[Gmod-gbrowse-cmts] SF.net SVN: gmod:[22122] Generic-Genome-Browser/trunk

[<ls...@us...>]

Revision: 22122
          http://gmod.svn.sourceforge.net/gmod/?rev=22122&view=rev
Author:   lstein
Date:     2009-09-28 20:25:38 +0000 (Mon, 28 Sep 2009)

Log Message:
-----------
all asynchronous methods now moved into Bio::Graphics::Browser2::Action

Modified Paths:
--------------
    Generic-Genome-Browser/trunk/cgi-bin/gbrowse_img
    Generic-Genome-Browser/trunk/conf/plugins/FilterTest.pm
    Generic-Genome-Browser/trunk/htdocs/js/ajax_upload.js
    Generic-Genome-Browser/trunk/htdocs/js/autocomplete.js
    Generic-Genome-Browser/trunk/htdocs/js/buttons.js
    Generic-Genome-Browser/trunk/htdocs/js/controller.js
    Generic-Genome-Browser/trunk/htdocs/js/login.js
    Generic-Genome-Browser/trunk/htdocs/js/toggle.js
    Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Action.pm
    Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm
    Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm
    Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/RenderPanels.pm
    Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/UploadSet.pm

Modified: Generic-Genome-Browser/trunk/cgi-bin/gbrowse_img
===================================================================
--- Generic-Genome-Browser/trunk/cgi-bin/gbrowse_img	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/cgi-bin/gbrowse_img	2009-09-28 20:25:38 UTC (rev 22122)
@@ -4,7 +4,7 @@
 
 use strict;
 
-use Bio::Graphics::Browser;
+use Bio::Graphics::Browser2;
 use Bio::Graphics::Browser2::Render;
 use Bio::Graphics::Browser2::Util;
 use Digest::MD5 'md5_hex';

Modified: Generic-Genome-Browser/trunk/conf/plugins/FilterTest.pm
===================================================================
--- Generic-Genome-Browser/trunk/conf/plugins/FilterTest.pm	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/conf/plugins/FilterTest.pm	2009-09-28 20:25:38 UTC (rev 22122)
@@ -73,7 +73,6 @@
     warn $@ if $@;
     return $filter,"$key (filter incorrect)" if $@;  # error occurred
     
-    my $value   = $config->{filter_value};
     my $new_key = $FILTERS[ $config->{filter} ][1] =~ m/\$value/
 	          ? "$key ($FILTERS[$config->{filter}][0] $value)"
                   : "$key ($FILTERS[$config->{filter}][0])" ;

Modified: Generic-Genome-Browser/trunk/htdocs/js/ajax_upload.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/ajax_upload.js	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/htdocs/js/ajax_upload.js	2009-09-28 20:25:38 UTC (rev 22122)
@@ -65,7 +65,7 @@
   $('upload_status').innerHTML = '<b>Uploading...</b>';
   $('ajax_upload').hide();
   if (Ajax_Status_Updater==null)
-     Ajax_Status_Updater = new Ajax.PeriodicalUpdater($('upload_status'),'#',{parameters:{new_file_upload_status:1}});
+     Ajax_Status_Updater = new Ajax.PeriodicalUpdater($('upload_status'),'#',{parameters:{action:'upload_status'}});
   else
      Ajax_Status_Updater.start();
   return true;
@@ -86,7 +86,9 @@
    $(indicator).innerHTML = "<image src='/gbrowse2/images/buttons/ajax-loader.gif' />";
    new Ajax.Request(document.URL, {
         method:      'post',
-        parameters:  {deleteUploadTrack:trackName},
+        parameters:  {action: 'delete_upload',
+	              track:  trackName
+		      },
         onSuccess:   function (transport) {
                  Controller.update_sections(new Array(userdata_table_id));
 		 }

Modified: Generic-Genome-Browser/trunk/htdocs/js/autocomplete.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/autocomplete.js	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/htdocs/js/autocomplete.js	2009-09-28 20:25:38 UTC (rev 22122)
@@ -8,7 +8,7 @@
                     	 document.URL,
                          {indicator:          'indicator1',
                           parameters:         'action=autocomplete',
-                          paramName:          'autocomplete',
+                          paramName:          'prefix',
 			  minChars:           2
                          }
 	 );

