diff --git a/uk/ac/sanger/artemis/ExternalProgram.java b/uk/ac/sanger/artemis/ExternalProgram.java
index 21aa93610d94f4b2dd501eea149685669b48ce5c..080bc9c5c9d568c90a4aa7fb23cdda1fe484d9c3 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 1.7 2005-09-05 17:37:49 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.8 2005-09-06 15:39:44 tjc Exp $
**/
package uk.ac.sanger.artemis;
@@ -42,7 +42,7 @@ import java.util.Enumeration;
* and contains methods for invoking it.
*
* @author Kim Rutherford
- * @version $Id: ExternalProgram.java,v 1.7 2005-09-05 17:37:49 tjc Exp $
+ * @version $Id: ExternalProgram.java,v 1.8 2005-09-06 15:39:44 tjc Exp $
**/
public class ExternalProgram
@@ -121,18 +121,18 @@ public class ExternalProgram
// sequence_file_names will be set by prepareRun()
final File file_of_filenames = prepareRun(features, sequence_file_names);
- final Integer job_control_id =
- Options.getOptions().getIntegerProperty("jcon_" + getName() +
- "_program_id");
+// final Integer job_control_id =
+// Options.getOptions().getIntegerProperty("jcon_" + getName() +
+// "_program_id");
- final Integer min_jc_jobs =
- Options.getOptions().getIntegerProperty("jcon_min_jobs");
+// final Integer min_jc_jobs =
+// Options.getOptions().getIntegerProperty("jcon_min_jobs");
- String jcon_template =
- Options.getOptions().getProperty("jcon_" + getName() + "_template");
+// String jcon_template =
+// Options.getOptions().getProperty("jcon_" + getName() + "_template");
- final String jcon_batch_queue =
- Options.getOptions().getProperty("jcon_batch_queue");
+// final String jcon_batch_queue =
+// Options.getOptions().getProperty("jcon_batch_queue");
// if(job_control_id != null &&
// min_jc_jobs != null &&
@@ -183,6 +183,9 @@ public class ExternalProgram
args[4] = "-d"; args[5] = getProgramOptions();
}
+ if(System.getProperty("debug") != null)
+ System.out.println("CALL SSH CLIENT "+getRealName());
+
uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
new uk.ac.sanger.artemis.j2ssh.SshPSUClient(args);
ssh.start();
@@ -313,6 +316,18 @@ public class ExternalProgram
// store the file number to use for the next sequence file - the key is
// a File containing the directory of there Entry that contains the
// Feature and the value is the next file number to use
+
+ Entry entry = features.elementAt(0).getEntry();
+ RemoteFileNode node = null;
+
+ if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
+ instanceof RemoteFileDocument)
+ {
+ RemoteFileDocument nodeDoc =
+ (RemoteFileDocument)(((DocumentEntry)entry.getEMBLEntry()).getDocument());
+ node = nodeDoc.getRemoteFileNode();
+ }
+
final java.util.Hashtable file_number_hash = new java.util.Hashtable();
for(final Enumeration e = feature_count_hash.keys() ;
@@ -320,14 +335,14 @@ public class ExternalProgram
{
final File directory =(File) e.nextElement();
- final long old_file_number = getFileNumber(directory);
+ final long old_file_number = getFileNumber(directory, node);
final long feature_count =
((Long) feature_count_hash.get(directory)).longValue();
file_number_hash.put(directory, new Long(old_file_number));
- setFileNumber(directory, old_file_number + feature_count);
+ setFileNumber(directory, old_file_number + feature_count, node);
}
// write the sequences out
@@ -413,7 +428,7 @@ public class ExternalProgram
new File(new File(first_directory, getName()),
getName() + "_" +
"file_of_filenames." +
- (getFileNumber(first_directory) - 1));
+ (getFileNumber(first_directory, node) - 1));
final Writer filenames_writer = new FileWriter(file_of_filenames);
@@ -426,6 +441,10 @@ public class ExternalProgram
filenames_printwriter.close();
filenames_writer.close();
+ if(System.getProperty("debug") != null)
+ System.out.println("WRITTEN "+file_of_filenames.getCanonicalPath());
+
+
return file_of_filenames;
}
@@ -518,15 +537,41 @@ public class ExternalProgram
* file_counter_filename. If the file doesn't exist, it is created and
* initialised.
