allow user to open database entry using gene or sequence ID

uk/ac/sanger/artemis/components/ProjectProperty.java

@@ -72,6 +72,8 @@ import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
 import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
+import uk.ac.sanger.artemis.components.database.DatabaseJPanel;
 import uk.ac.sanger.artemis.util.Document;
 import uk.ac.sanger.artemis.util.FileDocument;
 
@@ -89,6 +91,7 @@ public class ProjectProperty extends JFrame
   private static HashMap<String, HashMap<String, String>> centralProjects;
   private static HashMap<String, HashMap<String, String>> userProjects;
   private Splash splash;
+  private DatabaseEntrySource entry_source;
   
   private final static int REFERENCE = 1;
   private final static int ANNOTATION = 2;
@@ -690,6 +693,36 @@ public class ProjectProperty extends JFrame
     }
   }
   
+  /**
+   * Open a database entry
+   * @param splash
+   * @param featureName gene or sequence ID
+   */
+  private void openDatabase(final Splash splash, final String featureName)
+  {
+    String loc = System.getProperty("chado");
+    int idx;
+    if((idx = loc.indexOf("?")) > -1 && loc.indexOf("?user=") == -1)
+      loc = loc.substring(0, idx+1) + "user=" + loc.substring(idx+1);
+
+    if( entry_source == null || 
+       !entry_source.getLocation().endsWith(loc) )
+    {
+      entry_source = new DatabaseEntrySource();
+      boolean promptUser = true;
+      if(System.getProperty("read_only") != null)
+      {
+        promptUser = false;
+        entry_source.setReadOnly(true);
+      }
+      if(!entry_source.setLocation(promptUser))
+        return;
+    }
+    DatabaseJPanel.getEntryEditFromDatabase(
+        entry_source, splash, ProjectProperty.this, featureName);
+  }
+  
+  
   /**
    * Escape the spaces with a double backslash (i.e. '\\ ').
    * @param s
@@ -799,10 +832,19 @@ public class ProjectProperty extends JFrame
       {
         public void run() 
         {
+          final String[] args = getArgs();
+          if(System.getProperty("chado") != null &&
+             args != null &&
+             args.length == 1 &&
+             args[0].indexOf(":") == -1)
+          {
+            openDatabase(splash, args[0]);
+            return;
+          }
+          
           setCursor(new Cursor(Cursor.WAIT_CURSOR));
           try
           {
-            String[] args = getArgs();
             final ArtemisMain main_window;
             if (splash == null)
             {

uk/ac/sanger/artemis/components/database/DatabaseJPanel.java

@@ -65,6 +65,7 @@ import java.awt.event.KeyEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.Toolkit;
 import java.awt.Cursor;
@@ -79,8 +80,8 @@ public class DatabaseJPanel extends JPanel
 {
   /** */
   private static final long serialVersionUID = 1L;
-  private JLabel status_line = new JLabel("");
-  private boolean splitGFFEntry = false;
+  private static JLabel status_line = new JLabel("");
+  private static boolean splitGFFEntry = false;
   private JTree tree;
   private DatabaseDocument doc;
   private static Vector<String> opening = new Vector<String>();
@@ -140,7 +141,7 @@ public class DatabaseJPanel extends JPanel
       public void keyPressed(KeyEvent e) 
       {
         if (e.getKeyCode() == KeyEvent.VK_ENTER)
-          getEntryEditFromDatabase(entry_source, splash_main,
+          getEntryEditFromDatabase(entry_source, splash_main, DatabaseJPanel.this,
               openGeneText.getText().trim());
       } 
     });
@@ -150,7 +151,7 @@ public class DatabaseJPanel extends JPanel
     {
       public void actionPerformed(ActionEvent e)
       {
-        getEntryEditFromDatabase(entry_source, splash_main,
+        getEntryEditFromDatabase(entry_source, splash_main, DatabaseJPanel.this,
             openGeneText.getText().trim());
       }
     });
@@ -238,7 +239,7 @@ public class DatabaseJPanel extends JPanel
    * @throws Exception 
    */
   private static EntryEdit show(final DatabaseEntrySource entry_source,
-                          final JComponent srcComponent,
+                          final Component srcComponent,
                           final JLabel status_line,
                           final Splash splash_main,
                           final InputStreamProgressListener stream_progress_listener,
@@ -393,8 +394,9 @@ public class DatabaseJPanel extends JPanel
    * @param splash_main
    * @param featureName
    */
-  private void getEntryEditFromDatabase(final DatabaseEntrySource entry_source,
+  public static void getEntryEditFromDatabase(final DatabaseEntrySource entry_source,
                          final Splash splash_main,
+                         final Component comp,
                          final String featureName)
   {
     SwingWorker entryWorker = new SwingWorker()
@@ -405,10 +407,10 @@ public class DatabaseJPanel extends JPanel
         Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
         try
         {
-          DatabaseJPanel.this.setCursor(cbusy);
+          comp.setCursor(cbusy);
           
           EntryEdit ee = show(entry_source, 
-             DatabaseJPanel.this, status_line, splash_main,
+             comp, status_line, splash_main,
              stream_progress_listener, ":" + featureName,
              true, splitGFFEntry);
           goTo(ee, featureName);
@@ -416,14 +418,14 @@ public class DatabaseJPanel extends JPanel
         catch (Exception npe)
         {
           //npe.printStackTrace();
-          JOptionPane.showMessageDialog(DatabaseJPanel.this, 
+          JOptionPane.showMessageDialog(comp, 
               featureName + " not opened/found!", 
               "Failed to Open", JOptionPane.WARNING_MESSAGE);
           logger4j.debug(featureName + " not found!");
         }
         finally
         {
-          DatabaseJPanel.this.setCursor(cdone);
+          comp.setCursor(cdone);
         }
         return null;
       }
@@ -448,7 +450,7 @@ public class DatabaseJPanel extends JPanel
   private static EntryEdit openEntry(
       final String srcfeatureId,
       final DatabaseEntrySource entry_source, 
-      final JComponent srcComponent,
+      final Component srcComponent,
       final JLabel status_line,
       final InputStreamProgressListener stream_progress_listener,
       final boolean splitGFFEntry,
@@ -596,7 +598,7 @@ public class DatabaseJPanel extends JPanel
    * An InputStreamProgressListener used to update the error label with the
    * current number of chars read.
    */
-  private final InputStreamProgressListener stream_progress_listener =
+  private static final InputStreamProgressListener stream_progress_listener =
     new InputStreamProgressListener() 
   {
     public void progressMade(final InputStreamProgressEvent event)