svn commit: r1529931 - in /airavata/sandbox/gsissh/src/main: java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java java/org/apache/airavata/gsi/ssh/util/SSHUtils.java resources/PBSTemplate.xslt

[la...@apache.org]

Author: lahiru
Date: Mon Oct  7 15:05:40 2013
New Revision: 1529931

URL: http://svn.apache.org/r1529931
Log:
new changes to get the vanilassh wroking with br2.

Modified:
    airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
    airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
    airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
    airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt

Modified: airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
URL: http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java?rev=1529931&r1=1529930&r2=1529931&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java (original)
+++ airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java Mon Oct  7 15:05:40 2013
@@ -119,8 +119,7 @@ public class JobDescriptor {
      * @param minutes
      */
     public void setMaxWallTime(String minutes) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
-                CommonUtils.maxWallTimeCalculator(Integer.getInteger(minutes)));
+        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(minutes);
 
     }
 

Modified: airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
URL: http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java?rev=1529931&r1=1529930&r2=1529931&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java (original)
+++ airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java Mon Oct  7 15:05:40 2013
@@ -78,12 +78,14 @@ public class PBSCluster implements Clust
 
         this.authenticationInfo = authenticationInfo;
 
-        System.setProperty(X509_CERT_DIR, (String) ((GSIAuthenticationInfo)authenticationInfo).getProperties().
-                get(X509_CERT_DIR));
+        if (authenticationInfo instanceof GSIAuthenticationInfo) {
+            System.setProperty(X509_CERT_DIR, (String) ((GSIAuthenticationInfo) authenticationInfo).getProperties().
+                    get("X509_CERT_DIR"));
+        }
 
-        if(installedPath.endsWith("/")){
+        if (installedPath.endsWith("/")) {
             this.installedPath = installedPath;
-        }else {
+        } else {
             this.installedPath = installedPath + "/";
         }
 
@@ -125,7 +127,7 @@ public class PBSCluster implements Clust
 
         } else if (authenticationInfo instanceof SSHPublicKeyFileAuthentication) {
             SSHPublicKeyFileAuthentication sshPublicKeyFileAuthentication
-                    = (SSHPublicKeyFileAuthentication)authenticationInfo;
+                    = (SSHPublicKeyFileAuthentication) authenticationInfo;
 
             String privateKeyFile = sshPublicKeyFileAuthentication.
                     getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
@@ -159,14 +161,14 @@ public class PBSCluster implements Clust
 
             // Set the user info
             SSHKeyPasswordHandler sshKeyPasswordHandler
-                    = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
+                    = new SSHKeyPasswordHandler((SSHKeyAuthentication) authenticationInfo);
 
             session.setUserInfo(sshKeyPasswordHandler);
 
         } else if (authenticationInfo instanceof SSHPublicKeyAuthentication) {
 
             SSHPublicKeyAuthentication sshPublicKeyAuthentication
-                    = (SSHPublicKeyAuthentication)authenticationInfo;
+                    = (SSHPublicKeyAuthentication) authenticationInfo;
 
             Identity identityFile;
 
@@ -192,7 +194,7 @@ public class PBSCluster implements Clust
 
             // Set the user info
             SSHKeyPasswordHandler sshKeyPasswordHandler
-                    = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
+                    = new SSHKeyPasswordHandler((SSHKeyAuthentication) authenticationInfo);
 
             session.setUserInfo(sshKeyPasswordHandler);
 
@@ -200,7 +202,9 @@ public class PBSCluster implements Clust
 
         // Not a good way, but we dont have any choice
         if (session instanceof ExtendedSession) {
-            ((ExtendedSession) session).setAuthenticationInfo((GSIAuthenticationInfo)authenticationInfo);
+            if (authenticationInfo instanceof GSIAuthenticationInfo) {
+                ((ExtendedSession) session).setAuthenticationInfo((GSIAuthenticationInfo) authenticationInfo);
+            }
         }
 
         try {
@@ -281,7 +285,7 @@ public class PBSCluster implements Clust
                     " connecting user name - "
                     + serverInfo.getUserName(), e);
         } finally {
-            if(tempPBSFile != null){
+            if (tempPBSFile != null) {
                 tempPBSFile.delete();
             }
         }

Modified: airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
URL: http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java?rev=1529931&r1=1529930&r2=1529931&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java (original)
+++ airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java Mon Oct  7 15:05:40 2013
@@ -21,10 +21,13 @@
 package org.apache.airavata.gsi.ssh.util;
 
 import com.jcraft.jsch.*;
+import com.sun.tools.javac.util.Paths;
+import org.apache.airavata.gsi.ssh.api.CommandOutput;
 import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
 import org.apache.airavata.gsi.ssh.api.SSHApiException;
 import org.apache.airavata.gsi.ssh.api.ServerInfo;
 import org.apache.airavata.gsi.ssh.config.ConfigReader;
+import org.apache.airavata.gsi.ssh.impl.SystemCommandOutput;
 import org.apache.airavata.gsi.ssh.jsch.ExtendedJSch;
 import org.slf4j.*;
 
