diff --git a/uk/ac/sanger/artemis/ExternalProgram.java b/uk/ac/sanger/artemis/ExternalProgram.java
index 61779cc39c93020e1a65e92adec135b67e122b74..bb83140740abd0256ab41d324593d1dd1766cb5a 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 1.5 2005-08-12 16:01:48 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ExternalProgram.java,v 1.6 2005-08-17 17:03:06 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 1.5 2005-08-12 16:01:48 tjc Exp $
+ * @version $Id: ExternalProgram.java,v 1.6 2005-08-17 17:03:06 tjc Exp $
**/
public class ExternalProgram
@@ -152,6 +152,7 @@ public class ExternalProgram
String [] args = { "-f", file_of_filenames.getPath(),
"-cmd", getRealName(),
"-d", getProgramOptions()};
+
uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
new uk.ac.sanger.artemis.j2ssh.SshPSUClient(args);
ssh.start();
diff --git a/uk/ac/sanger/artemis/components/ArtemisMain.java b/uk/ac/sanger/artemis/components/ArtemisMain.java
index 2c1671d07709f0e746cc521e6e65b81387e348c1..7cd6ca7a0b80a454f03d95abc4f330312c0d65a1 100644
--- a/uk/ac/sanger/artemis/components/ArtemisMain.java
+++ b/uk/ac/sanger/artemis/components/ArtemisMain.java
@@ -20,12 +20,13 @@
* 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/ArtemisMain.java,v 1.17 2005-08-17 08:43:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.18 2005-08-17 17:03:06 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.components.filetree.FileManager;
+import uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.sequence.Bases;
@@ -46,7 +47,7 @@ import java.io.*;
* The main window for the Artemis sequence editor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ArtemisMain.java,v 1.17 2005-08-17 08:43:05 tjc Exp $
+ * @version $Id: ArtemisMain.java,v 1.18 2005-08-17 17:03:06 tjc Exp $
**/
public class ArtemisMain extends Splash
@@ -78,6 +79,22 @@ public class ArtemisMain extends Splash
};
makeMenuItem(file_menu, "Open File Manager ...", menu_listener);
+
+ ActionListener menu_listener_ssh = new ActionListener()
+ {
+ private LocalAndRemoteFileManager fm;
+ public void actionPerformed(ActionEvent event)
+ {
+ if(fm == null)
+ fm = new LocalAndRemoteFileManager(ArtemisMain.this);
+ else
+ fm.setVisible(true);
+ }
+ };
+ makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
+
+
+
final EntrySourceVector entry_sources = getEntrySources(this);
for(int source_index=0; source_index<entry_sources.size();
diff --git a/uk/ac/sanger/artemis/components/filetree/FileList.java b/uk/ac/sanger/artemis/components/filetree/FileList.java
index e32322eadf835e5a280f60a7b19fa8e1bfa23497..2888f5e6f96a42b72b69e0427d3c8ccdab7f7e07 100644
--- a/uk/ac/sanger/artemis/components/filetree/FileList.java
+++ b/uk/ac/sanger/artemis/components/filetree/FileList.java
@@ -33,7 +33,7 @@ public class FileList
private Vector vdir;
private Vector vfile;
private static SshFileManager ssh_client = new SshFileManager();
-
+
public FileList()
{
}
@@ -125,7 +125,15 @@ public class FileList
*/
public Vector fileVector()
{
- return vfile;
+ final Vector vfile_filtered = new Vector();
+ for(int i=0; i<vfile.size(); i++)
+ {
+ String sfile = (String)vfile.get(i);
+ if(!sfile.startsWith("."))
+ vfile_filtered.add(sfile);
+ }
+
+ return vfile_filtered;
}
diff --git a/uk/ac/sanger/artemis/components/filetree/FileManager.java b/uk/ac/sanger/artemis/components/filetree/FileManager.java
index 85aca7e09dbf8bf8fb5289c05775f71b01f22f7b..706662834060f9ffbc225568e4387539f9a6846e 100644
--- a/uk/ac/sanger/artemis/components/filetree/FileManager.java
+++ b/uk/ac/sanger/artemis/components/filetree/FileManager.java
@@ -30,6 +30,9 @@ import java.io.FileFilter;
import java.awt.event.*;
import java.awt.geom.*;
import java.awt.*;
+import java.util.Properties;
+import java.util.Vector;
+import java.util.Enumeration;
public class FileManager extends JFrame
{
@@ -54,7 +57,7 @@ public class FileManager extends JFrame
{
super("File Manager");
- FileTree ftree = new FileTree(new File(System.getProperty("user.dir")),
+ FileTree ftree = new FileTree(getLocalDirectories(),
frame, filter);
JScrollPane jsp = new JScrollPane(ftree);
JPanel pane = (JPanel)getContentPane();
@@ -73,6 +76,45 @@ public class FileManager extends JFrame
setVisible(true);
}
+ /**
+ *
+ * Look in j2ssh.properties for local directories.