Modified: Generic-Genome-Browser/trunk/htdocs/js/buttons.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/buttons.js	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/htdocs/js/buttons.js	2009-09-28 20:25:38 UTC (rev 22122)
@@ -97,7 +97,7 @@
 		      handle:  'titlebar',
 		      scroll:   window,
 		      onUpdate: function() {
-		      var postData = Sortable.serialize(div_name,{name:'label'});
+		      var postData = Sortable.serialize(div_name,{name:'label'})+';action=change_track_order';
 		      new Ajax.Request(document.URL,{method:'post',postBody:postData});
 		    }
 		  }

Modified: Generic-Genome-Browser/trunk/htdocs/js/controller.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/controller.js	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/htdocs/js/controller.js	2009-09-28 20:25:38 UTC (rev 22122)
@@ -271,7 +271,7 @@
    set_display_option:
    function(option,value) {
 
-     var param = {set_display_option: 1};
+     var param = {action: 'set_display_option'};
      param[option] = value;
      new Ajax.Request(document.URL,
             {
@@ -387,7 +387,7 @@
 
     if (force == null) force=false;
 
-    var request_str = "add_tracks=1";
+    var request_str = "action=add_tracks";
     var found_track = false;
     for (var i = 0; i < track_names.length; i++) {
       var track_name = track_names[i];
@@ -461,7 +461,7 @@
        new Ajax.Request(document.URL,{
          method:     'post',
          parameters: {
-           rerender_track:  1,
+           action:          'rerender_track',
            track_id:        gbtrack.track_id
          },
          onSuccess: function(transport) {
@@ -527,7 +527,7 @@
 
     new Ajax.Request(document.URL,{
       method:     'post',
-      parameters: $H({ retrieve_multiple: 1, 
+      parameters: $H({ action:        'retrieve_multiple', 
                        track_ids:     track_ids
 		    }).toQueryString()  + track_key_str,
       onSuccess: function(transport) {
@@ -654,7 +654,7 @@
       method:     'post',
       parameters: form_element.serialize() +"&"+ $H({
             plugin_action: plugin_action,
-            reconfigure_plugin: 1
+	    action:  'reconfigure_plugin'
           }).toQueryString(),
 
       onSuccess: function(transport) {
@@ -729,13 +729,19 @@
     new Ajax.Request(document.URL,{
       method:     'post',
       parameters: form_element.serialize() +"&"+ $H({
-            edited_file: edited_file,
-            commit_file_edit: 1
+            action:      'commit_file_edit',
+            edited_file: edited_file
           }).toQueryString(),
       onSuccess: function(transport) {
         var results      = transport.responseJSON;
         var file_created = results.file_created;
 	var tracks       = results.tracks;
+	var error        = results.error;
+	
+	if (error) {
+           alert(error);
+           return; 
+        }        
 
         Controller.wipe_div(external_utility_div_id); 
 
@@ -788,8 +794,8 @@
     new Ajax.Request(document.URL,{
       method:     'post',
       parameters: {
-        delete_upload_file: 1,
-        file: file_name
+        action: 'delete_upload_file',
+	file:   file_name
       },
       onSuccess: function(transport) {
         Controller.each_track(file_name,function(gbtrack) {
@@ -812,8 +818,8 @@
     new Ajax.Request(document.URL,{
       method:     'post',
       parameters:{
-            add_url:    1,
-            eurl:       eurl
+            action: 'add_url',
+            eurl:    eurl
       },
       onSuccess: function(transport) {
         var results     = transport.responseJSON;

Modified: Generic-Genome-Browser/trunk/htdocs/js/login.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/login.js	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/htdocs/js/login.js	2009-09-28 20:25:38 UTC (rev 22122)
@@ -582,7 +582,7 @@
 function login_get_account(username,session,remember,openid) {
     new Ajax.Request(document.URL,{
         method:      'post',
-        parameters: {authorize_login: 1,
+        parameters: {action:   'authorize_login',
                      username: username,
                      session:  session,
                      remember: remember,

Modified: Generic-Genome-Browser/trunk/htdocs/js/toggle.js
===================================================================
--- Generic-Genome-Browser/trunk/htdocs/js/toggle.js	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/htdocs/js/toggle.js	2009-09-28 20:25:38 UTC (rev 22122)
@@ -6,7 +6,8 @@
 }
 
 function setVisState (element_name,is_visible) {
-  var postData = 'div_visible_'+ element_name + '=' + is_visible;
+  var visibility = is_visible ? 'show' : 'hide';
+  var postData   = 'action=show_hide_section;'+visibility+'='+element_name;
   new Ajax.Request(document.URL,{method:'post',postBody:postData});
 }
 
