSHApiException extends Exception {
-
-    public SSHApiException(String message) {
-        super(message);
-    }
-
-    public SSHApiException(String message, Exception e) {
-        super(message, e);
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
deleted file mode 100644
index d3c2160..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.apache.airavata.gfac.ssh.api;/*
- *
- * 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.
- *
- */
-
-/**
- * Encapsulate server information.
- */
-public class ServerInfo {
-
-    private String host;
-    private String userName;
-    private int port = 22;
-
-    public ServerInfo(String userName, String host) {
-        this.userName = userName;
-        this.host = host;
-    }
-
-    public ServerInfo(String userName,String host,  int port) {
-        this.host = host;
-        this.userName = userName;
-        this.port = port;
-    }
-
-    public String getHost() {
-        return host;
-    }
-
-    public void setHost(String host) {
-        this.host = host;
-    }
-
-    public String getUserName() {
-        return userName;
-    }
-
-    public void setUserName(String userName) {
-        this.userName = userName;
-    }
-
-    public int getPort() {
-        return port;
-    }
-
-    public void setPort(int port) {
-        this.port = port;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java
deleted file mode 100644
index 6b4e913..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package org.apache.airavata.gfac.ssh.api.authentication;/*
- *
- * 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.
- *
- */
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 10/4/13
- * Time: 11:25 AM
- */
-
-/**
- * An empty interface that represents authentication data to the API.
- */
-public interface AuthenticationInfo {
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java
deleted file mode 100644
index 1f327f0..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package org.apache.airavata.gfac.ssh.api.authentication;/*
- *
- * 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.
- *
- */
-
-import org.ietf.jgss.GSSCredential;
-
-import java.util.Properties;
-
-/**
- * Authentication data. Could be MyProxy user name, password, could be GSSCredentials
- * or could be SSH keys.
- */
-public abstract class GSIAuthenticationInfo implements AuthenticationInfo {
-
-    public Properties properties = new Properties();
-
-    public abstract GSSCredential getCredentials() throws SecurityException;
-
-    public Properties getProperties() {
-        return properties;
-    }
-
-    public void setProperties(Properties properties) {
-        this.properties = properties;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java
deleted file mode 100644
index ebd79f2..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package org.apache.airavata.gfac.ssh.api.authentication;/*
- *
- * 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.
- *
- */
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 10/4/13
- * Time: 2:39 PM
- */
-
-/**
- * Abstracts out common methods for SSH key authentication.
- */
-public interface SSHKeyAuthentication extends AuthenticationInfo {
-
-    /**
-     * This is needed only if private key and public keys are encrypted.
-     * If they are not encrypted we can just return null.
-     * @return User should return pass phrase if keys are encrypted. If not null.
-     */
-    String getPassPhrase();
-
-    /**
-     * Callback with the banner message. API user can get hold of banner message
-     * by implementing this method.
-     * @param message The banner message.
-     */
-    void bannerMessage(String message);
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java
deleted file mode 100644
index fd884f8..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java
+++ /dev/null
@@ -1,43 +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.api.authentication;
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 10/4/13
- * Time: 11:22 AM
- */
-
-/**
- * Password authentication for vanilla SSH.
- */
-public interface SSHPasswordAuthentication extends AuthenticationInfo {
-
-    /**
-     * Gets the password for given host name and given user name.
-     * @param userName The connecting user name name.
-     * @param hostName The connecting host.
-     * @return Password for the given user.
-     */
-    String getPassword(String userName, String hostName);
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java
deleted file mode 100644
index dcedfec..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java
+++ /dev/null
@@ -1,54 +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.api.authentication;
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 10/4/13
- * Time: 9:48 AM
- */
-
-
-/**
- * Public key authentication for vanilla SSH.
- * The public key and private key are returned as byte arrays. Useful when we store private key/public key
- * in a secure storage such as credential store. API user should implement this.
- */
-public interface SSHPublicKeyAuthentication extends SSHKeyAuthentication {
-
-    /**
-     * Gets the public key as byte array.
-     * @param userName The user who is trying to SSH
-     * @param hostName The host which user wants to connect to.
-     * @return The public key as a byte array.
-     */
-    byte[] getPrivateKey(String userName, String hostName);
-
-    /**
-     * Gets the private key as byte array.
-     * @param userName The user who is trying to SSH
-     * @param hostName The host which user wants to connect to.
-     * @return The private key as a byte array.
-     */
-    byte[] getPublicKey(String userName, String hostName);
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/13c2e79e/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java
deleted file mode 100644
index e22b9af..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.apache.airavata.gfac.ssh.api.authentication;/*
- *
- * 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.
- *
- */
-
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 10/4/13
- * Time: 9:52 AM
- */
-
-/**
- * Public key authentication for vanilla SSH.
- * The public key and private key stored files are returned. API user should implement this.
- */
-public interface SSHPublicKeyFileAuthentication extends SSHKeyAuthentication {
-
-    /**
-     * The file which contains the public key.
-     * @param userName The user who is trying to SSH
-     * @param hostName The host which user wants to connect to.
-     * @return The name of the file which contains the public key.
-     */
-    String getPublicKeyFile(String userName, String hostName);
-
-    /**
-     * The file which contains the public key.
-     * @param userName The user who is trying to SSH
-     * @param hostName The host which user wants to connect to.
-     * @return The name of the file which contains the private key.
-     */
-    String getPrivateKeyFile(String userName, String hostName);
-
-
-}


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