**/
- protected long getFileNumber(final File directory)
+ private long getFileNumber(final File directory,
+ final RemoteFileNode node)
throws IOException
{
try
{
- final FileReader file_reader =
- new FileReader(new File(directory, File.separatorChar +
+ final Reader file_reader;
+ if(node == null)
+ file_reader =
+ new FileReader(new File(directory, File.separatorChar +
getName() + File.separatorChar +
file_counter_filename));
+ else
+ {
+ String dir = node.getRootDir()+ File.separatorChar +
+ node.getFullName();
+ int index = dir.lastIndexOf(File.separatorChar);
+ dir = dir.substring(0,index) + File.separatorChar + getName();
+ byte[] contents = node.getFileContents(null, dir+
+ File.separatorChar+file_counter_filename);
+ if(contents == null)
+ {
+ if(System.getProperty("debug") != null)
+ System.out.println("getFileNumber() creating "+dir+
+ File.separatorChar+file_counter_filename);
+
+ node.mkdir(dir);
+ return setFileNumber(directory, 1, node);
+ }
+
+ file_reader = new StringReader(new String(contents));
+
+ if(System.getProperty("debug") != null)
+ System.out.println("getFileNumber()\n"+new String(contents));
+ }
final BufferedReader reader = new BufferedReader(file_reader);
@@ -534,10 +579,10 @@ public class ExternalProgram
final String comment_line = reader.readLine();
if(comment_line == null || comment_line.length() == 0)
- return setFileNumber(directory, guessNumber(directory));
+ return setFileNumber(directory, guessNumber(directory), node);
if(!comment_line.startsWith("#"))
- return setFileNumber(directory, guessNumber(directory));
+ return setFileNumber(directory, guessNumber(directory), node);
final String number_line = reader.readLine();
@@ -547,7 +592,7 @@ public class ExternalProgram
}
catch(NumberFormatException e)
{
- return setFileNumber(directory, guessNumber(directory));
+ return setFileNumber(directory, guessNumber(directory), node);
}
finally
{
@@ -558,11 +603,11 @@ public class ExternalProgram
catch(FileNotFoundException e)
{
// create a new file_number_counter file
- return setFileNumber(directory, guessNumber(directory));
+ return setFileNumber(directory, guessNumber(directory), node);
}
catch(IOException e)
{
- return setFileNumber(directory, guessNumber(directory));
+ return setFileNumber(directory, guessNumber(directory), node);
}
}
@@ -571,22 +616,37 @@ public class ExternalProgram
* (eg. directory + "/blastp/" + new_file_number).
**/
protected long setFileNumber(final File directory,
- final long new_file_number)
+ final long new_file_number, final RemoteFileNode node)
throws IOException
{
makeDirectory(new File(directory, getName()));
- final FileWriter file_writer =
- new FileWriter(new File(directory, File.separatorChar +
- getName() + File.separatorChar +
- file_counter_filename));
+ File local_file = new File(directory, File.separatorChar +
+ getName() + File.separatorChar +
+ file_counter_filename);
+ final FileWriter file_writer = new FileWriter(local_file);
final PrintWriter print_writer = new PrintWriter(file_writer);
print_writer.println("# the file is machine generated - do not edit");
print_writer.println(new_file_number);
print_writer.close();
file_writer.close();
+
+ if(node != null)
+ {
+ String dir = node.getRootDir()+ File.separatorChar +
+ node.getFullName();
+ int index = dir.lastIndexOf(File.separatorChar);
+ dir = dir.substring(0,index) + File.separatorChar +
+ getName() + File.separatorChar;
+
+ if(System.getProperty("debug") != null)
+ System.out.println("setFileNumber() "+
+ local_file.getCanonicalPath()+" --> "+dir);
+
+ node.put(dir, local_file, null, true);
+ }
return new_file_number;
}
diff --git a/uk/ac/sanger/artemis/components/filetree/FileList.java b/uk/ac/sanger/artemis/components/filetree/FileList.java
index bf6801c8ac8d6c7b29f062f80cf54aa3fcb69e10..c9cc8092b6fa71bd8e0a3b281a680b04793c1b1b 100644
--- a/uk/ac/sanger/artemis/components/filetree/FileList.java
+++ b/uk/ac/sanger/artemis/components/filetree/FileList.java
@@ -108,9 +108,10 @@ public class FileList
* Put a file
*
*/
