read only option

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7314 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/ArtemisMain.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/ArtemisMain.java,v 1.28 2008-01-21 16:15:39 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.29 2008-04-25 09:58:29 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -52,7 +52,7 @@ import javax.swing.JOptionPane;
  *  The main window for the Artemis sequence editor.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: ArtemisMain.java,v 1.28 2008-01-21 16:15:39 tjc Exp $
+ *  @version $Id: ArtemisMain.java,v 1.29 2008-04-25 09:58:29 tjc Exp $
  **/
 
 public class ArtemisMain extends Splash 
@@ -137,7 +137,7 @@ public class ArtemisMain extends Splash
     {
       public void actionPerformed(ActionEvent event)
       {
-        launchDatabaseJFrame(true);
+        launchDatabaseJFrame();
       }
     };
 
@@ -256,7 +256,7 @@ public class ArtemisMain extends Splash
   * Launch database manager window
   *
   */
-  private void launchDatabaseJFrame(final boolean prompt_user)
+  private void launchDatabaseJFrame()
   {
     SwingWorker entryWorker = new SwingWorker()
     {
@@ -264,7 +264,11 @@ public class ArtemisMain extends Splash
       {
         getStatusLabel().setText("Connecting ...");
         DatabaseEntrySource entry_source = new DatabaseEntrySource();
-        if(!entry_source.setLocation(prompt_user))
+        boolean promptUser = true;
+        if(System.getProperty("read_only") != null)
+          promptUser = false;
+        
+        if(!entry_source.setLocation(promptUser))
           return null;
 
         JFrame frame = new JFrame("Organism List");
@@ -366,7 +370,12 @@ public class ArtemisMain extends Splash
         Splash.logger4j.info("OPEN ENTRY "+new_entry_name);
         getStatusLabel().setText("Connecting ...");
         DatabaseEntrySource entry_source = new DatabaseEntrySource();
-        if(!entry_source.setLocation(true))
+
+        boolean promptUser = true;
+        if(System.getProperty("read_only") != null)
+          promptUser = false;
+        
+        if(!entry_source.setLocation(promptUser))
           return;
         
         last_entry_edit =

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 1.60 2008-03-07 12:20:44 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryEdit.java,v 1.61 2008-04-25 09:58:29 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -67,7 +67,7 @@ import java.util.Vector;
  *  Each object of this class is used to edit an EntryGroup object.
  *
  *  @author Kim Rutherford
- *  @version $Id: EntryEdit.java,v 1.60 2008-03-07 12:20:44 tjc Exp $
+ *  @version $Id: EntryEdit.java,v 1.61 2008-04-25 09:58:29 tjc Exp $
  *
  */
 public class EntryEdit extends JFrame
@@ -163,6 +163,8 @@ public class EntryEdit extends JFrame
         getEntryGroup().getBases().addSequenceChangeListener(ctm, 0);
         ctm.setEntryGroup(getEntryGroup());
         
+        if(!getEntryGroup().getDefaultEntry().getEMBLEntry().isReadOnly())
+        {
           commitButton = new CommitButton();
           getEntryGroup().addFeatureChangeListener(commitButton);
           getEntryGroup().addEntryChangeListener(commitButton);
@@ -170,6 +172,7 @@ public class EntryEdit extends JFrame
           xBox.add(commitButton);
         }
       }
+    }
 
     //final int font_height;
     //final int font_base_line;
@@ -1091,7 +1094,7 @@ public class EntryEdit extends JFrame
           db = true;
       }
 
-      if(db)
+      if(db && !getEntryGroup().getDefaultEntry().getEMBLEntry().isReadOnly())
       {
         final JMenuItem commit = new JMenuItem("Commit to Database");
         commit.addActionListener(new ActionListener()

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

@@ -63,6 +63,8 @@ public class DatabaseEntrySource implements EntrySource, Serializable
 
   private boolean splitGFFEntry;
   
