diff --git a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
index db2c9467adfcbc14dd9283f82f5c04efc7f2626a..25c1f6b7eecc84878eeceb6281cc76facda3cf51 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
@@ -113,18 +113,20 @@ public class SshFileManager
private SftpClient getSftpClient()
throws IOException
{
- SftpClient sftp;
+ SftpClient sftp;
try
{
+ if(!ssh.hasActiveSftpClient())
+ return ssh.openSftpClient();
+
sftp = ssh.getActiveSftpClient();
- return sftp;
+ return sftp;
}
catch(IOException ioe)
- {}
- return ssh.openSftpClient();
+ {}
+ return ssh.openSftpClient();
}
-
/**
*
* Remote directory listing
@@ -134,18 +136,17 @@ public class SshFileManager
throws IOException
{
SftpClient sftp = getSftpClient();
+ Object list[] = null;
try
{
- sftp.cd(remoteRootDir);
+ list = sftp.ls(remoteRootDir).toArray();
}
catch(java.io.FileNotFoundException fnf)
{
return false;
}
- Object list[] = sftp.ls().toArray();
-
dir_list = new Hashtable();
file_list = new Hashtable();
@@ -153,8 +154,6 @@ public class SshFileManager
{
SftpFile sfile = (SftpFile)list[i];
FileAttributes fat = sfile.getAttributes();
-// String modTime = fat.getModTimeString();
-// long modTime = fat.getModifiedTime().longValue()*1000;
if(sfile.isDirectory() || sfile.isLink())
dir_list.put(sfile.getFilename(), fat);
@@ -162,7 +161,6 @@ public class SshFileManager
file_list.put(sfile.getFilename(), fat);
}
-// sftp.quit();
return true;
}
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index e87f7f992a49ce6ac01376b127240ad188891010..124d576058c932e45e009ee5da9c883b81453f2e 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -191,17 +191,14 @@ public class SshPSUClient extends Thread
private boolean waitUntilFileAppears(String file)
throws InterruptedException, IOException
{
- SftpClient sftp;
-
for(int i=0; i < 500; i++)
{
if(System.getProperty("debug") != null)
System.out.println("waitUntilFileAppears() "+file);
Thread.currentThread().sleep(1000);
- sftp = getSftpClient();
try
{
- if(fileExists(sftp, file))
+ if(fileExists(getSftpClient() , file))
return true;
}
catch(SshException sshe)
@@ -211,15 +208,10 @@ public class SshPSUClient extends Thread
System.out.println("waitUntilFileAppears()");
sshe.printStackTrace();
}
-// sftp = getSftpClient();
try
{
-
rescue();
continue;
-// if(fileExists(sftp, file))
-// return true;
-
} catch(Exception exp) {}
}
}
@@ -230,8 +222,17 @@ public class SshPSUClient extends Thread
private boolean fileExists(SftpClient sftp, String file)
throws SshException, IOException
{
- Object list[] = sftp.ls(wdir).toArray();
-
+ Object list[] = null;
+ try
+ {
+ list = sftp.ls(wdir).toArray();
+ }
+ catch(SshException sshe)
+ {
+ sftp = getSftpClient();
+ list = sftp.ls(wdir).toArray();
+ }
+
for(int j=0; j<list.length;j++)
{
if( ((SftpFile)list[j]).getFilename().equals(file) )
@@ -387,15 +388,12 @@ public class SshPSUClient extends Thread
{
if(System.getProperty("debug") != null)
{
- System.out.println("runBlastOrFasta() - 3");
+ System.out.println("NOT STARTED runBlastOrFasta() ----- 3 "+filename);
exp.printStackTrace();
}
rescue();
}
- if(System.getProperty("debug") != null)
- System.out.println("STARTED session");
-
String outputfile = wdir+filename+".out";
final String actualCMD;
@@ -414,7 +412,22 @@ public class SshPSUClient extends Thread
// run the application
if(System.getProperty("debug") != null)
System.out.println(actualCMD);
- session.executeCommand(actualCMD);
+
+ try
+ {
+ session.executeCommand(actualCMD);
+ }
+ catch(IOException exp)
+ {
+ if(System.getProperty("debug") != null)
+ {
+ System.out.println("runBlastOrFasta() - 3");
+ exp.printStackTrace();
+ }
+ }
+
+ if(System.getProperty("debug") != null)
+ System.out.println("STARTED session "+filename);
// Reading from the session InputStream
StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
@@ -437,8 +450,6 @@ public class SshPSUClient extends Thread
ie.printStackTrace();
}
- sftp = getSftpClient();
-
if(System.getProperty("debug") != null)
{
// stdout & stderr
@@ -446,17 +457,10 @@ public class SshPSUClient extends Thread
System.out.println("STDERR "+filename+"\n"+stderrh.getOutput());
}
-// ByteArrayOutputStream os = new ByteArrayOutputStream();
-// sftp.get(outputfile, os);
-// System.out.println(os.toString());
-
-
try
{
+ sftp = getSftpClient();
sftp.get(outputfile, filepath+".out");
-
- if(System.getProperty("debug") != null)
- System.out.println("GET SUCCESS "+filepath+".out");
}
catch(Exception ioe)
{
@@ -466,20 +470,22 @@ public class SshPSUClient extends Thread
ioe.printStackTrace();
}
rescue();
+ sftp = getSftpClient();
sftp.get(outputfile, filepath+".out");
}
+ if(System.getProperty("debug") != null)
+ System.out.println("GET SUCCESS "+filepath+".out");
if(!keep)
{
sftp.rm(outputfile);
sftp.rm(wdir+filename);
- sftp.rm(outputfile+".err");
}
-
+ sftp = getSftpClient();
+ sftp.rm(outputfile+".err");
session.close();
}
- sftp.quit();
return true;
}
@@ -489,21 +495,42 @@ public class SshPSUClient extends Thread
* Return an active SftpClient object
*
*/
- private SftpClient getSftpClient()
+ private synchronized SftpClient getSftpClient()
throws IOException
{
SftpClient sftp;
+
try
{
+ if(!ssh.hasActiveSftpClient())
+ return ssh.openSftpClient();
+
sftp = ssh.getActiveSftpClient();
return sftp;
}
- catch(IOException ioe)
+ catch(SshException sshe)
+ {
+ try
+ {
+ sftp = ssh.openSftpClient();
+ return sftp;
+ }
+ catch(IOException ioe)
+ {
+ if(System.getProperty("debug") != null)
+ {
+ System.out.println("getSftpClient() -- 2");
+ ioe.printStackTrace();
+ }
+ rescue();
+ }
+ }
+ catch(IOException ioe2)
{
if(System.getProperty("debug") != null)
{
System.out.println("getSftpClient()");
- ioe.printStackTrace();
+ ioe2.printStackTrace();
}
rescue();
}
@@ -542,11 +569,16 @@ public class SshPSUClient extends Thread
int read;
while((read = in.read(buffer)) > 0)
buff.append(new String(buffer, 0, read));
+
+ in.close();
+ }
+ catch(Exception ioe)
+ {
+ ioe.printStackTrace();
}
- catch(IOException ioe){}
}
- public String getOutput()
+ public synchronized String getOutput()
{
return buff.toString();
}