+ *
+ */
+ private File[] getLocalDirectories()
+ {
+ final Properties settings = new Properties();
+ ClassLoader cl = getClass().getClassLoader();
+ // try out of the classpath
+ try
+ {
+ settings.load(cl.getResourceAsStream("j2ssh.properties"));
+ }
+ catch (Exception e)
+ {
+ }
+
+ Enumeration enum_prop = settings.propertyNames();
+ Vector dirs = new Vector();
+
+ dirs.add(new File(System.getProperty("user.home")));
+ dirs.add(new File(System.getProperty("user.dir")));
+
+ while(enum_prop.hasMoreElements())
+ {
+ final String property = (String)enum_prop.nextElement();
+ File f = new File(settings.getProperty(property));
+ if(property.startsWith("localdir") && f.exists())
+ dirs.add(f);
+ }
+
+ File fdirs[] = new File[dirs.size()];
+ for(int i=0; i<dirs.size(); i++)
+ fdirs[i] = (File)dirs.get(i);
+
+ return fdirs;
+ }
+
protected JComboBox getFileFileterComboBox(final FileTree ftree)
{
String[] filters = { "Artemis Files", "Sequence Files",
@@ -229,45 +271,6 @@ public class FileManager extends JFrame
JMenu fileMenu = new JMenu("File");
mBar.add(fileMenu);
- JMenuItem fileMenuGoto = new JMenuItem("Go to Directory ...");
- fileMenuGoto.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- String dir = ftree.getRoot().getAbsolutePath();
- String newDir = JOptionPane.showInputDialog(FileManager.this,
- "Go to Directory:",dir);
-
- if(newDir == null)
- return;
-
- newDir = newDir.trim();
- File newDirFile = new File(newDir);
-
- if(newDirFile.exists() &&
- newDirFile.canRead() &&
- !newDir.equals(dir))
- ftree.newRoot(newDir);
- else
- {
- String error = null;
- if(!newDirFile.exists())
- error = new String(newDir+" doesn't exist!");
- else if(!newDirFile.canRead())
- error = new String(newDir+" cannot be read!");
- else if(newDir.equals(dir))
- error = new String("Same directory!");
-
- if(error != null)
- JOptionPane.showMessageDialog(FileManager.this,
- error, "Warning",
- JOptionPane.WARNING_MESSAGE);
- }
- }
- });
- fileMenu.add(fileMenuGoto);
- fileMenu.add(new JSeparator());
-
JMenuItem fileMenuClose = new JMenuItem("Close");
fileMenuClose.addActionListener(new ActionListener()
{
@@ -278,138 +281,6 @@ public class FileManager extends JFrame
});
fileMenu.add(fileMenuClose);
- // tool bar set up
- JToolBar toolBar = new JToolBar();
- Dimension buttonSize = new Dimension(22,24);
-
- JButton upBt = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
-
- g2.setColor(new Color(0,128,0));
- float loc1[][] = { {11,18}, {7,18}, {7,14},
- {3,14}, {11,4} };
-
- g2.fill(makeShape(loc1));
- g2.setColor(Color.green);
-
- float loc2[][] = { {11,18}, {15,18}, {15,14},
- {19,14}, {11,4} };
- g2.fill(makeShape(loc2));
-
- setSize(22,24);
- }
- };
- upBt.setPreferredSize(buttonSize);
- upBt.setMinimumSize(buttonSize);
-
- upBt.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- FileManager.this.setCursor(cbusy);
- File root = ftree.getRoot();
- String parent = root.getParent();
- if(parent != null)
- ftree.newRoot(parent);
- FileManager.this.setCursor(cdone);
- }
- });
- toolBar.add(upBt);
-
-// yeastpub
- JButton shortCut1 = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
- Font font = new Font("Monospaced", Font.BOLD, 14);
- g2.setFont(font);
-
- g2.setColor(Color.black);
- g2.drawString("Y",4,18);
- g2.setColor(Color.red);
- g2.drawString("P",10,15);
- setSize(22,24);
- }
- };
- shortCut1.setPreferredSize(buttonSize);
- shortCut1.setMinimumSize(buttonSize);
- shortCut1.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ftree.newRoot("/nfs/disk222/yeastpub");
- }
- });
-
- if((new File("/nfs/disk222/yeastpub")).exists())
- toolBar.add(shortCut1);
-
-// pathdata
- JButton shortCut2 = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
- Font font = new Font("Monospaced", Font.BOLD, 14);
- g2.setFont(font);
-
- g2.setColor(Color.black);
- g2.drawString("P",4,18);
- g2.setColor(Color.red);
- g2.drawString("D",10,15);
- setSize(22,24);
- }
- };
- shortCut2.setPreferredSize(buttonSize);
- shortCut2.setMinimumSize(buttonSize);
- shortCut2.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ftree.newRoot("/nfs/pathdata/");
- }
- });
-
- if((new File("/nfs/pathdata/")).exists())
- toolBar.add(shortCut2);
-
-// home button
- JButton homeBt = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
-
- g2.setColor(Color.blue);
- float loc1[][] = { {3,14}, {11,3}, {19,14},
- {17,14}, {17,18}, {5,18}, {5,14} };
- g2.fill(makeShape(loc1));
-
- setSize(22,24);
- }
- };
- homeBt.setPreferredSize(buttonSize);
- homeBt.setMinimumSize(buttonSize);
- homeBt.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ftree.newRoot(System.getProperty("user.home"));
- }
- });
- toolBar.add(homeBt);
-
- toolBar.add(Box.createVerticalStrut(35));
- pane.add(toolBar, BorderLayout.NORTH);
-
return mBar;
}
diff --git a/uk/ac/sanger/artemis/components/filetree/FileNode.java b/uk/ac/sanger/artemis/components/filetree/FileNode.java
index 6542722e7c292e2c4d383102599d9c0a697e1529..94c66d4842b14328ebdcf3fec2233bcb0f59a1ab 100644
--- a/uk/ac/sanger/artemis/components/filetree/FileNode.java
+++ b/uk/ac/sanger/artemis/components/filetree/FileNode.java
@@ -34,6 +34,7 @@ import java.util.*;
public class FileNode extends DefaultMutableTreeNode
implements Transferable, Serializable
{
+ private boolean isDir;
/** true if explored */
private boolean explored = false;
/** data flavour of a file node */
@@ -50,6 +51,7 @@ public class FileNode extends DefaultMutableTreeNode
public FileNode(File file)
{
setUserObject(file);
+ this.isDir = file.isDirectory();
}
/** Determine if this is a directory */
@@ -62,9 +64,13 @@ public class FileNode extends DefaultMutableTreeNode
public boolean isExplored() { return explored; }
/** Determine if this is a directory */
public boolean isDirectory()
+ {
+ return isDir;
+ }
+
+ protected void setDirectory(boolean isDir)
{
- File file = getFile();
- return file.isDirectory();
+ this.isDir = isDir;
}
/**
diff --git a/uk/ac/sanger/artemis/components/filetree/FileTree.java b/uk/ac/sanger/artemis/components/filetree/FileTree.java
