diff --git a/uk/ac/sanger/artemis/ExternalProgram.java b/uk/ac/sanger/artemis/ExternalProgram.java
index 940670af664859e96bab63315277f1a1f0ed0bad..824c6cc4736ddc5458c7cc3c13b644f144370bb1 100644
--- a/uk/ac/sanger/artemis/ExternalProgram.java
+++ b/uk/ac/sanger/artemis/ExternalProgram.java
@@ -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 1.15 2007-02-28 16:12:04 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.16 2007-03-01 16:27:24 tjc Exp $
**/
package uk.ac.sanger.artemis;
@@ -49,12 +49,14 @@ import javax.swing.JProgressBar;
* and contains methods for invoking it.
*
* @author Kim Rutherford
- * @version $Id: ExternalProgram.java,v 1.15 2007-02-28 16:12:04 tjc Exp $
+ * @version $Id: ExternalProgram.java,v 1.16 2007-03-01 16:27:24 tjc Exp $
**/
public class ExternalProgram
{
-
+ public static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(ExternalProgram.class);
+
final public static int AA_PROGRAM = 0;
final public static int DNA_PROGRAM = 1;
final public static int APPLICATION = 2;
@@ -159,8 +161,7 @@ public class ExternalProgram
(getRealName().indexOf("blast") > -1 || getRealName().startsWith("fast")) )
{
- if(System.getProperty("debug") != null)
- System.out.println("GET READY TO CALL SSH CLIENT "+getRealName());
+ logger4j.debug("GET READY TO CALL SSH CLIENT "+getRealName());
final Feature this_feature = features.elementAt(0);
Entry entry = this_feature.getEntry();
@@ -194,8 +195,7 @@ public class ExternalProgram
args[4] = "-d"; args[5] = getProgramOptions();
}
- if(System.getProperty("debug") != null)
- System.out.println("CALL SSH CLIENT "+getRealName());
+ logger4j.debug("CALL SSH CLIENT "+getRealName());
uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
new uk.ac.sanger.artemis.j2ssh.SshPSUClient(args);
@@ -493,8 +493,7 @@ public class ExternalProgram
filenames_printwriter.close();
filenames_writer.close();
- if(System.getProperty("debug") != null)
- System.out.println("WRITTEN "+file_of_filenames.getCanonicalPath());
+ logger4j.debug("WRITTEN "+file_of_filenames.getCanonicalPath());
return file_of_filenames;
@@ -619,8 +618,7 @@ public class ExternalProgram
if(contents == null)
{
- if(System.getProperty("debug") != null)
- System.out.println("getFileNumber() creating "+dir+
+ logger4j.debug("getFileNumber() creating "+dir+
fs+file_counter_filename);
node.mkdir(dir);
@@ -629,8 +627,7 @@ public class ExternalProgram
file_reader = new StringReader(new String(contents));
- if(System.getProperty("debug") != null)
- System.out.println("getFileNumber()\n"+new String(contents));
+ logger4j.debug("getFileNumber()\n"+new String(contents));
}
final BufferedReader reader = new BufferedReader(file_reader);
@@ -702,9 +699,8 @@ public class ExternalProgram
dir = dir.substring(0,index) + fs +
getName() + fs;
- if(System.getProperty("debug") != null)
- System.out.println("setFileNumber() "+
- local_file.getCanonicalPath()+" --> "+dir);
+ logger4j.debug("setFileNumber() "+
+ local_file.getCanonicalPath()+" --> "+dir);
node.put(dir, local_file, null, true);
}
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index 5acefc1bb3cd64d45776855e18d2026b5f947054..2b18ca03d5085e21cbad5d1b8dbd9bb4c0083c0a 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -1,4 +1,4 @@
-/* ExternalProgram.java
+/* SshPSUClient.java
*
* created: Aug 2005
*
@@ -26,19 +26,11 @@ package uk.ac.sanger.artemis.j2ssh;
import uk.ac.sanger.artemis.components.MessageDialog;
-import javax.swing.JOptionPane;
import javax.swing.JFileChooser;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.JPasswordField;
-import javax.swing.SwingConstants;
-import java.awt.GridLayout;
import java.io.File;
import java.io.FileReader;
import java.io.InputStream;
-import java.io.InputStreamReader;
import java.io.BufferedReader;
import java.io.IOException;
@@ -61,6 +53,8 @@ import com.sshtools.j2ssh.configuration.ConfigurationLoader;
*/
public class SshPSUClient extends Thread
{
+ public static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(SshPSUClient.class);
// defaults
private String listfilepath = null;
private String cmd = null;
@@ -113,7 +107,7 @@ public class SshPSUClient extends Thread
}
catch(Exception exp)
{
- System.out.println("SshPSUClient.rescue()");
+ logger4j.warn("SshPSUClient.rescue()");
exp.printStackTrace();
}
return ssh;
@@ -132,8 +126,7 @@ public class SshPSUClient extends Thread
if(ssh == null)
return;
- if(System.getProperty("debug") != null)
- System.out.println("RUN "+program);
