remote ssh exec in working dir

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3644 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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 1.6 2005-08-17 17:03:06 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.7 2005-09-05 17:37:49 tjc Exp $
  **/
 
 package uk.ac.sanger.artemis;
@@ -30,6 +30,7 @@ import uk.ac.sanger.artemis.io.EntryInformation;
 import uk.ac.sanger.artemis.io.EntryInformationException;
 import uk.ac.sanger.artemis.io.DocumentEntry;
 import uk.ac.sanger.artemis.io.Qualifier;
+import uk.ac.sanger.artemis.components.filetree.RemoteFileNode;
 
 import java.io.*;
 import java.text.*;
@@ -41,7 +42,7 @@ import java.util.Enumeration;
  *  and contains methods for invoking it.
  *
  *  @author Kim Rutherford
- *  @version $Id: ExternalProgram.java,v 1.6 2005-08-17 17:03:06 tjc Exp $
+ *  @version $Id: ExternalProgram.java,v 1.7 2005-09-05 17:37:49 tjc Exp $
  **/
 
 public class ExternalProgram 
@@ -149,9 +150,38 @@ public class ExternalProgram
         if( System.getProperty("j2ssh") != null &&
             (getRealName().indexOf("blast") > -1 || getRealName().startsWith("fast")) )
         {
-          String [] args = { "-f", file_of_filenames.getPath(),
-                             "-cmd", getRealName(),
-                             "-d", getProgramOptions()};
+
+          final Feature this_feature = features.elementAt(0);
+          Entry entry = this_feature.getEntry();
+          String [] args;
+
+          if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
+                            instanceof RemoteFileDocument)
+          {
+            RemoteFileDocument nodeDoc =
+               (RemoteFileDocument)(((DocumentEntry)entry.getEMBLEntry()).getDocument());
+            RemoteFileNode node = nodeDoc.getRemoteFileNode();
+
+            String wdir = node.getRootDir()+"/"+node.getFullName();
+            int index = wdir.lastIndexOf("/");
+            wdir = wdir.substring(0,index);
+
+            args = new String[9];
+
+            args[0] = "-f";    args[1] = file_of_filenames.getPath();
+            args[2] = "-cmd";  args[3] = getRealName();
+            args[4] = "-wdir"; args[5] = wdir; 
+            args[6] = "-d";    args[7] = getProgramOptions();
+            args[8] = "-keep";
+          }
+          else
+          {
+            args = new String[6];
+
+            args[0] = "-f";    args[1] = file_of_filenames.getPath();
+            args[2] = "-cmd";  args[3] = getRealName();
+            args[4] = "-d";    args[5] = getProgramOptions();
+          }
 
           uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
                 new uk.ac.sanger.artemis.j2ssh.SshPSUClient(args);

uk/ac/sanger/artemis/j2ssh/SshPSUClient.java

@@ -65,11 +65,12 @@ public class SshPSUClient extends Thread
   private String bsub     = null;
   private String logfile  = null;
   private String db       = null;
-  private String wdir     = "/nfs/pathscratch1/scratch";
+  private String wdir     = null;
 
   //
   private SshClient ssh;
   private String user;
+  private boolean keep = false;
 
   public SshPSUClient(String args[])
   {
@@ -90,6 +91,8 @@ public class SshPSUClient extends Thread
           db = args[i+1];
         else if(args[i].equals("-wdir") && i < args.length-1)
           wdir = args[i+1];
+        else if(args[i].equals("-keep"))
+          keep = true;
       }
     }
 
@@ -102,9 +105,6 @@ public class SshPSUClient extends Thread
   {
     String program = cmd;
 
-    // get properties from j2ssh.properties
-    Properties settings = getProperties();
-
     boolean completed = false;
     try
     {
@@ -113,7 +113,7 @@ public class SshPSUClient extends Thread
       if(ssh == null)
         return;
 
-      completed = runBlastOrFasta(ssh, program, settings);
+      completed = runBlastOrFasta(ssh, program);
 
       // Quit
       //ssh.disconnect();
@@ -212,7 +212,7 @@ public class SshPSUClient extends Thread
         db = "%uniprot";
     } 
 
-    if(settings.getProperty("wdir") != null)
+    if(wdir == null && settings.getProperty("wdir") != null)
       wdir = settings.getProperty("wdir");
 
     if(cmd != null)
@@ -240,9 +240,11 @@ public class SshPSUClient extends Thread
   * Run fasta or blast on the server ssh'ed into
   *
   */
-  private boolean runBlastOrFasta(SshClient ssh, String program, Properties settings)
+  private boolean runBlastOrFasta(SshClient ssh, String program)
                     throws IOException
   {
+    Properties settings = getProperties();
+
     // prompt for local listfile
     if(listfilepath == null)
     {
@@ -268,11 +270,12 @@ public class SshPSUClient extends Thread
 
       try
       {
+        if(!keep)
           wdir = wdir+"/"+user;
         sftp.mkdir(wdir);
         wdir = wdir+"/"+program+"/";
-        sftp.mkdir(wdir);
 
+        sftp.mkdir(wdir);
         sftp.put(filepath, wdir+filename);
       }
       catch(IOException ioe)
@@ -335,8 +338,12 @@ public class SshPSUClient extends Thread
 //    System.out.println(os.toString());
 
       sftp.get(outputfile, filepath+".out");
+
+      if(!keep)
+      {
         sftp.rm(outputfile);
         sftp.rm(wdir+filename);
+      }
 
       session.close();
     }