index cd86e466b3b628700df6f045f9f24d55b1bc347f..4aa4a555d48c4f4b68397f10a4ee56b790752850 100644
--- a/uk/ac/sanger/artemis/components/filetree/FileTree.java
+++ b/uk/ac/sanger/artemis/components/filetree/FileTree.java
@@ -60,7 +60,7 @@ public class FileTree extends JTree implements DragGestureListener,
{
/** root directory */
- private File root;
+ private File root[];
/** store of directories that are opened */
private Vector openNode;
/** file separator */
@@ -78,13 +78,14 @@ public class FileTree extends JTree implements DragGestureListener,
/** file filter */
private FileFilter filter = null;
+
/**
*
* @param rt root directory
* @param f frame
*
*/
- public FileTree(File rt, final JFrame f,
+ public FileTree(File rt[], final JFrame f,
FileFilter filter)
{
this.root = rt;
@@ -193,7 +194,7 @@ public class FileTree extends JTree implements DragGestureListener,
if(source.getText().equals("Refresh"))
{
if(node == null)
- newRoot(root.getAbsolutePath());
+ return;
else if(node.isLeaf())
refresh((FileNode)node.getParent());
else
@@ -369,7 +370,8 @@ public class FileTree extends JTree implements DragGestureListener,
*/
public void newRoot(String newRoot)
{
- root = new File(newRoot);
+// root = new File(newRoot);
+
DefaultTreeModel model = (DefaultTreeModel)getModel();
model = createTreeModel(root);
setModel(model);
@@ -383,7 +385,7 @@ public class FileTree extends JTree implements DragGestureListener,
*/
public File getRoot()
{
- return root;
+ return null;
}
/**
@@ -495,12 +497,24 @@ public class FileTree extends JTree implements DragGestureListener,
* to the given directory
*
*/
- private DefaultTreeModel createTreeModel(File root)
+ private DefaultTreeModel createTreeModel(File root[])
{
- FileNode rootNode = new FileNode(root);
- rootNode.explore(filter);
- openNode = new Vector();
- openNode.add(rootNode);
+ FileNode rootNode = new FileNode(new File(""));
+ rootNode.setDirectory(true);
+
+ for(int i=0; i<root.length; i++)
+ {
+ FileNode node = new FileNode(root[i]);
+
+ if(i == 0)
+ {
+ node.explore(filter);
+ openNode = new Vector();
+ openNode.add(node);
+ }
+ rootNode.add(node);
+ }
+
return new DefaultTreeModel(rootNode);
}
@@ -935,8 +949,10 @@ public class FileTree extends JTree implements DragGestureListener,
public static void main(String[] args)
{
JFrame tree_frame = new JFrame("File Manager");
- FileTree ftree = new FileTree(new File(System.getProperty("user.home")),
- tree_frame,null);
+
+ File dirs[] = new File[1];
+ dirs[0] = new File(System.getProperty("user.home"));
+ FileTree ftree = new FileTree(dirs, tree_frame, null);
JScrollPane jsp = new JScrollPane(ftree);
tree_frame.getContentPane().add(jsp);
tree_frame.pack();
diff --git a/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java b/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
index b105a2e9c78404e48805148f64a1ad96c3bac0be..810e917ee4f5618deaab256c56a838c9b7f128bd 100644
--- a/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
+++ b/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
@@ -21,6 +21,7 @@
package uk.ac.sanger.artemis.components.filetree;
+import uk.ac.sanger.artemis.j2ssh.SshLogin;
import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.Options;
@@ -30,6 +31,10 @@ import java.io.FileFilter;
import java.awt.event.*;
import java.awt.geom.*;
import java.awt.*;
+import java.util.Properties;
+import java.util.Enumeration;
+import java.util.Vector;
+import javax.swing.border.Border;
public class LocalAndRemoteFileManager extends JFrame
{
@@ -54,19 +59,24 @@ public class LocalAndRemoteFileManager extends JFrame
{
super("File Manager");
+ FileList flist = new FileList();
final JPanel localPanel = new JPanel(new BorderLayout());
- FileTree ftree = new FileTree(new File(System.getProperty("user.dir")),
- frame, filter);
+
+ FileTree ftree = new FileTree(getLocalDirectories(), this, filter);
JScrollPane localTree = new JScrollPane(ftree);
localPanel.add(localTree,BorderLayout.CENTER);
+ final JLabel local_status_line = getStatusLabel("LOCAL");
+ localPanel.add(local_status_line,BorderLayout.NORTH);
+
final JPanel remotePanel = new JPanel(new BorderLayout());
- FileList flist = new FileList();
- String pwd = flist.pwd();
- SshFileTree sshtree = new SshFileTree(pwd);
+ SshFileTree sshtree = new SshFileTree( getRemoteDirectories(flist.pwd()) );
JScrollPane remoteTree = new JScrollPane(sshtree);
remotePanel.add(remoteTree,BorderLayout.CENTER);
+
+ final JLabel remote_status_line = getStatusLabel("REMOTE");
+ remotePanel.add(remote_status_line,BorderLayout.NORTH);
final JSplitPane treePane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,
localPanel,remotePanel);
@@ -76,7 +86,7 @@ public class LocalAndRemoteFileManager extends JFrame
pane.add(treePane, BorderLayout.CENTER);
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- Dimension panelSize = new Dimension(210, (int)(screen.getHeight()/3));
+ Dimension panelSize = new Dimension(240, (int)(screen.getHeight()/2));
setJMenuBar(makeMenuBar(pane,ftree,sshtree,localPanel,remotePanel,treePane,panelSize));
localPanel.add(getFileFileterComboBox(ftree), BorderLayout.SOUTH);
@@ -90,6 +100,82 @@ public class LocalAndRemoteFileManager extends JFrame
setVisible(true);
}
+ /**
+ *
+ * Create a status JLabel with bevelled border
+ *
+ */
+ private JLabel getStatusLabel(String status)
+ {
+ final JLabel status_line = new JLabel(status);
+ Border loweredbevel = BorderFactory.createLoweredBevelBorder();
+ Border raisedbevel = BorderFactory.createRaisedBevelBorder();
+ Border compound = BorderFactory.createCompoundBorder(raisedbevel,loweredbevel);
+ status_line.setBorder(compound);
+
+ final FontMetrics fm =
+ this.getFontMetrics(status_line.getFont());
+ final int font_height = fm.getHeight()+10;
+
+ status_line.setMinimumSize(new Dimension(100, font_height));
+ status_line.setPreferredSize(new Dimension(100, font_height));
+ return status_line;
+ }
+
+ /**
+ *
+ * Look in j2ssh.properties for local directories.
