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From ramin...@apache.org
Subject git commit: Made changes to SCP connection creator and add third-party transfer.AIRAVATA-1300
Date Mon, 23 Jun 2014 21:56:57 GMT
Repository: airavata
Updated Branches:
  refs/heads/master bc20a06d1 -> 64582600a


Made changes to SCP connection creator and add third-party
transfer.AIRAVATA-1300

Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/64582600
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/64582600
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/64582600

Branch: refs/heads/master
Commit: 64582600a429fc71fdf6d823a3a83cba0d880578
Parents: bc20a06
Author: raminder <raminder@apache.org>
Authored: Mon Jun 23 17:56:33 2014 -0400
Committer: raminder <raminder@apache.org>
Committed: Mon Jun 23 17:56:33 2014 -0400

----------------------------------------------------------------------
 .../gfac/ssh/handler/SSHInputHandler.java       |   5 +
 .../apache/airavata/gsi/ssh/api/Cluster.java    |   8 ++
 .../gsi/ssh/impl/GSISSHAbstractCluster.java     |  18 ++-
 .../apache/airavata/gsi/ssh/util/SSHUtils.java  | 117 +++++++++++++++++++
 4 files changed, 147 insertions(+), 1 deletion(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/64582600/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
index b237a81..4c1345d 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
@@ -123,10 +123,15 @@ public class SSHInputHandler extends AbstractHandler {
         String substring = paramValue.substring(i + 1);
         try {
             String targetFile = app.getInputDataDirectory() + File.separator + substring;
+            if(paramValue.startsWith("scp:")){
+            	paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
+            	cluster.scpThirdParty(paramValue, targetFile);
+            }else{
             if(paramValue.startsWith("file")){
                 paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
             }
             cluster.scpTo(targetFile, paramValue);
+            }
             return targetFile;
         } catch (SSHApiException e) {
             throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());

http://git-wip-us.apache.org/repos/asf/airavata/blob/64582600/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
index 4454624..b3ecc16 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
@@ -72,6 +72,14 @@ public interface Cluster {
     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

http://git-wip-us.apache.org/repos/asf/airavata/blob/64582600/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
index 0ddea0f..118bf91 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
@@ -135,7 +135,7 @@ public class GSISSHAbstractCluster implements Cluster {
             logDebug("The private key file for vanilla SSH " + privateKeyFile);
 
             String publicKeyFile = sshPublicKeyFileAuthentication.
-                    getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
+                    getPublicKeyFile(serverInfo.getUserName(), serverInfo.getHost());
 
             logDebug("The public key file for vanilla SSH " + publicKeyFile);
 
@@ -374,6 +374,22 @@ public class GSISSHAbstractCluster implements Cluster {
                     + serverInfo.getHost() + ":rFile", e);
         }
     }
+    
+    public void scpThirdParty(String remoteFileSource, String remoteFileTarget) throws SSHApiException
{
+        try {
+            if(!session.isConnected()){
+                session.connect();
+            }
+            log.info("Transfering from:" + remoteFileSource + " To: " + remoteFileTarget);
+            SSHUtils.scpThirdParty(remoteFileSource, remoteFileTarget, session);
+        } catch (IOException e) {
+            throw new SSHApiException("Failed during scping  file:" + remoteFileSource +
" to remote file "
+                    +remoteFileTarget , e);
+        } catch (JSchException e) {
+            throw new SSHApiException("Failed during scping  file:" + remoteFileSource +
" to remote file "
+                    +remoteFileTarget, e);
+        }
+    }
 
     public void makeDirectory(String directoryPath) throws SSHApiException {
         try {

http://git-wip-us.apache.org/repos/asf/airavata/blob/64582600/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
index 02547a0..f36d2d0 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
@@ -583,6 +583,123 @@ public class SSHUtils {
         }
     }
 
+    /**
+     * 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');
+                }
+
+//                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();
+                
+                while (true) {
+                    int len = in.read(buf, 0, buf.length);
+                    if (len <= 0) break;
+                    out.write(buf, 0, len); 
+                }
+//                // 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().equals("")) {
+            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


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