@@ -51,7 +52,9 @@
      pad.style.display = 'none';
      control.className = 'titlebar';
    }
-   var postData = 'track_collapse_'+ escape(element_name) + '=' + (closeit ? 1 : 0);
+   
+   var direction = closeit ? 'collapse' : 'open';
+   var postData  = 'action=open_collapse_track;'+direction+'='+escape(element_name);
    new Ajax.Request(document.URL,{method:'post',postBody:postData});
    return false;
 }

Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Action.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Action.pm	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Action.pm	2009-09-28 20:25:38 UTC (rev 22122)
@@ -26,6 +26,27 @@
 sub session     {shift->render->session}
 sub segment     {shift->render->segment}
 
+sub handle_legacy_calls {
+    my $class  = shift;
+    my ($q,$render) = @_;
+
+    # redirect to galaxy form submission
+    if ($q->param('galaxy')) {
+	return (302,undef,$render->galaxy_link($render->state));
+    }
+
+    # redirect to the imagelink
+    if (my $format = $q->param('make_image')) {
+	return (302,undef,$render->image_link($render->state,$format));
+    }
+
+    if ($q->param('clear_dsn') || $q->param('reset_dsn')) {
+	return (302,undef,"?action=reset_dsn");
+    }
+
+    return;
+}
+
 # each ACTION_* method corresponds to a "action=*" parameter on the CGI stack
 sub ACTION_navigate {
     my $self   = shift;
@@ -133,4 +154,335 @@
     return ( 200, 'application/json', {} );
 }
 