+ *
+ */
+ private File[] getLocalDirectories()
+ {
+ final Properties settings = SshLogin.getProperties();
+ Enumeration enum_prop = settings.propertyNames();
+ Vector dirs = new Vector();
+
+ dirs.add(new File(System.getProperty("user.home")));
+ dirs.add(new File(System.getProperty("user.dir")));
+
+ while(enum_prop.hasMoreElements())
+ {
+ final String property = (String)enum_prop.nextElement();
+ File f = new File(settings.getProperty(property));
+ if(property.startsWith("localdir") && f.exists())
+ dirs.add(f);
+ }
+
+ File fdirs[] = new File[dirs.size()];
+ for(int i=0; i<dirs.size(); i++)
+ fdirs[i] = (File)dirs.get(i);
+
+ return fdirs;
+ }
+
+ /**
+ *
+ * Look in j2ssh.properties for remote directories.
+ *
+ */
+ private String[] getRemoteDirectories(String pwd)
+ {
+ final Properties settings = SshLogin.getProperties();
+ Enumeration enum_prop = settings.propertyNames();
+ Vector dirs = new Vector();
+ dirs.add(pwd);
+ while(enum_prop.hasMoreElements())
+ {
+ final String property = (String)enum_prop.nextElement();
+ if(property.startsWith("remotedir"))
+ dirs.add(settings.getProperty(property));
+ }
+
+ String sdirs[] = new String[dirs.size()];
+ for(int i=0; i<dirs.size(); i++)
+ sdirs[i] = (String)dirs.get(i);
+
+ return sdirs;
+ }
+
protected JComboBox getFileFileterComboBox(final FileTree ftree)
{
String[] filters = { "Artemis Files", "Sequence Files",
@@ -248,45 +334,6 @@ public class LocalAndRemoteFileManager extends JFrame
JMenu fileMenu = new JMenu("File");
mBar.add(fileMenu);
- JMenuItem fileMenuGoto = new JMenuItem("Go to Directory ...");
- fileMenuGoto.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- String dir = ftree.getRoot().getAbsolutePath();
- String newDir = JOptionPane.showInputDialog(LocalAndRemoteFileManager.this,
- "Go to Directory:",dir);
-
- if(newDir == null)
- return;
-
- newDir = newDir.trim();
- File newDirFile = new File(newDir);
-
- if(newDirFile.exists() &&
- newDirFile.canRead() &&
- !newDir.equals(dir))
- ftree.newRoot(newDir);
- else
- {
- String error = null;
- if(!newDirFile.exists())
- error = new String(newDir+" doesn't exist!");
- else if(!newDirFile.canRead())
- error = new String(newDir+" cannot be read!");
- else if(newDir.equals(dir))
- error = new String("Same directory!");
-
- if(error != null)
- JOptionPane.showMessageDialog(LocalAndRemoteFileManager.this,
- error, "Warning",
- JOptionPane.WARNING_MESSAGE);
- }
- }
- });
- fileMenu.add(fileMenuGoto);
- fileMenu.add(new JSeparator());
-
JRadioButtonMenuItem prefV = new JRadioButtonMenuItem("Vertical Split");
fileMenu.add(prefV);
prefV.addActionListener(new ActionListener()
@@ -342,137 +389,12 @@ public class LocalAndRemoteFileManager extends JFrame
fileMenu.add(fileMenuClose);
// remote tool bar set up
- JToolBar remoteToolBar = new JToolBar();
- Dimension buttonSize = new Dimension(22,24);
-
- JButton remoteUpBt = new UpButton();
- remoteUpBt.setPreferredSize(buttonSize);
- remoteUpBt.setMinimumSize(buttonSize);
-
- remoteUpBt.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- LocalAndRemoteFileManager.this.setCursor(cbusy);
- sshtree.up();
- LocalAndRemoteFileManager.this.setCursor(cdone);
- }
- });
- remoteToolBar.add(remoteUpBt);
-
- remoteToolBar.add(Box.createVerticalStrut(35));
- remotePanel.add(remoteToolBar, BorderLayout.NORTH);
+// JToolBar remoteToolBar = new JToolBar();
+// remotePanel.add(remoteToolBar, BorderLayout.NORTH);
// local tool bar set up
- JToolBar toolBar = new JToolBar();
-
- JButton upBt = new UpButton();
- upBt.setPreferredSize(buttonSize);
- upBt.setMinimumSize(buttonSize);
-
- upBt.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- LocalAndRemoteFileManager.this.setCursor(cbusy);
- File root = ftree.getRoot();
- String parent = root.getParent();
- if(parent != null)
- ftree.newRoot(parent);
- LocalAndRemoteFileManager.this.setCursor(cdone);
- }
- });
- toolBar.add(upBt);
-
-// yeastpub
- JButton shortCut1 = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
- Font font = new Font("Monospaced", Font.BOLD, 14);
- g2.setFont(font);
-
- g2.setColor(Color.black);
- g2.drawString("Y",4,18);
- g2.setColor(Color.red);
- g2.drawString("P",10,15);
- setSize(22,24);
- }
- };
- shortCut1.setPreferredSize(buttonSize);
- shortCut1.setMinimumSize(buttonSize);
- shortCut1.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ftree.newRoot("/nfs/disk222/yeastpub");
- }
- });
-
- if((new File("/nfs/disk222/yeastpub")).exists())
- toolBar.add(shortCut1);
-
-// pathdata
- JButton shortCut2 = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
- Font font = new Font("Monospaced", Font.BOLD, 14);
- g2.setFont(font);
-
- g2.setColor(Color.black);
- g2.drawString("P",4,18);
- g2.setColor(Color.red);
- g2.drawString("D",10,15);
- setSize(22,24);
- }
- };
- shortCut2.setPreferredSize(buttonSize);
- shortCut2.setMinimumSize(buttonSize);
- shortCut2.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ftree.newRoot("/nfs/pathdata/");
- }
- });
-
- if((new File("/nfs/pathdata/")).exists())
- toolBar.add(shortCut2);
-
-// home button
- JButton homeBt = new JButton()
- {
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
-
- g2.setColor(Color.blue);
- float loc1[][] = { {3,14}, {11,3}, {19,14},
