diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index a903f48f2f30ab397a9634de745edb660d3b6fb7..70c015d858437a25caf64a87b287036cee63cce6 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -142,135 +142,13 @@ public class SshPSUClient extends Thread
{
ConfigurationLoader.initialize(false);
- int result = AuthenticationProtocolState.FAILED;
+ SshClient ssh = login();
+ if(ssh == null)
+ return;
- SshClient ssh = null;
-
- // login
- while(result != AuthenticationProtocolState.COMPLETE)
- {
- if(!setLogin())
- return;
-
- // Create a password authentication instance
- PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
- user = ufield.getText().trim();
- pwd.setUsername(user);
- pwd.setPassword(new String(pfield.getPassword()));
-
- // Make a client connection
- ssh = new SshClient();
- hostname = hostfield.getText().trim();
- if(portfield.getText().trim().equals(""))
- port = -1;
- else
- port = Integer.parseInt(portfield.getText().trim());
-
- if(port < 0)
- ssh.connect(hostname);
- else
- ssh.connect(hostname,port);
-
- // Try the authentication
- result = ssh.authenticate(pwd);
- }
-
- // prompt for local listfile
- if(listfilepath == null)
- {
- JFileChooser chooser = new JFileChooser();
- int returnVal = chooser.showOpenDialog(null);
- if(returnVal == JFileChooser.APPROVE_OPTION)
- listfilepath = chooser.getSelectedFile().getAbsolutePath();
- else
- return;
- }
-
- SftpClient sftp = ssh.openSftpClient();
-
- // loop over sequence files in the listfile
- Vector seqfile = readListFile(listfilepath);
- for(int i=0; i<seqfile.size();i++)
- {
- String filepath = (String)seqfile.get(i);
- int index = filepath.lastIndexOf(System.getProperty("file.separator"));
- String filename = filepath;
- if(index > -1)
- filename = filename.substring(index+1);
-
- try
- {
- wdir = wdir+"/"+user;
- sftp.mkdir(wdir);
- wdir = wdir+"/"+program+"/";
- sftp.mkdir(wdir);
-
- sftp.put(filepath, wdir+filename);
- }
- catch(IOException ioe)
- {}
-
- SessionChannelClient session = ssh.openSessionChannel();
-
- String outputfile = wdir+filename+".out";
- final String actualCMD;
-
- if( (cmd.indexOf("fasta33") > -1) ||
- (cmd.indexOf("fastx33") > -1) )
- {
- if(settings.getProperty(db) != null)
- db = settings.getProperty(db);
- actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
- cmd+" "+wdir+filename+" "+db;
- }
- else
- actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
- cmd+" "+db+" "+wdir+filename;
-
- // run the application
- if(System.getProperty("debug") != null)
- System.out.println(actualCMD);
- session.executeCommand(actualCMD);
-
- // Reading from the session InputStream
- StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
- StdoutStdErrHandler stderrh = new StdoutStdErrHandler(session, false);
-
- stdouth.start();
- stderrh.start();
-
- boolean isFile = false;
- try
- {
- // make sure we hang around for stdout
- while(stdouth.isAlive() || stderrh.isAlive())
- Thread.currentThread().sleep(10);
-
- isFile = waitUntilFileAppears(sftp, filename+".out");
- }
- catch(InterruptedException ie)
- {
- ie.printStackTrace();
- }
-
- 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();
- }
+ completed = runBlastOrFasta(ssh, program, settings);
// Quit
- sftp.quit();
ssh.disconnect();
}
catch(IOException ioe){}
@@ -338,6 +216,47 @@ public class SshPSUClient extends Thread
return false;
}
+ /**
+ *
+ * Log the user in.
+ *
+ */
+ private SshClient login()
+ throws IOException
+ {
+ SshClient ssh = null;
+ int result = AuthenticationProtocolState.FAILED;
+
+ while(result != AuthenticationProtocolState.COMPLETE)
+ {
+ if(!setLogin())
+ return null;
+
+ // Create a password authentication instance
+ PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
+ user = ufield.getText().trim();
+ pwd.setUsername(user);
+ pwd.setPassword(new String(pfield.getPassword()));
+
+ // Make a client connection
+ ssh = new SshClient();
+ hostname = hostfield.getText().trim();
+ if(portfield.getText().trim().equals(""))
+ port = -1;
+ else
+ port = Integer.parseInt(portfield.getText().trim());
+
+ if(port < 0)
+ ssh.connect(hostname);
+ else
+ ssh.connect(hostname,port);
+
+ // Try the authentication
+ result = ssh.authenticate(pwd);
+ }
+ return ssh;
+ }
+
/**
*
* Set the login information.
@@ -440,6 +359,111 @@ public class SshPSUClient extends Thread
return settings;
}
+ /**
+ *
+ * Run fasta or blast on the server ssh'ed into
+ *
+ */
+ private boolean runBlastOrFasta(SshClient ssh, String program, Properties settings)
+ throws IOException
+ {
+ // prompt for local listfile
+ if(listfilepath == null)
+ {
+ JFileChooser chooser = new JFileChooser();
+ int returnVal = chooser.showOpenDialog(null);
+ if(returnVal == JFileChooser.APPROVE_OPTION)
+ listfilepath = chooser.getSelectedFile().getAbsolutePath();
+ else
+ return false;
+ }
+
+ SftpClient sftp = ssh.openSftpClient();
+
+ // loop over sequence files in the listfile
+ Vector seqfile = readListFile(listfilepath);
+ for(int i=0; i<seqfile.size();i++)
+ {
+ String filepath = (String)seqfile.get(i);
+ int index = filepath.lastIndexOf(System.getProperty("file.separator"));
+ String filename = filepath;
+ if(index > -1)
+ filename = filename.substring(index+1);
+
+ try
+ {
+ wdir = wdir+"/"+user;
+ sftp.mkdir(wdir);
+ wdir = wdir+"/"+program+"/";
+ sftp.mkdir(wdir);
+
+ sftp.put(filepath, wdir+filename);
+ }
+ catch(IOException ioe)
+ {}
+
+ SessionChannelClient session = ssh.openSessionChannel();
+
+ String outputfile = wdir+filename+".out";
+ final String actualCMD;
+
+ if( (cmd.indexOf("fasta33") > -1) ||
+ (cmd.indexOf("fastx33") > -1) )
+ {
+ if(settings.getProperty(db) != null)
+ db = settings.getProperty(db);
+ actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
+ cmd+" "+wdir+filename+" "+db;
+ }
+ else
+ actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
+ cmd+" "+db+" "+wdir+filename;
+
+ // run the application
+ if(System.getProperty("debug") != null)
+ System.out.println(actualCMD);
+ session.executeCommand(actualCMD);
+
+ // Reading from the session InputStream
+ StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
+ StdoutStdErrHandler stderrh = new StdoutStdErrHandler(session, false);
+
+ stdouth.start();
+ stderrh.start();
+
+ boolean isFile = false;
+ try
+ {
+ // make sure we hang around for stdout
+ while(stdouth.isAlive() || stderrh.isAlive())
+ Thread.currentThread().sleep(10);
+
+ isFile = waitUntilFileAppears(sftp, filename+".out");
+ }
+ catch(InterruptedException ie)
+ {
+ ie.printStackTrace();
+ }
+
+ 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");
+ session.close();
+ }
+ sftp.quit();
+
+ return true;
+ }
+
/**
*
* Thread to handle stdout/stderr reading without blocking.