+ logger4j.debug("RUN "+program);
completed = runBlastOrFasta(program);
@@ -178,7 +171,7 @@ public class SshPSUClient extends Thread
}
catch (IOException e)
{
- System.out.println("Problem reading list file");
+ logger4j.warn("Problem reading list file");
}
return seqfiles;
}
@@ -193,9 +186,8 @@ public class SshPSUClient extends Thread
{
for(int i=0; i < 500; i++)
{
- if(System.getProperty("debug") != null)
- System.out.println("waitUntilFileAppears() "+file);
- Thread.currentThread().sleep(1000);
+ logger4j.debug("waitUntilFileAppears() "+file);
+ Thread.sleep(1000);
try
{
if(fileExists(getSftpClient() , file))
@@ -205,7 +197,7 @@ public class SshPSUClient extends Thread
{
if(System.getProperty("debug") != null)
{
- System.out.println("waitUntilFileAppears()");
+ logger4j.warn("waitUntilFileAppears()");
sshe.printStackTrace();
}
try
@@ -337,9 +329,9 @@ public class SshPSUClient extends Thread
}
catch(SshException sshe)
{
+ logger4j.debug("runBlastOrFasta()");
if(System.getProperty("debug") != null)
{
- System.out.println("runBlastOrFasta()");
sshe.printStackTrace();
}
rescue();
@@ -357,14 +349,13 @@ public class SshPSUClient extends Thread
{
sftp.put(filepath, wdir+filename);
- if(System.getProperty("debug") != null)
- System.out.println("PUT SUCCESS "+wdir+filename);
+ logger4j.debug("PUT SUCCESS "+wdir+filename);
}
catch(SshException ioe)
{
+ logger4j.debug("runBlastOrFasta() - 2");
if(System.getProperty("debug") != null)
{
- System.out.println("runBlastOrFasta() - 2");
ioe.printStackTrace();
}
rescue();
@@ -372,8 +363,7 @@ public class SshPSUClient extends Thread
sftp.put(filepath, wdir+filename);
}
- if(System.getProperty("debug") != null)
- System.out.println("STARTING session");
+ logger4j.debug("STARTING session");
SessionChannelClient session = null;
@@ -386,9 +376,9 @@ public class SshPSUClient extends Thread
}
catch(IOException exp)
{
+ logger4j.debug("NOT STARTED runBlastOrFasta() ----- 3 "+filename);
if(System.getProperty("debug") != null)
{
- System.out.println("NOT STARTED runBlastOrFasta() ----- 3 "+filename);
exp.printStackTrace();
}
rescue();
@@ -427,8 +417,7 @@ public class SshPSUClient extends Thread
}
// run the application
- if(System.getProperty("debug") != null)
- System.out.println(actualCMD);
+ logger4j.debug(actualCMD);
try
{
@@ -436,15 +425,14 @@ public class SshPSUClient extends Thread
}
catch(IOException exp)
{
+ logger4j.debug("runBlastOrFasta() - 3");
if(System.getProperty("debug") != null)
{
- System.out.println("runBlastOrFasta() - 3");
exp.printStackTrace();
}
}
- if(System.getProperty("debug") != null)
- System.out.println("STARTED session "+filename);
+ logger4j.debug("STARTED session "+filename);
// Reading from the session InputStream
StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
@@ -458,7 +446,7 @@ public class SshPSUClient extends Thread
{
// make sure we hang around for stdout
while(stdouth.isAlive() || stderrh.isAlive())
- Thread.currentThread().sleep(10);
+ Thread.sleep(10);
isFile = waitUntilFileAppears(filename+".out");
}
@@ -467,12 +455,10 @@ public class SshPSUClient extends Thread
ie.printStackTrace();
}
- if(System.getProperty("debug") != null)
- {
- // stdout & stderr
- System.out.println("STDOUT "+filename+"\n"+stdouth.getOutput());
- System.out.println("STDERR "+filename+"\n"+stderrh.getOutput());
- }
+ // stdout & stderr
+ logger4j.debug("STDOUT "+filename+"\n"+stdouth.getOutput());
+ logger4j.debug("STDERR "+filename+"\n"+stderrh.getOutput());
+
try
{
@@ -481,9 +467,9 @@ public class SshPSUClient extends Thread
}
catch(Exception ioe)
{
+ logger4j.debug("runBlastOrFasta() - 3");
if(System.getProperty("debug") != null)
{
- System.out.println("runBlastOrFasta() - 3");
ioe.printStackTrace();
}
rescue();
@@ -491,8 +477,7 @@ public class SshPSUClient extends Thread
sftp.get(outputfile, filepath+".out");
}
- if(System.getProperty("debug") != null)
- System.out.println("GET SUCCESS "+filepath+".out");
+ logger4j.debug("GET SUCCESS "+filepath+".out");
if(!keep)
{
@@ -534,9 +519,9 @@ public class SshPSUClient extends Thread
}
catch(IOException ioe)
{
+ logger4j.debug("getSftpClient() -- 2");
if(System.getProperty("debug") != null)
{
- System.out.println("getSftpClient() -- 2");
ioe.printStackTrace();
}
rescue();
@@ -544,9 +529,9 @@ public class SshPSUClient extends Thread
}
catch(IOException ioe2)
{
+ logger4j.debug("getSftpClient()");
if(System.getProperty("debug") != null)
{
- System.out.println("getSftpClient()");
ioe2.printStackTrace();
}
rescue();