- {17,14}, {17,18}, {5,18}, {5,14} };
- g2.fill(makeShape(loc1));
-
- setSize(22,24);
- }
- };
- homeBt.setPreferredSize(buttonSize);
- homeBt.setMinimumSize(buttonSize);
- homeBt.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ftree.newRoot(System.getProperty("user.home"));
- }
- });
- toolBar.add(homeBt);
-
- toolBar.add(Box.createVerticalStrut(35));
- localPanel.add(toolBar, BorderLayout.NORTH);
+// JToolBar toolBar = new JToolBar();
+// localPanel.add(toolBar, BorderLayout.NORTH);
return mBar;
}
@@ -516,6 +438,40 @@ public class LocalAndRemoteFileManager extends JFrame
}
}
+ class TextButton extends JButton
+ {
+ private String s1;
+ private String s2;
+ private Color c;
+
+ public TextButton(String text)
+ {
+ this(text, Color.black);
+ }
+
+ public TextButton(String text, Color c)
+ {
+ super();
+ this.s1 = text.substring(0);
+ this.s2 = text.substring(1);
+ }
+
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+ Font font = new Font("Monospaced", Font.BOLD, 14);
+ g2.setFont(font);
+
+ g2.setColor(c);
+ g2.drawString(s1,4,18);
+ g2.setColor(Color.red);
+ g2.drawString(s2,10,15);
+ setSize(22,24);
+ }
+ }
+
+
public static void main(String args[])
{
final javax.swing.LookAndFeel look_and_feel =
diff --git a/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java b/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
index 4e7a678a716f57b9e8dbee715831beaddb72b90f..2b03b010434db0d5549716ac9900cfb4cc6dc29b 100644
--- a/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
+++ b/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
@@ -47,8 +47,6 @@ public class RemoteFileNode extends DefaultMutableTreeNode
/** parent directory listing */
private transient FileList parentList; // make transient for
- /** jemboss properties */
- private transient Properties mysettings; // Transferable to work
/** remote server file roots */
private transient String froots;
/** file separator for server files */
@@ -59,25 +57,27 @@ public class RemoteFileNode extends DefaultMutableTreeNode
static DataFlavor remoteFlavors[] = { REMOTEFILENODE,
DataFlavor.stringFlavor };
+ public RemoteFileNode(boolean isDir)
+ {
+ this.isDir = isDir;
+ }
/**
*
- * @param mysettings jemboss properties
* @param froots remote server file roots
* @param file file for this node
* @param parentList parent directory listing
* @param parent parent to this node
*
*/
- public RemoteFileNode(Properties mysettings, String froots,
- String file, FileList parentList, String parent)
+ public RemoteFileNode(String froots, String file,
+ FileList parentList, String parent)
{
- this(mysettings, froots, file, parentList, parent, false);
+ this(froots, file, parentList, parent, false);
}
/**
*
- * @param mysettings jemboss properties
* @param froots remote server file roots
* @param file file for this node
* @param parentList parent directory listing
@@ -85,11 +85,10 @@ public class RemoteFileNode extends DefaultMutableTreeNode
* @param ldir true if the node is a directory
*
*/
- public RemoteFileNode(Properties mysettings, String froots,
- String file, FileList parentList, String parent,
- boolean ldir)
+ public RemoteFileNode(String froots, String file,
+ FileList parentList, String parent,
+ boolean ldir)
{
- this.mysettings = mysettings;
this.froots = froots;
this.parentList = parentList;
isDir = ldir;
@@ -143,11 +142,6 @@ public class RemoteFileNode extends DefaultMutableTreeNode
/** @return true if explored */
public boolean isExplored() { return explored; }
- protected void setDir(boolean isDir)
- {
- this.isDir = isDir;
- }
-
/**
*
* Get the server name
@@ -190,7 +184,7 @@ public class RemoteFileNode extends DefaultMutableTreeNode
flist.getDirList(dir);
Vector children = flist.fileVector();
for(int i=0;i<children.size();i++)
- add(new RemoteFileNode(mysettings,froots,(String)children.get(i),
+ add(new RemoteFileNode(froots,(String)children.get(i),
flist,fullname));
}
explored = true;
diff --git a/uk/ac/sanger/artemis/components/filetree/SshFileTree.java b/uk/ac/sanger/artemis/components/filetree/SshFileTree.java
index 19be4f2a0d514dccb5912bb23ac831eef8762594..a064863df4278e36846e3a490a883a9331920736 100644
--- a/uk/ac/sanger/artemis/components/filetree/SshFileTree.java
+++ b/uk/ac/sanger/artemis/components/filetree/SshFileTree.java
@@ -56,7 +56,7 @@ public class SshFileTree extends JTree implements DragGestureListener,
/** properties */
private Properties mysettings;
/** remote directory roots */
- private static String froots;
+ private static String froots[];
/** popup menu */
private JPopupMenu popup;
/** file separator */
@@ -80,7 +80,7 @@ public class SshFileTree extends JTree implements DragGestureListener,
* @param froots remote directory roots
*
*/
- public SshFileTree(String froots)
+ public SshFileTree(String froots[])
{
this.froots = froots;
@@ -193,14 +193,31 @@ public class SshFileTree extends JTree implements DragGestureListener,
* the tree.
*
*/
+/*
public void up()
{
File current = new File(froots);
- froots = current.getParentFile().getAbsolutePath();
+ String new_froots = current.getParentFile().getAbsolutePath();
+ newRoot(new_froots);
+ }
+*/
+
+ /**
+ *
+ * Define a directory root for the file tree
+ * @param newRoot directory to use as the root for
+ * the tree.
