diff --git a/uk/ac/sanger/artemis/ExternalProgram.java b/uk/ac/sanger/artemis/ExternalProgram.java
index 03f5d469cdabb271d2b0577706affd1cf80709cd..9a73b7c7ba8f47ad6b6ae630ca7c817bf7ee77af 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 1.2 2004-06-09 13:00:09 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.3 2005-08-11 16:12:43 tjc Exp $
**/
package uk.ac.sanger.artemis;
@@ -41,7 +41,7 @@ import java.util.Enumeration;
* and contains methods for invoking it.
*
* @author Kim Rutherford
- * @version $Id: ExternalProgram.java,v 1.2 2004-06-09 13:00:09 tjc Exp $
+ * @version $Id: ExternalProgram.java,v 1.3 2005-08-11 16:12:43 tjc Exp $
**/
public class ExternalProgram
@@ -146,6 +146,18 @@ public class ExternalProgram
// {
try
{
+ if(System.getProperty("j2ssh") != null)
+ {
+ String [] args = { "-f", file_of_filenames.getPath(),
+ "-cmd", getRealName(),
+ "-d", getProgramOptions()};
+ uk.ac.sanger.artemis.j2ssh.SftpPSUClient ssh =
+ new uk.ac.sanger.artemis.j2ssh.SftpPSUClient( args );
+ ssh.start();
+
+ return null;
+ }
+
final String [] arguments;
switch(program_type)
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 1cf849977b12a241bf58452db01387c6475c050c..b50665037cbb851cb00d4e6970a11755082c6e9a 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -24,6 +24,8 @@
package uk.ac.sanger.artemis.chado;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.sequence.SequenceChangeListener;
import uk.ac.sanger.artemis.sequence.SequenceChangeEvent;
import uk.ac.sanger.artemis.io.QualifierVector;
@@ -37,7 +39,8 @@ import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.FeatureChangeListener;
import uk.ac.sanger.artemis.FeatureChangeEvent;
-
+import uk.ac.sanger.artemis.EntryChangeListener;
+import uk.ac.sanger.artemis.EntryChangeEvent;
import java.util.Vector;
import javax.swing.JOptionPane;
@@ -48,7 +51,7 @@ import javax.swing.JOptionPane;
*
**/
public class ChadoTransactionManager
- implements FeatureChangeListener, SequenceChangeListener
+ implements FeatureChangeListener, EntryChangeListener, SequenceChangeListener
{
private Vector sql = new Vector();
@@ -117,6 +120,22 @@ public class ChadoTransactionManager
}
}
+ public void entryChanged(EntryChangeEvent event)
+ {
+ System.out.println("HERE");
+ if(event.getType() == EntryChangeEvent.FEATURE_ADDED)
+ System.out.println("HERE FEATURE_ADDED");
+
+ Feature feature = event.getFeature();
+
+ if(feature == null)
+ System.out.println("HERE feature == null");
+ else
+ System.out.println("HERE feature != null");
+
+ System.out.println(event.getEntry().getName());
+ }
+
/**
*
* Return a string containing one qualifier per line. These are the
diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index e0c92bbc006935ea8f40e49a56eec993585a05ce..f2a760e2558a322e0db6d9107d04edbf5d92b26d 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.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/components/EntryEdit.java,v 1.18 2005-08-08 10:56:46 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryEdit.java,v 1.19 2005-08-11 16:12:43 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -56,7 +56,7 @@ import javax.swing.border.BevelBorder;
* Each object of this class is used to edit an EntryGroup object.
*
* @author Kim Rutherford
- * @version $Id: EntryEdit.java,v 1.18 2005-08-08 10:56:46 tjc Exp $
+ * @version $Id: EntryEdit.java,v 1.19 2005-08-11 16:12:43 tjc Exp $
*
*/
public class EntryEdit extends JFrame
@@ -939,6 +939,7 @@ public class EntryEdit extends JFrame
{
final ChadoTransactionManager ctm = new ChadoTransactionManager();
getEntryGroup().addFeatureChangeListener(ctm);
+ getEntryGroup().addEntryChangeListener(ctm);
JMenuItem commit = new JMenuItem("Commit to Database");
commit.addActionListener(new ActionListener()
diff --git a/uk/ac/sanger/artemis/components/RunMenu.java b/uk/ac/sanger/artemis/components/RunMenu.java
index 8fc5f2a1d685975035d2e85425f2c904f403a61c..f912871313680f06973b92d04e383bdbe948121a 100644
--- a/uk/ac/sanger/artemis/components/RunMenu.java
+++ b/uk/ac/sanger/artemis/components/RunMenu.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/components/RunMenu.java,v 1.7 2004-12-21 13:46:47 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/RunMenu.java,v 1.8 2005-08-11 16:12:43 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
@@ -43,7 +43,7 @@ import javax.swing.*;
* A JMenu of external commands/functions.