+sub ACTION_share_track {
+    my $self = shift;
+    my $q    = shift;
+
+    my $track_name = $q->param('track') or croak;
+    my $html = $self->render->share_track($track_name);
+    return ( 200, 'text/html', $html );
+}
+
+sub ACTION_retrieve_multiple {
+    my $self = shift;
+    my $q    = shift;
+
+    my $render = $self->render;
+
+    $render->init_plugins();
+    $render->init_remote_sources();
+
+    my %track_html;
+    my @track_ids = $q->param('track_ids');
+
+    foreach my $track_id (@track_ids) {
+	my $track_key = $q->param( 'tk_' . $track_id ) or next;
+	warn "retrieving $track_id=>$track_key" if DEBUG;
+	
+	$track_html{$track_id} = $render->render_deferred_track(
+	    cache_key  => $track_key,
+	    track_id   => $track_id,
+            ) || '';
+    }
+
+    my $return_object = { track_html => \%track_html, };
+    return ( 200, 'application/json', $return_object );
+}
+
+sub ACTION_add_tracks {
+    my $self = shift;
+    my $q    = shift;
+
+    my $render = $self->render;
+    
+
+    my @track_names = $q->param('track_names');
+
+    $render->init_database();
+    $render->init_plugins();
+    $render->init_remote_sources();
+
+    my $track_data = $render->add_tracks(\@track_names);
+    my $return_object = { track_data => $track_data, };
+
+    return ( 200, 'application/json', $return_object );
+}
+
+sub ACTION_reconfigure_plugin {
+    my $self   = shift;
+    my $q      = shift;
+    $self->render->init_plugins();
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_rerender_track {
+    my $self  = shift;
+    my $q     = shift;
+
+    my $render   = $self->render;
+    my $track_id = $q->param('track_id');
+
+    $render->init_database();
+    $render->init_plugins();
+    $render->init_remote_sources();
+
+    my ( $track_keys, $display_details, $details_msg )
+	= $render->background_individual_track_render($track_id);
+
+    my $return_object = {
+	track_keys      => $track_keys,
+	display_details => $display_details,
+	details_msg     => $details_msg,
+    };
+    return (200,'application/json',$return_object);
+}
+
+sub ACTION_commit_file_edit {
+    my $self = shift;
+    my $q    = shift;
+
+    my $data        = $q->param('a_data');
+    my $edited_file = $q->param('edited_file');
+
+    return ( 204, 'text/plain', undef ) unless ( $edited_file and $data );
+
+    $self->render->init_remote_sources();
+    my ($file_created,$tracks,$error) = $self->render->handle_edit( $edited_file, $self->state, $data );
+
+    my $return_object = {
+	file_created   => $file_created,
+	tracks         => $tracks,
+	error          => "$error"
+    };
+
+    return (200,'application/json',$return_object);
+}
+
+sub ACTION_add_url {
+    my $self = shift;
+    my $q    = shift;
+
+    my $data   = $q->param('eurl');
+    my $render = $self->render;
+
+    $render->init_remote_sources;
+    $render->remote_sources->add_source($data);
+    $render->add_track_to_state($data);
+    warn "adding $data to remote sources" if DEBUG;
+    return (200,'application/json',{url_created=>1});
+}
+
+sub ACTION_delete_upload_file {
+    my $self = shift;
+    my $q    = shift;
+
+    my $render = $self->render;
+    my $file   = $q->param('file');
+    warn "deleting file $file " if DEBUG;
+
+    $render->init_remote_sources();
+    $render->uploaded_sources->clear_file($file);
+    $render->remote_sources->delete_source($file);
+    $render->remove_track_from_state($file);
+
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_show_hide_section {
+    my $self = shift;
+    my $q    = shift;
+
+    my @show = $q->param('show');
+    my @hide = $q->param('hide');
+
+    my $settings = $self->state;
+    $settings->{section_visible}{$_} = 0 foreach @hide;
+    $settings->{section_visible}{$_} = 1 foreach @show;
+
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_open_collapse_track {
+    my $self = shift;
+    my $q    = shift;
+
+    my @open     = $q->param('open');
+    my @collapse = $q->param('collapse');
+
+    my $settings = $self->state;
+    $settings->{track_collapsed}{$_} = 1 foreach @collapse;
+    $settings->{track_collapsed}{$_} = 0 foreach @open;
+
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_change_track_order {
+    my $self = shift;
+    my $q    = shift;
+
+    warn "change_track_order()";
+
+    my $settings = $self->state;
+    my @labels   = $q->param('label[]') or return;
+    foreach (@labels) {
+	s/%5F/_/g;
+	s/:(overview|region|detail)$// if m/^(plugin|file|http|ftp):/;
+    }
+    my %seen;
+    @{ $settings->{tracks} } = grep { length() > 0 && !$seen{$_}++ }
+    ( @labels, @{ $settings->{tracks} } );
+
+    return (204,'text/plain',undef);    
+}
+
+sub ACTION_set_display_option {
+    my $self = shift;
+
+    # this is a little bogus because update_options() is going to
+    # read from the CGI parameter list directly.
+    $self->render->update_options;  
+    return (204,'text/plain',undef);        
+}
+
+sub ACTION_bookmark {
+    my $self = shift;
+    return (302,undef,$self->render->bookmark_link($self->state));
+}
+
+sub ACTION_autocomplete {
+    my $self   = shift;
+    my $q      = shift;
+    my $render = $self->render;
+
+    my $match  = $q->param('prefix') or croak;
+
+    my $search = $render->get_search_object;
+    my $matches= $search->features_by_prefix($match,100);
+    my $autocomplete = $render->format_autocomplete($matches,$match);
+    return (200,'text/html',$autocomplete);
+}
+
+sub ACTION_reset_dsn {
+    my $self = shift;
+    warn "here I am";
+    $self->data_source->clear_cached_config();
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_authorize_login {
+    my $self = shift;
+    my $q    = shift;
+    my $username = $q->param('username') or croak;
+    my $session  = $q->param('session')  or croak;
+    my $openid   = $q->param('openid')   or croak;
+
+    my ($id,$nonce) = $self->render->authorize_user($username,$session,$openid);
+    return (200,'application/json',{id=>$id,authority=>$nonce});
+}
+
+# DEBUGGING METHOD
+sub ACTION_new_test_track {
+    my $self = shift;
+    my $q    = shift;
+
+    my $render   = $self->render;
+    my $userdata = Bio::Graphics::Browser2::UploadSet->new($render->data_source,
+							   $render->state,
+							   $render->language);
+    warn "Adding test track for ",$render->state->{uploadid}," path = ",($userdata->name_file('test'))[1];
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_upload_file {
+    my $self = shift;
+    my $q    = shift;
+
+    my $fh = $q->param('file') or return(204,'text/plain',undef);
+
+    my $render   = $self->render;
+    my $state    = $self->state;
+    my $session  = $render->session;
+
+    my $userdata = Bio::Graphics::Browser2::UserTracks->new($render->data_source,
+							    $render->state,
+							    $render->language);
+    warn "created userdata $userdata";
+
+    my $name = File::Basename::basename($fh );
+    $state->{current_upload} = $name;
+    $session->flush();
+    $session->unlock();
+
+    my ($result,$msg) = $userdata->upload_track($name,$fh);
+
+    return $msg ? (200,
+		   'text/html',
+		   "<pre style='background-color:pink'>$msg</pre>".
+		   a({
+		       -href    =>'javascript:void(0)',
+		       -onClick =>"\$('upload_status').innerHTML=''"
+		     },
+		     '[Remove]'
+		   )
+	)
+	: (200,'text/plain','');
+}
+
+sub ACTION_delete_upload {
+    my $self  = shift;
+    my $q     = shift;
+
+    my $track  = $q->param('track') or croak;
+    my $render = $self->render;
+
+    my $userdata = Bio::Graphics::Browser2::UserTracks->new($render->data_source,
+							    $render->state,
+							    $render->language);
+    $userdata->delete_track($track);
+    return (204,'text/plain',undef);
+}
+
+sub ACTION_upload_status {
+    my $self = shift;
+    my $q    = shift;
+
+    my $status    = 'status unknown';
+    my $file_name = 'Unknown';
+
+    my $state      = $self->state;
+    my $render     = $self->render;
+
+    if ($file_name = $state->{current_upload}) {
+	my $userdata = Bio::Graphics::Browser2::UserTracks->new($render->data_source,
+								$render->state,
+								$render->language);
+	$status      = $userdata->status($file_name);
+	return (200,'text/html',"<b>$file_name:</b> <i>$status</i>");
+    } else {
+	return (204,'text/plain',undef);
+    }
+}
+
+
 1;
+
+__END__
+
+# some dead code follows here
+
+# This looks like an older version of the retrieve_multiple request
+
+# Slightly different -- process a tracks request in the background.
+#     if ( my @labels = param('render') ) {    # deferred rendering requested
+#         $self->init_database();
+#         $self->init_plugins();
+#         $self->init_remote_sources();
+#         my $features = $self->region->features;
+#         my $seg      = $self->features2segments($features)->[0];    # likely wrong
+
+#         $self->set_segment($seg);
+
+#         my $deferred_data = $self->render_deferred( labels => \@labels );
+# 	return (200,'application/json',$deferred_data);
+#     }
+

Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render/HTML.pm	2009-09-28 20:25:38 UTC (rev 22122)
@@ -314,7 +314,7 @@
 	      -head     => \@extra_headers,
 	     );
   push @args,(-lang=>($self->language_code)[0]) if $self->language_code;
-  my $autocomplete = ''; # $self->setting('autocomplete') ? 'initAutocomplete()' : '';
+  my $autocomplete = '';
   push @args,(-onLoad=>"initialize_page();$set_dragcolors;$autocomplete");
 
   return start_html(@args);
@@ -583,7 +583,7 @@
       );
 
   my @segment_showing_links =(
-      a({-href=>'?bookmark=1'},'['.$self->tr('BOOKMARK').']'),
+      a({-href=>'?action=bookmark'},'['.$self->tr('BOOKMARK').']'),
       a({-href=>'#',
 	 -onMouseDown=>'visibility("upload_tracks_panel",1);new Effect.ScrollTo("upload_tracks_panel");setTimeout(\'new Effect.Highlight("upload_tracks_panel_title")\',1000)'},
       '['.$self->tr('Add_your_own_tracks').']'),
@@ -643,7 +643,7 @@
     }
 
     my $action = $galaxy_url =~ /\?/ ? "$galaxy_url&URL=$URL" : "$galaxy_url?URL=$URL";
-    
+
     my $html = start_multipart_form(-name  => 'galaxyform',
 				    -action => $action,
 				    -method => 'POST');
@@ -1213,8 +1213,9 @@
       action="$url"
       enctype="multipart/form-data"
        method="post">
-        <input type="file"   name="new_file_upload" id="new_upload_field" />
-        <input type="submit" name="new_file_submit" value="Upload"/>
+        <input type="file"   name="file"        id="upload_field" />
+        <input type="submit" name="submit"      value="Upload" />
+        <input type="hidden" name="action"      value="upload_file" />
         <a href="javascript:void(0)" onClick="this.parentNode.remove()">Remove</a>
 </form>
 END

Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/Render.pm	2009-09-28 20:25:38 UTC (rev 22122)
@@ -248,15 +248,9 @@
 