+  private boolean readOnly = false;
+
   /**
    * Create a new DatabaseEntrySource.
    */
@@ -110,14 +112,14 @@ public class DatabaseEntrySource implements EntrySource, Serializable
       InputStreamProgressListener progress_listener)
       throws OutOfRangeException, NoSequenceException, IOException
   {
-    return makeFromID(null, id, schema, false, progress_listener, null);
+    return makeFromID(null, id, schema, progress_listener, null);
   }
   
   public Entry getEntry(String id, String schema,
       InputStreamProgressListener progress_listener, Range range)
       throws OutOfRangeException, NoSequenceException, IOException
   {
-    return makeFromID(null, id, schema, false, progress_listener, range);
+    return makeFromID(null, id, schema, progress_listener, range);
   }
 
   /**
@@ -143,7 +145,7 @@ public class DatabaseEntrySource implements EntrySource, Serializable
    * jdbc:postgresql://host:port/database?user=username
    * 
    */
-  public boolean setLocation(final boolean prompt_user)
+  public boolean setLocation(final boolean promptUser)
   {
     Container bacross = new Container();
     bacross.setLayout(new GridLayout(6, 2, 5, 5));
@@ -210,12 +212,15 @@ public class DatabaseEntrySource implements EntrySource, Serializable
       }
     }
 
+    if(promptUser)
+    {
       int n = JOptionPane.showConfirmDialog(null, bacross,
                                           "Enter Database Address",
                                           JOptionPane.OK_CANCEL_OPTION,
                                           JOptionPane.QUESTION_MESSAGE);
       if(n == JOptionPane.CANCEL_OPTION)
         return false;
+    }
     
     location = "jdbc:postgresql://" + 
                inServer.getText().trim() + ":" +
@@ -253,15 +258,12 @@ public class DatabaseEntrySource implements EntrySource, Serializable
    *          The id of the entry in the database
    * @param schema
    *          The schema of the entry in the database
-   * @param read_only
-   *          true if and only if a read-only Entry should be created (some are
-   *          always read only).
    * @exception OutOfRangeException
    *              Thrown if one of the features in the Entry is out of range of
    *              the Bases object.
    */
   private Entry makeFromID(final Bases bases, final String id,
-                             final String schema, final boolean read_only,
+                             final String schema, 
                              InputStreamProgressListener progress_listener, 
                              final Range range)
              throws OutOfRangeException, IOException
@@ -270,11 +272,6 @@ public class DatabaseEntrySource implements EntrySource, Serializable
     {
       DatabaseDocumentEntry db_entry = null;
 
-      if(read_only)
-      {
-      }
-      else
-      {
       DatabaseDocument doc = new DatabaseDocument(location, pfield, id,
                                                   schema, splitGFFEntry, 
                                                   progress_listener);
@@ -282,7 +279,8 @@ public class DatabaseEntrySource implements EntrySource, Serializable
       if(range != null)
         doc.setRange(range);
       db_entry = new DatabaseDocumentEntry(doc, null);
-      }
+        
+      db_entry.setReadOnly(isReadOnly());
       
       final Bases real_bases;
 
@@ -356,4 +354,14 @@ public class DatabaseEntrySource implements EntrySource, Serializable
   {
     return pfield;
   }
+
+  public boolean isReadOnly()
+  {
+    return readOnly;
+  }
+
+  public void setReadOnly(boolean readOnly)
+  {
+    this.readOnly = readOnly;
+  }
 }

uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java

@@ -145,7 +145,15 @@ public class LocalAndRemoteFileManager extends JFrame
     { 
       setTitle("Database and File Manager");
       entry_source = new DatabaseEntrySource();
-      if(!entry_source.setLocation(true))
+      
+      boolean promptUser = true;
+      if(System.getProperty("read_only") != null)
+      {
+        promptUser = false;
+        entry_source.setReadOnly(true);
+      }
+      
+      if(!entry_source.setLocation(promptUser))
         return;
     
       JLabel label  = new JLabel(" Database Loading...");