*
* @author Kim Rutherford
- * @version $Id: RunMenu.java,v 1.7 2004-12-21 13:46:47 tjc Exp $
+ * @version $Id: RunMenu.java,v 1.8 2005-08-11 16:12:43 tjc Exp $
**/
public class RunMenu extends SelectionMenu
@@ -171,6 +171,9 @@ public class RunMenu extends SelectionMenu
final ExternalProgramMonitor monitor =
program.run(selection_features, Splash.getLogger());
+ if(monitor == null)
+ return;
+
monitor.addExternalProgramListener(new ExternalProgramListener()
{
public void statusChanged(final ExternalProgramEvent e)
@@ -288,53 +291,53 @@ public class RunMenu extends SelectionMenu
/**
*
**/
- private int[] getIds()
- {
- final FeatureVector selected_features = getSelection().getAllFeatures();
- final Vector ids_vector = new Vector();
+//private int[] getIds()
+//{
+// final FeatureVector selected_features = getSelection().getAllFeatures();
+// final Vector ids_vector = new Vector();
- for(int feature_index = 0; feature_index < selected_features.size();
- ++feature_index)
- {
- final Feature this_feature = selected_features.elementAt(feature_index);
-
- try
- {
- final Qualifier job_qualifier =
- this_feature.getQualifierByName("job");
-
- final StringVector values = job_qualifier.getValues();
+// for(int feature_index = 0; feature_index < selected_features.size();
+// ++feature_index)
+// {
+// final Feature this_feature = selected_features.elementAt(feature_index);
- if(values != null && values.size() > 0)
- {
- for(int value_index=0; value_index<values.size();
- ++value_index)
- {
- final String job_value = values.elementAt(value_index);
- final StringVector bits = StringVector.getStrings(job_value);
+// try
+// {
+// final Qualifier job_qualifier =
+// this_feature.getQualifierByName("job");
+//
+// final StringVector values = job_qualifier.getValues();
- if(bits.size() > 4 && bits.elementAt(2).equals("task:"))
- {
- try
- {
- final Integer task_id = Integer.valueOf(bits.elementAt(3));
-
- if(!ids_vector.contains(task_id))
- ids_vector.add(task_id);
- }
- catch(NumberFormatException e) {}
- }
- }
- }
- }
- catch(InvalidRelationException e) {}
- }
+// if(values != null && values.size() > 0)
+// {
+// for(int value_index=0; value_index<values.size();
+// ++value_index)
+// {
+// final String job_value = values.elementAt(value_index);
+// final StringVector bits = StringVector.getStrings(job_value);
+
+// if(bits.size() > 4 && bits.elementAt(2).equals("task:"))
+// {
+// try
+// {
+// final Integer task_id = Integer.valueOf(bits.elementAt(3));
+
+// if(!ids_vector.contains(task_id))
+// ids_vector.add(task_id);
+// }
+// catch(NumberFormatException e) {}
+// }
+// }
+// }
+// }
+// catch(InvalidRelationException e) {}
+// }
- final int[] ids = new int[ids_vector.size()];
+// final int[] ids = new int[ids_vector.size()];
- for(int i=0 ; i<ids.length ; ++i)
- ids[i] =((Integer)ids_vector.elementAt(i)).intValue();
+// for(int i=0 ; i<ids.length ; ++i)
+// ids[i] =((Integer)ids_vector.elementAt(i)).intValue();
- return ids;
- }
+// return ids;
+//}
}
diff --git a/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java
index 52f37dc6189eee2b82b3b6d09e0dcc5759d24420..684a52b53ccb0dff5a0c0ca1ee1297c9f1a9a2c5 100644
--- a/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java
@@ -50,7 +50,7 @@ import java.util.logging.SimpleFormatter;
/**
*
*/
-public class SftpPSUClient
+public class SftpPSUClient extends Thread
{
private String hostname = null;
@@ -65,7 +65,7 @@ public class SftpPSUClient
public SftpPSUClient(String args[])
{
-
+ // process arguments
if(args != null && args.length > 0)
{
for(int i=0; i<args.length; i++)
@@ -90,8 +90,12 @@ public class SftpPSUClient
wdir = args[i+1];
}
}
+ }
- // get properties
+ public void run()
+ {
+ String program = cmd;
+ // get properties from j2ssh.properties
Properties settings = getProperties();
if(hostname == null && settings.getProperty("host") != null)
hostname = settings.getProperty("host");
@@ -108,8 +112,10 @@ public class SftpPSUClient
else
db = "%uniprot";
}
- if(cmd.equals("blast") && settings.getProperty("blast") != null)
- cmd = settings.getProperty("blast");
+ if(cmd.equals("blastp") && settings.getProperty("blastp") != null)
+ cmd = settings.getProperty("blastp");