 # handle asynchronous events
 #
-# asynchronous requests:
-#
-# div_visible_<label>=bool              Turn on/off visibility of track with <label>
-# track_collapse_<label>=bool           Collapse/uncollapse track with <label>
-# label[]=<label1>,label[]=<label2>...  Change track order
-# render=<label1>,render=<label2>...    Render the specified tracks
-# navigate=
-#
-# returns ($http_status,$mime_type,$body_data)
+# Asynchronous requests. See Bio::Graphics::Browser2::Action for dispatch
+# table. Each request returns a three element list of format:
+#    ($http_status,$mime_type,$body_data)
 sub asynchronous_event {
     my $self     = shift;
     my $settings = $self->state;
@@ -264,350 +258,32 @@
 
     warn "event(",(join ' ',param()),")" if DEBUG;
 
-    # the big IF/ELSE statement that follows is HORRIBLE,
-    # so we are slowly cleaning this up with a more orderly
-    # dispatch object.
-    if (my $action = param('action')) {
+    # TO ADD AN ASYNCHRONOUS REQUEST...
+    # 1. Give the request a unique name, such as "foo"
+    # 2. Arrange for the client to POST or GET the document URL with a CGI
+    #    argument list that includes "action=foo".
+    # 3. Modify Bio::Graphics::Browser2::Action to include a method named
+    #    ACTION_foo that processes the request. The method will receive 
+    #    the CGI object as its argument, and is expected to return
+    #    a three-item list consisting of the HTTP status code, the MIME type,
+    #    and the message contents in the appropriate format for the MIME type.
+    #    Within the method call $self->render()
+    #    to get this Bio::Graphics::Browser2::Render object.
+
+    # legacy URLs
+    if (my @result = Bio::Graphics::Browser2::Action->handle_legacy_calls($CGI::Q,$self)) {
+	return @result;
+    }
+
+    elsif (my $action = param('action')) {
 	my $dispatch = Bio::Graphics::Browser2::Action->new($self);
 	my $method   = "ACTION_${action}";
 	return $dispatch->$method($CGI::Q);
     }
 