+ *
+ */
+/*
+ protected void newRoot(final String froots)
+ {
+ this.froots = froots;
DefaultTreeModel model = (DefaultTreeModel)getModel();
model = createTreeModel(froots);
setModel(model);
}
+*/
/**
*
@@ -457,8 +474,8 @@ public class SshFileTree extends JTree implements DragGestureListener,
}
else
{
- childNode = new RemoteFileNode(mysettings,froots,
- child,null,path,ldir);
+ childNode = new RemoteFileNode(froots[0],child,
+ null,path,ldir);
//find the index for the child
int num = parentNode.getChildCount();
@@ -578,18 +595,28 @@ public class SshFileTree extends JTree implements DragGestureListener,
* @return tree model
*
*/
- private DefaultTreeModel createTreeModel(String root)
+ private DefaultTreeModel createTreeModel(String froot[])
{
setCursor(cbusy);
- File f = new File(root);
- RemoteFileNode rootNode = new RemoteFileNode(mysettings,froots,
- f.getName(),null,null);
-
- rootNode.setDir(true);
- rootNode.explore();
- openNode = new Vector();
- openNode.add(rootNode);
+ RemoteFileNode rootNode = new RemoteFileNode(true);
+
+ for(int i=0; i<froots.length; i++)
+ {
+ File f = new File(froot[i]);
+ RemoteFileNode node = new RemoteFileNode(froots[i], f.getName(),
+ null, null, true);
+ rootNode.add(node);
+ if(i == 0)
+ {
+ node.explore();
+ openNode = new Vector();
+ openNode.add(node);
+ }
+ }
+
+
+
setCursor(cdone);
return new DefaultTreeModel(rootNode);
}
@@ -991,7 +1018,8 @@ public class SshFileTree extends JTree implements DragGestureListener,
}
JFrame frame = new JFrame("SSH :: File Manager");
- JScrollPane jsp = new JScrollPane(new SshFileTree("/nfs/team81/tjc"));
+ String roots[] = { "/nfs/team81/tjc" };
+ JScrollPane jsp = new JScrollPane(new SshFileTree(roots));
frame.getContentPane().add(jsp);
frame.pack();
frame.setVisible(true);
diff --git a/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java
deleted file mode 100644
index 684a52b53ccb0dff5a0c0ca1ee1297c9f1a9a2c5..0000000000000000000000000000000000000000
--- a/uk/ac/sanger/artemis/j2ssh/SftpPSUClient.java
+++ /dev/null
@@ -1,427 +0,0 @@
-/* ExternalProgram.java
- *
- * created: Aug 2005
- *
- * This file is part of Artemis
- *
- * Copyright(C) 2005 Genome Research Limited
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or(at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- *
- **/
-
-package uk.ac.sanger.artemis.j2ssh;
-
-
-import javax.swing.*;
-import java.awt.*;
-import java.io.*;
-import com.sshtools.j2ssh.SshClient;
-import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
-import com.sshtools.j2ssh.authentication.PasswordAuthenticationClient;
-import com.sshtools.j2ssh.io.UnsignedInteger32;
-import com.sshtools.j2ssh.session.SessionChannelClient;
-import com.sshtools.j2ssh.sftp.FileAttributes;
-import com.sshtools.j2ssh.sftp.SftpFile;
-import com.sshtools.j2ssh.sftp.SftpFileOutputStream;
-import com.sshtools.j2ssh.SftpClient;
-import com.sshtools.j2ssh.configuration.ConfigurationLoader;
-
-import java.util.Vector;
-import java.util.Properties;
-import java.util.logging.FileHandler;
-import java.util.logging.Handler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import java.util.logging.SimpleFormatter;
-
-/**
- *
- */
-public class SftpPSUClient extends Thread
-{
-
- private String hostname = null;
- private String user = null;
- private String listfilepath = null;
- private String cmd = null;
- private String bsub = null;
- private String logfile = null;
- private String db = null;
- private String wdir = "/nfs/pathscratch1/scratch";
- private int port = -1;
-
- public SftpPSUClient(String args[])
- {
- // process arguments
- if(args != null && args.length > 0)
- {
- for(int i=0; i<args.length; i++)
- {
- if(args[i].equals("-h") && i < args.length-1)
- hostname = args[i+1];
- else if(args[i].equals("-u") && i < args.length-1)
- user = args[i+1];
- else if(args[i].equals("-f") && i < args.length-1)
- listfilepath = args[i+1];
- else if(args[i].equals("-cmd") && i < args.length-1)
- cmd = args[i+1];
- else if(args[i].equals("-bsub") && i < args.length-1)
- bsub = args[i+1];
- else if(args[i].equals("-l") && i < args.length-1)
- logfile = args[i+1];
- else if(args[i].equals("-p") && i < args.length-1)
- port = Integer.parseInt(args[i+1]);
- else if(args[i].equals("-d") && i < args.length-1)
- db = args[i+1];
- else if(args[i].equals("-wdir") && i < args.length-1)
- wdir = args[i+1];
- }
- }
- }
-
- 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");
- if(port < 0 && settings.getProperty("port") != null)
- port = Integer.parseInt(settings.getProperty("port"));
- if(bsub == null && settings.getProperty("bsub") != null)
- bsub = settings.getProperty("bsub");
- if(user == null)
- user = System.getProperty("user.name");
- if(db == null)
- {
- if(settings.getProperty("default_db") != null)
- db = settings.getProperty("default_db");
- else
- db = "%uniprot";
- }
- 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
- {
- // Setup a logfile
- if(logfile != null)
- {
- Handler fh = new FileHandler(logfile);
- fh.setFormatter(new SimpleFormatter());
- Logger.getLogger("com.sshtools").setUseParentHandlers(false);
- Logger.getLogger("com.sshtools").addHandler(fh);
- Logger.getLogger("com.sshtools").setLevel(Level.ALL);
- }
- else
- Logger.getLogger("com.sshtools").setLevel(Level.OFF);
-
- ConfigurationLoader.initialize(false);
-
-// 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));
-
- // Create a password authentication instance
- PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
- // Get the users name
-
- 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,
- "LOGIN",
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[1]);
-
- if(select == 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);
- pwd.setPassword(new String(pfield.getPassword()));
-
- // Try the authentication
- int result = ssh.authenticate(pwd);
-
- // Evaluate the result
- if(result == AuthenticationProtocolState.COMPLETE)
- {
- 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();
- 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);
-
- wdir = wdir+"/"+user+"/";
- try
- {
- 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)
