From a425a1cbcc390b065e6bb447a1e29f4099e53119 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 12 Jun 2009 15:47:50 +0000
Subject: [PATCH] retrieve and init vamsas session from vdoc at URL

---
 src/jalview/bin/Jalview.java |   21 ++++++++++-------
 src/jalview/gui/Desktop.java |   53 +++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 65 insertions(+), 9 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index a2ef369..ed51cee 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -86,9 +86,9 @@ public class Jalview
                       + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                       + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
 //                      + "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
-                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
-                      +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
-                      +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+                      +"\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+                      +"\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                       + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
 //                      + "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
 //                      + "-vses vamsas-session\tJoin session with given URN\n"
@@ -219,9 +219,14 @@ public class Jalview
       boolean inSession = false;
       if (vamsasImport!=null)
       {
-        try {
-          inSession = desktop.vamsasImport(new File(vamsasImport));
-            
+          try {
+            String viprotocol = Jalview.checkProtocol(vamsasImport);
+            if (viprotocol == jalview.io.FormatAdapter.FILE) {
+              inSession = desktop.vamsasImport(new File(vamsasImport));
+            } else if (viprotocol == jalview.io.FormatAdapter.URL) {
+              inSession = desktop.vamsasImport(new URL(vamsasImport));
+            }
+          
           } catch (Exception e)
           {
             System.err.println("Exeption when importing "+vamsasImport+" as a vamsas document.");
@@ -231,8 +236,8 @@ public class Jalview
             System.err.println("Failed to import "+vamsasImport+" as a vamsas document.");
           } else {
             System.out.println("Imported Successfully into new session "+desktop.getVamsasApplication().getCurrentSession());
-        }
-      } 
+          }
+      }
       if (vamsasSession!=null) {
         if (vamsasImport!=null) {
        // close the newly imported session and import the Jalview specific remnants into the new session later on.
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index f9689db..484bcde 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -24,8 +24,15 @@ import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
 import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
 import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.channels.ReadableByteChannel;
 import java.util.*;
 
 import javax.swing.*;
@@ -1125,8 +1132,52 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * @param file 
    * @return true if import was a success and a session was started.
    */
+  public boolean vamsasImport(URL url)
+  {
+    // TODO: create progress bar
+    if (v_client != null)
+    {
+      
+      jalview.bin.Cache.log
+      .error("Implementation error - load session from a running session is not supported.");
+      return false;     
+    }
+    
+    try
+      {
+      // copy the URL content to a temporary local file
+      // TODO: be a bit cleverer here with nio (?!)
+      File file = File.createTempFile("vdocfromurl", ".vdj");
+      FileOutputStream fos = new FileOutputStream(file);
+      BufferedInputStream bis = new BufferedInputStream(url.openStream());
+      byte[] buffer = new byte[2048];
+      int ln;
+      while ((ln = bis.read(buffer))>-1)
+      {
+        fos.write(buffer,0,ln);
+      }
+      bis.close();
+      fos.close();
+      v_client = new jalview.gui.VamsasApplication(this, file, url.toExternalForm());
+      } catch (Exception ex)
+      {
+        jalview.bin.Cache.log.error(
+                "Failed to create new vamsas session from contents of URL "+url,ex);
+        return false;
+      }
+      setupVamsasConnectedGui();
+      v_client.initial_update(); // TODO: thread ?
+      return v_client.inSession();
+    }
+
+  /**
+   * import file into a new vamsas session (uses jalview.gui.VamsasApplication) 
+   * @param file 
+   * @return true if import was a success and a session was started.
+   */
   public boolean vamsasImport(File file)
   {
+    // TODO: create progress bar
     if (v_client != null)
     {
 
@@ -1137,7 +1188,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     try
     {
-      v_client = new jalview.gui.VamsasApplication(this, file);
+      v_client = new jalview.gui.VamsasApplication(this, file,null);
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error(
-- 
1.7.10.2