-    # everything below here should be migrated into Bio::Graphics::Browser2::Action
-
-    if ( my $track_name = param('share_track') ) {
-        my $html = $self->share_track($track_name);
-        return ( 200, 'text/html', $html );
+    else {
+	return;
     }
-
-    if ( my $element = param('update') ) {
-        warn "UPDATE HAS BEEN DEPRECATED";
-        my $html = $self->asynchronous_update_element($element);
-	return (200,'text/html',$html);
-    }
-
-    if ( param('retrieve_multiple') ) {
-        $self->init_plugins();
-        $self->init_remote_sources();
-
-        my %track_html;
-        my @track_ids = param('track_ids');
-
-        foreach my $track_id (@track_ids) {
-            my $track_key = param( 'tk_' . $track_id ) or next;
-	    warn "retrieving $track_id=>$track_key" if DEBUG;
-            $track_html{$track_id} = $self->render_deferred_track(
-                cache_key  => $track_key,
-                track_id   => $track_id,
-            ) || '';
-        }
-
-        my $return_object = { track_html => \%track_html, };
-        return ( 200, 'application/json', $return_object );
-    }
-
-    if ( my $action = param('add_tracks') ) {
-        my @track_names = param('track_names');
-
-        $self->init_database();
-        $self->init_plugins();
-        $self->init_remote_sources();
-        my %track_data;
-
-        foreach my $track_name ( @track_names ) {
-	    warn "add_track_to_state($track_name)" if DEBUG;
-
-            $self->add_track_to_state($track_name);
-	    next unless $self->segment;
-
-	    my @track_ids = $self->expand_track_names($track_name);
-
-	    for my $track_id (@track_ids) {
-
-		warn "rendering track $track_id" if DEBUG;
-
-		my ( $track_keys, $display_details, $details_msg )
-		    = $self->background_individual_track_render($track_id);
-
-		my $track_key        = $track_keys->{$track_id};
-		my $track_section    = $self->get_section_from_label($track_id);
-		my $image_width      = $self->get_image_width;
-		my $image_element_id = $track_name . "_image";
-
-		my $track_html;
-		if ( $track_section eq 'detail' and not $display_details ) {
-		    my $image_width = $self->get_image_width;
-		    $track_html .= $self->render_grey_track(
-			track_id         => $track_name,
-			image_width      => $image_width,
-			image_height     => EMPTY_IMAGE_HEIGHT,
-			image_element_id => $track_name . "_image",
-			);
-		}
-		else {
-		    $track_html = $self->render_deferred_track(
-			cache_key  => $track_key,
-			track_id   => $track_id,
-			) || '';
-		}
-		$track_html = $self->wrap_track_in_track_div(
-		    track_id   => $track_id,
-		    track_name => $track_name,
-		    track_html => $track_html,
-		    );
-
-		my $panel_id = 'detail_panels';
-		if ( $track_id =~ /:overview$/ ) {
-		    $panel_id = 'overview_panels';
-		}
-		elsif ( $track_id =~ /:region$/ ) {
-		    $panel_id = 'region_panels';
-		}
-		warn "add_track() returning track_id=$track_id, key=$track_key, name=$track_name, panel_id=$panel_id" if DEBUG;
-		
-		$track_data{$track_id} = {
-		    track_key        => $track_key,
-		    track_id         => $track_id,
-		    track_name       => $track_name,
-		    track_html       => $track_html,
-		    track_section    => $track_section,
-		    image_element_id => $image_element_id,
-		    panel_id         => $panel_id,
-		    display_details  => $display_details,
-		    details_msg      => $details_msg,
-		};
-	    }
-	}
-
-        my $return_object = { track_data => \%track_data, };
-        return ( 200, 'application/json', $return_object );
-    }
-    if ( param('set_track_visibility') ) {
-        my $visible    = param('visible');
-        my $track_name = param('track_name');
-
-	param('track_name'),'=>',param('visible') if DEBUG;
-
-        if ($visible) {
-	    $self->init_plugins();
-	    $self->init_remote_sources();
-            $self->add_track_to_state($track_name);
-        }
-        else {
-            $self->remove_track_from_state($track_name);
-        }
-
-        return (204,'text/plain',undef);
-    }
-
-    if ( my $action = param('rerender_track') ) {
-        my $track_id = param('track_id');
-
-        $self->init_database();
-        $self->init_plugins();
-        $self->init_remote_sources();
-
-        my ( $track_keys, $display_details, $details_msg )
-            = $self->background_individual_track_render($track_id);
-
-        my $return_object = {
-            track_keys      => $track_keys,
-            display_details => $display_details,
-            details_msg     => $details_msg,
-        };
-        return (200,'application/json',$return_object);
-    }
-
-    if ( param('reconfigure_plugin') ) {
-        # init_plugins will do the configure call needed
-        $self->init_plugins();
-	return (204,'text/plain',undef);
-    }
-
-    if ( param('commit_file_edit') ) {
-        my $data        = param('a_data');
-        my $edited_file = param('edited_file');
-
-        return ( 204, 'text/plain', undef ) unless ( $edited_file and $data );
-        $self->init_remote_sources();
-        my ($file_created,$tracks) = $self->handle_edit( $edited_file, $self->state, $data );
-
-        my $return_object = {
-            file_created   => $file_created,
-	    tracks         => $tracks,
-        };
-
-        return (200,'application/json',$return_object);
-    }
-
-    if (param ('add_url')) {
-	my $data = param('eurl');
-	$self->init_remote_sources;
-	$self->remote_sources->add_source($data);
-	$self->add_track_to_state($data);