- {
- 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(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);
-
- int count = 0;
-
- while(!isFile && count < 100)
- {
- Thread.currentThread().sleep(5000);
- Object list[] = sftp.ls(wdir).toArray();
-
- for(int j=0; j<list.length;j++)
- {
- if(((SftpFile)list[j]).getFilename().equals(filename+".out"))
- isFile = true;
- }
- count++;
- }
- }
- catch(InterruptedException ie)
- {
- ie.printStackTrace();
- }
- catch(java.io.IOException ioe)
- {
- ioe.printStackTrace();
- }
-
- // stdout
- 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();
- }
-
- // Quit
- sftp.quit();
- ssh.disconnect();
- }
- else
- JOptionPane.showMessageDialog(null,
- "Problem logging in!\nCheck username and password.",
- "Authentication Problem",
- JOptionPane.ERROR_MESSAGE);
-
-
- } catch(IOException ioe){}
- finally
- {
- JOptionPane.showMessageDialog(null,
- "Finished \n" + program,
- "Process Finished",
- JOptionPane.INFORMATION_MESSAGE);
- }
- }
-
- private Vector readListFile(String file)
- {
- Vector seqfiles = new Vector();
- try
- {
- String line;
- BufferedReader in = new BufferedReader(new FileReader(file));
- while((line = in.readLine()) != null )
- {
- File seq = new File(line);
- if(seq.exists())
- {
- seqfiles.add(seq.getAbsolutePath());
- }
- }
- }
- catch (IOException e)
- {
- System.out.println("Problem reading list file");
- }
- return seqfiles;
- }
-
- private Properties getProperties()
- {
- Properties settings = new Properties();
- ClassLoader cl = this.getClass().getClassLoader();
- // try out of the classpath
- try
- {
- settings.load(cl.getResourceAsStream("j2ssh.properties"));
- }
- catch (Exception e)
- {
- }
- return settings;
- }
-
-
- class StdoutStdErrHandler extends Thread
- {
- private SessionChannelClient session;
- private boolean isStdout;
- private StringBuffer buff = new StringBuffer();
-
- protected StdoutStdErrHandler(SessionChannelClient session,
- boolean isStdout)
- {
- this.session = session;
- this.isStdout = isStdout;
- }
-
- public void run()
- {
- try
- {
- final InputStream in;
- if(isStdout)
- in = session.getInputStream();
- else
- in = session.getStderrInputStream();
-
- byte buffer[] = new byte[100];
- int read;
- while((read = in.read(buffer)) > 0)
- buff.append(new String(buffer, 0, read));
- }
- catch(IOException ioe){}
- }
-
- public String getOutput()
- {
- return buff.toString();
- }
-
- }
-
-
- /**
- * The main program for the PasswordConnect class
- *
- * @param args The command line arguments
- */
- public static void main(String args[])
- {
- new SftpPSUClient(args);
- }
-}
diff --git a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
index bd20d0f7a96f08947ebdcbc68876af421fc0aad0..9f73cbf01be628eaf6d7fbf0bfe540c5ae187381 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
@@ -77,162 +77,12 @@ public class SshFileManager
private String logfile = null;
private String wdir = "/nfs/pathscratch1/scratch";
- // login variables
- private String hostname = null;
- private String user = null;
- private int port = -1;
- private static JPasswordField pfield = new JPasswordField(16);
- private static JTextField portfield = new JTextField(16);
- private static JTextField hostfield = new JTextField(16);
- private static JTextField ufield = new JTextField(16);
private SshClient ssh;
public SshFileManager()
{
- try
- {
- // Setup a logfile
- if(logfile != null)
- {
- Handler fh = new FileHandler(logfile);
- fh.setFormatter(new SimpleFormatter());
- Logger.getLogger("com.sshtools").setUseParentHandlers(false);
- Logger.getLogger("com.sshtools").addHandler(fh);
- Logger.getLogger("com.sshtools").setLevel(Level.ALL);
- }
- else
- Logger.getLogger("com.sshtools").setLevel(Level.OFF);
- }
- catch(IOException ioe){}
-
- Properties settings = getProperties();
- try
- {
- ssh = login();
- }
- catch(IOException ioe){}
- }
-
- /**
- *
- * 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.
- *
- */
- private boolean setLogin()
- {
- JPanel promptPanel = new JPanel(new GridLayout(4,2));
-
- if(hostname != null && hostfield.getText().equals(""))
- hostfield.setText(hostname);
-
- if(port >-1 && portfield.getText().equals(""))
- portfield.setText(Integer.toString(port));
-
- if(user != null && ufield.getText().equals(""))
- ufield.setText(user);
-
- 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 AND RUN"};
-
- int select = JOptionPane.showOptionDialog(null, promptPanel,
- "LOGIN",
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[1]);
-
- if(select == 0)
- return false;
-
- return true;
- }
-
-
- /**
- *
- * Get the properties from the j2ssh.properties file.
- *
- */
- private Properties getProperties()
- {
- Properties settings = new Properties();
- ClassLoader cl = this.getClass().getClassLoader();
- // try out of the classpath
- try
- {
- settings.load(cl.getResourceAsStream("j2ssh.properties"));
- }
- catch (Exception e)
- {
- }
-
- if(hostname == null && settings.getProperty("host") != null)
- hostname = settings.getProperty("host");
- if(port < 0 && settings.getProperty("port") != null)
- port = Integer.parseInt(settings.getProperty("port"));
- if(user == null)
- user = System.getProperty("user.name");
-
- return settings;
+ SshLogin sshLogin = new SshLogin();
+ ssh = sshLogin.getSshClient();
}
public boolean remoteList(String remoteRootDir)
diff --git a/uk/ac/sanger/artemis/j2ssh/SshLogin.java b/uk/ac/sanger/artemis/j2ssh/SshLogin.java
index 5fdacae967c619e0b3524e169e93fdfbc80925f6..f40c249125ae5200c4ce96922e1d31f7f6aea601 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshLogin.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshLogin.java
@@ -74,6 +74,7 @@ public class SshLogin
{
try
{
+ logfile = System.getProperty("logfile");
// Setup a logfile
if(logfile != null)
{
@@ -89,7 +90,7 @@ public class SshLogin
catch(IOException ioe){}
if(settings == null)
- settings = getProperties();
+ settings = setProperties();
}
public SshClient getSshClient()
@@ -110,6 +111,11 @@ public class SshLogin
return ufield.getText().trim();
}
+ public static Properties getProperties()
+ {
+ return settings;
+ }
+
/**
*
* Log the user in.