@@ -50,6 +53,7 @@ public class SSHUtils {
 
     /**
      * We need to pass certificateLocation when we use SCPTo method standalone
+     *
      * @param serverInfo
      * @param authenticationInfo
      * @param certificateLocation
@@ -64,6 +68,7 @@ public class SSHUtils {
 
     /**
      * This can be used when use SCPTo method within SSHAPi because SSHApiFactory already set the system property certificateLocation
+     *
      * @param serverInfo
      * @param authenticationInfo
      * @param configReader
@@ -74,6 +79,7 @@ public class SSHUtils {
         this.authenticationInfo = authenticationInfo;
         this.configReader = configReader;
     }
+
     /**
      * This  method will scp the lFile to the rFile location
      *
@@ -82,8 +88,9 @@ public class SSHUtils {
      * @throws IOException
      * @throws JSchException
      * @throws org.apache.airavata.gsi.ssh.api.SSHApiException
+     *
      */
-    public Session scpTo(String rFile, String lFile) throws IOException, JSchException, SSHApiException {
+    public String scpTo(String rFile, String lFile) throws IOException, JSchException, SSHApiException {
         FileInputStream fis = null;
         String prefix = null;
         if (new File(lFile).isDirectory()) {
@@ -189,9 +196,12 @@ public class SSHUtils {
 
         channel.disconnect();
         session.disconnect();
-        return session;
+        int i = lFile.lastIndexOf("\\");
+        String substring = lFile.substring(i + 1);
+        return rFile + File.separator + substring;
     }
-    public static Session scpTo(String rFile, String lFile,Session session) throws IOException, JSchException, SSHApiException {
+
+    public static String scpTo(String rFile, String lFile, Session session) throws IOException, JSchException, SSHApiException {
         FileInputStream fis = null;
         String prefix = null;
         if (new File(lFile).isDirectory()) {
@@ -263,8 +273,45 @@ public class SSHUtils {
         out.close();
 
         channel.disconnect();
+        int i = lFile.lastIndexOf("\\");
+        String substring = lFile.substring(i + 1);
+        return rFile + File.separator + substring;
+    }
+
+    public static Session makeDirectory(String path, Session session) throws IOException, JSchException, SSHApiException {
+
+        // exec 'scp -t rfile' remotely
+        String command = "mkdir " + path;
+        Channel channel = session.openChannel("exec");
+        CommandOutput commandOutput = new SystemCommandOutput();
+        ((ChannelExec) channel).setCommand(command);
+
+        // get I/O streams for remote scp
+        OutputStream out = channel.getOutputStream();
+        InputStream in = channel.getInputStream();
+        ((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 - " + session.getHost() + ":" + session.getPort() +
+                    " connecting user name - "
+                    + session.getUserName(), e);
+        }
+
+        commandOutput.onOutput(channel);
+
+        channel.disconnect();
+        session.disconnect();
+
+        channel.disconnect();
         return session;
     }
+
     static int checkAck(InputStream in) throws IOException {
         int b = in.read();
         if (b == 0) return b;

Modified: airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt
URL: http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt?rev=1529931&r1=1529930&r2=1529931&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt (original)
+++ airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt Mon Oct  7 15:05:40 2013
@@ -11,15 +11,31 @@
 #! /bin/sh
 # PBS batch job script built by Globus job manager
 #
+    <xsl:if test="shellName != @xsl:nil">
 ##PBS -S <xsl:value-of select="ns:shellName"/>
+    </xsl:if>
+    <xsl:if test="queueName != @xsl:nil">
 #PBS -q <xsl:value-of select="ns:queueName"/>
+    </xsl:if>
+    <xsl:if test="mailOptions != @xsl:nil">
 #PBS -m <xsl:value-of select="ns:mailOptions"/>
+    </xsl:if>
+<xsl:if test="acountString != @xsl:nil">
 #PBS -A <xsl:value-of select="ns:acountString"/>
+    </xsl:if>
+    <xsl:if test="maxWallTime != @xsl:nil">
 #PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
+    </xsl:if>
+    <xsl:if test="standardOutFile != @xsl:nil">
 #PBS -o <xsl:value-of select="ns:standardOutFile"/>
+    </xsl:if>
+    <xsl:if test="standardOutFile != @xsl:nil">
 #PBS -e <xsl:value-of select="ns:standardErrorFile"/>
+    </xsl:if>
+    <xsl:if test="(nodes != @xsl:nil) and (processesPerNode != @xsl:nil)">
 #PBS -l nodes=<xsl:value-of select="ns:nodes"/>:ppn=<xsl:value-of select="ns:processesPerNode"/>
 <xsl:text>&#xa;</xsl:text>
+    </xsl:if>
 <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="."/>