- protected boolean put(String dir, File local_file, FTProgress monitor)
+ protected boolean put(String dir, File local_file,
+ FTProgress monitor, boolean force)
{
- return ssh_client.put(dir, local_file, monitor);
+ return ssh_client.put(dir, local_file, monitor, force);
}
diff --git a/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java b/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
index 7dcdfff78ebb9bc6f9baad2b6446adad58222072..1786af799faf3beb2a41a82eb48810b317e34e4c 100644
--- a/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
+++ b/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
@@ -197,7 +197,7 @@ public class RemoteFileNode extends DefaultMutableTreeNode
return flist.delete(getRootDir()+"/"+getFullName());
}
- protected boolean mkdir(String dir)
+ public boolean mkdir(String dir)
{
FileList flist = new FileList();
return flist.mkdir(dir);
@@ -211,7 +211,6 @@ public class RemoteFileNode extends DefaultMutableTreeNode
public boolean put(File local_file, FTProgress monitor)
{
- FileList flist = new FileList();
String dir;
if(!isDirectory())
{
@@ -222,9 +221,15 @@ public class RemoteFileNode extends DefaultMutableTreeNode
else
dir = getRootDir()+"/"+getFullName();
- return flist.put(dir, local_file, monitor);
+ return put(dir, local_file, monitor, false);
}
+ public boolean put(String dir, File local_file,
+ FTProgress monitor, boolean force)
+ {
+ FileList flist = new FileList();
+ return flist.put(dir, local_file, monitor, force);
+ }
public byte[] getFileContents(FTProgress monitor)
{
@@ -232,6 +237,12 @@ public class RemoteFileNode extends DefaultMutableTreeNode
return flist.getFileContents(getRootDir()+"/"+getFullName(), monitor);
}
+ public byte[] getFileContents(FTProgress monitor, String filename)
+ {
+ FileList flist = new FileList();
+ return flist.getFileContents(filename, monitor);
+ }
+
// Transferable
public DataFlavor[] getTransferDataFlavors()
{
diff --git a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
index c45aeeafbe7689adb05c1bd9b2abc015a2c1c5ff..dffd4b82ab18c2b96f9a959fd752fe083e90d07b 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
@@ -251,7 +251,7 @@ public class SshFileManager
*
*/
public boolean put(final String dir, final File local_file,
- final FTProgress monitor)
+ final FTProgress monitor, final boolean force)
{
SftpClient sftp = null;
@@ -268,7 +268,7 @@ public class SshFileManager
JOptionPane.ERROR_MESSAGE);
return false;
}
- else
+ else if(!force)
{
int n = JOptionPane.showConfirmDialog(null,
"Overwrite\n"+
@@ -352,10 +352,15 @@ public class SshFileManager
// sftp.quit();
return os.toByteArray();
}
+ catch(SshException se)
+ {
+ rescue();
+ return getFileContents(file, monitor);
+ }
catch(IOException ioe)
{
rescue();
- ioe.printStackTrace();
+// ioe.printStackTrace();
return null;
}
}
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index ca143bfb40a2c367bcc03d4164ae304cde1829f8..ab9df32a9e48061a9ac2ac264527bff1c8c05362 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -113,6 +113,9 @@ public class SshPSUClient extends Thread
if(ssh == null)
return;
+ if(System.getProperty("debug") != null)
+ System.out.println("RUN "+program);
+
completed = runBlastOrFasta(ssh, program);
// Quit
@@ -256,7 +259,7 @@ public class SshPSUClient extends Thread
return false;
}
- SftpClient sftp = ssh.openSftpClient();
+ SftpClient sftp = getSftpClient();
// loop over sequence files in the listfile
Vector seqfile = readListFile(listfilepath);
@@ -287,7 +290,7 @@ public class SshPSUClient extends Thread
String outputfile = wdir+filename+".out";
final String actualCMD;
-
+
if( (cmd.indexOf("fasta33") > -1) ||
(cmd.indexOf("fastx33") > -1) )
{
@@ -352,6 +355,24 @@ public class SshPSUClient extends Thread
return true;
}
+ /**
+ *
+ * Return an active SftpClient object
+ *
+ */
+ private SftpClient getSftpClient()
+ throws IOException
+ {
+ SftpClient sftp;
+ try
+ {
+ sftp = ssh.getActiveSftpClient();
+ return sftp;
+ }
+ catch(IOException ioe){}
+ return ssh.openSftpClient();
+ }
+
/**
*
* Thread to handle stdout/stderr reading without blocking.