@@ -208,7 +214,7 @@ public class SshLogin
* Get the properties from the j2ssh.properties file.
*
*/
- private Properties getProperties()
+ private Properties setProperties()
{
Properties settings = new Properties();
ClassLoader cl = this.getClass().getClassLoader();
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index b4e3d116af9f6ff926d5c4df1c08ed5f947799c2..c6ed411bf1e232aab13d277326415dee90e2feec 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -43,19 +43,10 @@ import java.io.IOException;
import java.util.Vector;
import java.util.Properties;
-import java.util.logging.FileHandler;
-import java.util.logging.Handler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import java.util.logging.SimpleFormatter;
import com.sshtools.j2ssh.SshClient;
-import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
-import com.sshtools.j2ssh.authentication.PasswordAuthenticationClient;
import com.sshtools.j2ssh.session.SessionChannelClient;
-import com.sshtools.j2ssh.sftp.FileAttributes;
import com.sshtools.j2ssh.sftp.SftpFile;
-import com.sshtools.j2ssh.sftp.SftpFileOutputStream;
import com.sshtools.j2ssh.SftpClient;
import com.sshtools.j2ssh.configuration.ConfigurationLoader;
@@ -76,14 +67,9 @@ public class SshPSUClient extends Thread
private String db = null;
private String wdir = "/nfs/pathscratch1/scratch";
- // login variables
- private String hostname = null;
- private String user = null;
- private int port = -1;
- private static JPasswordField pfield = new JPasswordField(16);
- private static JTextField portfield = new JTextField(16);
- private static JTextField hostfield = new JTextField(16);
- private static JTextField ufield = new JTextField(16);
+ //
+ private SshClient ssh;
+ private String user;
public SshPSUClient(String args[])
{
@@ -92,11 +78,7 @@ public class SshPSUClient extends Thread
{
for(int i=0; i<args.length; i++)
{
- if(args[i].equals("-h") && i < args.length-1)
- hostname = args[i+1];
- else if(args[i].equals("-u") && i < args.length-1)
- user = args[i+1];
- else if(args[i].equals("-f") && i < args.length-1)
+ if(args[i].equals("-f") && i < args.length-1)
listfilepath = args[i+1];
else if(args[i].equals("-cmd") && i < args.length-1)
cmd = args[i+1];
@@ -104,8 +86,6 @@ public class SshPSUClient extends Thread
bsub = args[i+1];
else if(args[i].equals("-l") && i < args.length-1)
logfile = args[i+1];
- else if(args[i].equals("-p") && i < args.length-1)
- port = Integer.parseInt(args[i+1]);
else if(args[i].equals("-d") && i < args.length-1)
db = args[i+1];
else if(args[i].equals("-wdir") && i < args.length-1)
@@ -113,26 +93,15 @@ public class SshPSUClient extends Thread
}
}
- try
- {
- // Setup a logfile
- if(logfile != null)
- {
- Handler fh = new FileHandler(logfile);
- fh.setFormatter(new SimpleFormatter());
- Logger.getLogger("com.sshtools").setUseParentHandlers(false);
- Logger.getLogger("com.sshtools").addHandler(fh);
- Logger.getLogger("com.sshtools").setLevel(Level.ALL);
- }
- else
- Logger.getLogger("com.sshtools").setLevel(Level.OFF);
- }
- catch(IOException ioe){}
+ SshLogin sshLogin = new SshLogin();
+ ssh = sshLogin.getSshClient();
+ user = sshLogin.getUser();
}
public void run()
{
String program = cmd;
+
// get properties from j2ssh.properties
Properties settings = getProperties();
@@ -141,14 +110,13 @@ public class SshPSUClient extends Thread
{
ConfigurationLoader.initialize(false);
- SshClient ssh = login();
if(ssh == null)
return;
completed = runBlastOrFasta(ssh, program, settings);
// Quit
- ssh.disconnect();
+ //ssh.disconnect();
}
catch(IOException ioe){}
finally
@@ -215,99 +183,6 @@ 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.
- *
- */
- private boolean setLogin()
- {
- JPanel promptPanel = new JPanel(new GridLayout(4,2));
-
- if(hostname != null && hostfield.getText().equals(""))
- hostfield.setText(hostname);
-
- if(port >-1 && portfield.getText().equals(""))
- portfield.setText(Integer.toString(port));
-
- if(user != null && ufield.getText().equals(""))
- ufield.setText(user);
-
- 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 AND RUN"};
-
- int select = JOptionPane.showOptionDialog(null, promptPanel,
- "LOGIN",
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[1]);
-
- if(select == 0)
- return false;
-
- return true;
- }
-
/**
*
@@ -327,14 +202,8 @@ public class SshPSUClient extends Thread
{
}
- if(hostname == null && settings.getProperty("host") != null)
- hostname = settings.getProperty("host");
- if(port < 0 && settings.getProperty("port") != null)
- port = Integer.parseInt(settings.getProperty("port"));
if(bsub == null && settings.getProperty("bsub") != null)
bsub = settings.getProperty("bsub");
- if(user == null)
- user = System.getProperty("user.name");
if(db == null)
{
if(settings.getProperty("default_db") != null)
@@ -404,7 +273,9 @@ public class SshPSUClient extends Thread
sftp.put(filepath, wdir+filename);
}
catch(IOException ioe)
- {}
+ {
+ ioe.printStackTrace();
+ }
SessionChannelClient session = ssh.openSessionChannel();