From 096a4fa3acd09199edc8fcfda2f0ce0532323e6b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 12 Aug 2005 16:01:48 +0000
Subject: [PATCH] set j2ssh for fasta and blast only
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3387 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/ExternalProgram.java | 9 +++++----
uk/ac/sanger/artemis/j2ssh/SshPSUClient.java | 20 +++++++++++++-------
2 files changed, 18 insertions(+), 11 deletions(-)
diff --git a/uk/ac/sanger/artemis/ExternalProgram.java b/uk/ac/sanger/artemis/ExternalProgram.java
index 8cceb2035..61779cc39 100644
--- a/uk/ac/sanger/artemis/ExternalProgram.java
+++ b/uk/ac/sanger/artemis/ExternalProgram.java
@@ -4,7 +4,7 @@
*
* This file is part of Artemis
*
- * Copyright(C) 1998-2003 Genome Research Limited
+ * Copyright(C) 1998-2005 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.4 2005-08-12 09:10:25 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.5 2005-08-12 16:01:48 tjc Exp $
**/
package uk.ac.sanger.artemis;
@@ -41,7 +41,7 @@ import java.util.Enumeration;
* and contains methods for invoking it.
*
* @author Kim Rutherford
- * @version $Id: ExternalProgram.java,v 1.4 2005-08-12 09:10:25 tjc Exp $
+ * @version $Id: ExternalProgram.java,v 1.5 2005-08-12 16:01:48 tjc Exp $
**/
public class ExternalProgram
@@ -146,7 +146,8 @@ public class ExternalProgram
// {
try
{
- if(System.getProperty("j2ssh") != null)
+ if( System.getProperty("j2ssh") != null &&
+ (getRealName().indexOf("blast") > -1 || getRealName().startsWith("fast")) )
{
String [] args = { "-f", file_of_filenames.getPath(),
"-cmd", getRealName(),
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index 1fb30ebce..7f56d29d1 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -129,6 +129,7 @@ public class SshPSUClient extends Thread
else if(cmd.equals("fastx") && settings.getProperty("fastx") != null)
cmd = settings.getProperty("fastx");
+ boolean completed = false;
try
{
// Setup a logfile
@@ -265,7 +266,9 @@ public class SshPSUClient extends Thread
actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
cmd+" "+db+" "+wdir+filename;
- System.out.println(actualCMD);
+ // run the application
+ if(System.getProperty("debug") != null)
+ System.out.println(actualCMD);
session.executeCommand(actualCMD);
// Reading from the session InputStream
@@ -307,17 +310,19 @@ public class SshPSUClient extends Thread
ioe.printStackTrace();
}
- // stdout
- System.out.println(stdouth.getOutput());
- System.out.println(stderrh.getOutput());
-
+ if(System.getProperty("debug") != null)
+ {
+ // stdout & stderr
+ System.out.println(stdouth.getOutput());
+ System.out.println(stderrh.getOutput());
+ }
// ByteArrayOutputStream os = new ByteArrayOutputStream();
// sftp.get(outputfile, os);
// System.out.println(os.toString());
sftp.get(outputfile, filepath+".out");
-
+ completed = true;
session.close();
}
@@ -335,7 +340,8 @@ public class SshPSUClient extends Thread
} catch(IOException ioe){}
finally
{
- JOptionPane.showMessageDialog(null,
+ if(completed)
+ JOptionPane.showMessageDialog(null,
"Finished \n" + program,
"Process Finished",
JOptionPane.INFORMATION_MESSAGE);
--
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