+ if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
+ cmd = settings.getProperty("fasta");
try
{
@@ -127,42 +133,53 @@ public class SftpPSUClient
ConfigurationLoader.initialize(false);
- if(hostname == null)
- hostname = (String)JOptionPane.showInputDialog(
- null, "Name of server machine:",
- "Server hostname",
- JOptionPane.PLAIN_MESSAGE, null,
- null, null);
+// if(hostname == null)
+// hostname = (String)JOptionPane.showInputDialog(
+// null, "Name of server machine:",
+// "Server hostname",
+// JOptionPane.PLAIN_MESSAGE, null,
+// null, null);
BufferedReader reader =
new BufferedReader(new InputStreamReader(System.in));
- // Make a client connection
- SshClient ssh = new SshClient();
- // Connect to the host
- if(port < 0)
- ssh.connect(hostname);
- else
- ssh.connect(hostname,port);
-
// Create a password authentication instance
PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
// Get the users name
- JPanel promptPanel = new JPanel(new GridLayout(2,2));
+ JPanel promptPanel = new JPanel(new GridLayout(4,2));
+
+ JTextField hostfield = new JTextField(16);
+ if(hostname != null)
+ hostfield.setText(hostname);
+
+ JTextField portfield = new JTextField(16);
+ if(port >-1)
+ portfield.setText(Integer.toString(port));
+
JTextField ufield = new JTextField(16);
if(user != null)
ufield.setText(user);
JPasswordField pfield = new JPasswordField(16);
+ JLabel hostlab = new JLabel(" Hostname:", SwingConstants.LEFT);
+ JLabel portlab = new JLabel(" Port:", SwingConstants.LEFT);
+
JLabel ulab = new JLabel(" Username:", SwingConstants.LEFT);
JLabel plab = new JLabel(" Password:", SwingConstants.LEFT);
//add labels etc
+ promptPanel.add(hostlab);
+ promptPanel.add(hostfield);
+
+ promptPanel.add(portlab);
+ promptPanel.add(portfield);
+
promptPanel.add(ulab);
promptPanel.add(ufield);
+
promptPanel.add(plab);
promptPanel.add(pfield);
-
+
Object[] options = { "CANCEL", "LOGIN"};
int select = JOptionPane.showOptionDialog(null, promptPanel,
@@ -173,9 +190,22 @@ public class SftpPSUClient
options,
options[1]);
-
if(select == 0)
- System.exit(0);
+ return;
+
+ // Make a client connection
+ SshClient ssh = new SshClient();
+ hostname = hostfield.getText().trim();
+ if(portfield.getText().trim().equals(""))
+ port = -1;
+ else
+ port = Integer.parseInt(portfield.getText().trim());
+
+ // Connect to the host
+ if(port < 0)
+ ssh.connect(hostname);
+ else
+ ssh.connect(hostname,port);
user = ufield.getText().trim();
pwd.setUsername(user);
@@ -194,7 +224,7 @@ public class SftpPSUClient
if(returnVal == JFileChooser.APPROVE_OPTION)
listfilepath = chooser.getSelectedFile().getAbsolutePath();
else
- System.exit(0);
+ return;
}
SftpClient sftp = ssh.openSftpClient();
@@ -219,11 +249,21 @@ public class SftpPSUClient
SessionChannelClient session = ssh.openSessionChannel();
String outputfile = wdir+filename+".out";
+ final String actualCMD;
- cmd = bsub+" -o "+ outputfile +" "+
+ if(cmd.indexOf("fasta33") > -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;
- System.out.println(cmd);
- session.executeCommand(cmd);
+
+ System.out.println(actualCMD);
+ session.executeCommand(actualCMD);
// Reading from the session InputStream
StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
@@ -267,9 +307,11 @@ public class SftpPSUClient
System.out.println(stdouth.getOutput());
System.out.println(stderrh.getOutput());
- ByteArrayOutputStream os = new ByteArrayOutputStream();
- sftp.get(outputfile, os);
- System.out.println(os.toString());
+// ByteArrayOutputStream os = new ByteArrayOutputStream();
+// sftp.get(outputfile, os);
+// System.out.println(os.toString());
+
+ sftp.get(outputfile, filepath+".out");
session.close();
}
@@ -280,15 +322,18 @@ public class SftpPSUClient
}
else
JOptionPane.showMessageDialog(null,
- "Problem logging in!\nCheck username and password.",
- "Authentication Problem",
- JOptionPane.ERROR_MESSAGE);
+ "Problem logging in!\nCheck username and password.",
+ "Authentication Problem",
+ JOptionPane.ERROR_MESSAGE);
} catch(IOException ioe){}
finally
{
- System.out.println("ENDED");
+ JOptionPane.showMessageDialog(null,
+ "Finished \n" + program,
+ "Process Finished",
+ JOptionPane.INFORMATION_MESSAGE);
}
}