-	warn "adding $data to remote sources" if DEBUG;
-	return (200,'application/json',{url_created=>1});
-    }
-
-    if ( param('delete_upload_file') ) {
-        my $file = param('file');
-	warn "deleting file $file " if DEBUG;
-        $self->init_remote_sources();
-        $self->uploaded_sources->clear_file($file);
-        $self->remote_sources->delete_source($file);
-        $self->remove_track_from_state($file);
-
-        return (204,'text/plain',undef);
-    }
-
-    # toggle the visibility of sections by looking for "div_visible_*"
-    # parameters
-    for my $p ( grep {/^div_visible_/} param() ) {
-        my $visibility = param($p);
-        $p =~ s/^div_visible_//;
-        $settings->{section_visible}{$p} = $visibility;
-        $events++;
-    }
-
-    # toggle the visibility of individual tracks
-    for my $p ( grep {/^track_collapse_/} param() ) {
-        my $collapsed = param($p);
-        $p =~ s/^track_collapse_//;
-	warn "\$settings->{track_collapsed}{$p} = $collapsed" if DEBUG;
-        $settings->{track_collapsed}{$p} = $collapsed;
-        $events++;
-    }
-
-    # Change the order of tracks if any "label[]" parameters are present
-    if ( my @labels = param('label[]') ) {
-        foreach (@labels) {
-	    s/%5F/_/g;
-	    s/:(overview|region|detail)$// if m/^(plugin|file|http|ftp):/;
-	}
-        my %seen;
-        @{ $settings->{tracks} } = grep { length() > 0 && !$seen{$_}++ }
-            ( @labels, @{ $settings->{tracks} } );
-        $events++;
-    }
-
-    # Slightly different -- process a tracks request in the background.
-    if ( my @labels = param('render') ) {    # deferred rendering requested
-        $self->init_database();
-        $self->init_plugins();
-        $self->init_remote_sources();
-        my $features = $self->region->features;
-        my $seg      = $self->features2segments($features)->[0];    # likely wrong
-
-        $self->set_segment($seg);
-
-        my $deferred_data = $self->render_deferred( labels => \@labels );
-	return (200,'application/json',$deferred_data);
-    }
-
-    # miscellaneous options
-    if (param('set_display_option')) {
-	$self->update_options();
-	$events++;
-    }
-
-    # redirect to the bookmark
-    if (param('bookmark')) {
-	return (302,undef,$self->bookmark_link($self->state));
-    }
-
-    # redirect to galaxy form submission
-    if (param('galaxy')) {
-	return (302,undef,$self->galaxy_link($self->state));
-    }
-
-    # redirect to the imagelink
-    if (my $format = param('make_image')) {
-	return (302,undef,$self->image_link($self->state,$format));
-    }
-
-    # autocomplete support
-    if (my $match  = param('autocomplete')) {
-	my $search = $self->get_search_object;
-	my $matches= $search->features_by_prefix($match,100);
-	my $autocomplete = $self->format_autocomplete($matches,$match);
-	return (200,'text/html',$autocomplete);
-    }
-
-    # clear a cached data source
-    if (param('clear_dsn') || param('reset_dsn')) {
-	$self->data_source->clear_cached_config();
-	return (204,'text/plain',undef);
-    }
-
-    # authorize an attempted login
-    if (param('authorize_login') && param('username') && param('session') && param('openid')) {
-	my ($id,$nonce) = $self->authorize_user(param('username'),param('session'),param('remember'),param('openid'));
-	return (200,'application/json',{id=>$id,authority=>$nonce});
-    }
-
-    # add a dummy track to the user data
-    if (param('new_test_track')) {
-	my $userdata = Bio::Graphics::Browser2::UploadSet->new($self->data_source,
-							      $self->state,
-							      $self->language);
-	warn "Adding test track for ",$self->state->{uploadid}," path = ",($userdata->name_file('test'))[1];
-	return (204,'text/plain',undef);
-    }
-
-    # new-style ajax upload
-    if (param('new_file_submit')) {
-	if (my $fh = param('new_file_upload')) {
-	    my $userdata = Bio::Graphics::Browser2::UserTracks->new($self->data_source,
-								   $self->state,
-								   $self->language);
-	    warn "created userdata $userdata";
-	    my $name = basename($fh );
-	    $self->state->{current_upload} = $name;
-	    $self->session->flush();
-	    $self->session->unlock();
-	    my ($result,$msg) = $userdata->upload_track($name,$fh);
-	    return $msg ? (200,
-			 'text/html',
-			 "<pre style='background-color:pink'>$msg</pre>".
-			 a({
-			     -href    =>'javascript:void(0)',
-			     -onClick =>"\$('upload_status').innerHTML=''"
-			   },
-			   '[Remove]'
-			 )
-		)
-		      : (200,'text/plain',undef);
-	}
-	return (204,'text/plain',undef);
-    }
-
-    if (param('new_file_upload_status')) {
-	my $status    = 'status unknown';
-	my $file_name = 'Unknown';
-
-	if ($file_name = $self->state->{current_upload}) {
-	    my $userdata = Bio::Graphics::Browser2::UserTracks->new($self->data_source,
-								   $self->state,
-								   $self->language);
-	    $status      = $userdata->status($file_name);
-	    return (200,'text/html',"<b>$file_name:</b> <i>$status</i>");
-        } else {
-	    return (204,'text/plain',undef);
-	}
-    }
-
-    if (my $track = param('deleteUploadTrack')) {
-	my $userdata = Bio::Graphics::Browser2::UserTracks->new($self->data_source,
-							       $self->state,
-							       $self->language);
-	$userdata->delete_track($track);
-	return (204,'text/plain',undef);
-    }
-
-    return unless $events;
-    warn "processing asynchronous event(s)" if DEBUG;
-    return (204,'text/plain',undef);
-    1;
 }
 
 sub authorize_user {
@@ -711,6 +387,81 @@
     return (\%track_keys, $display_details, $details_msg);
 }
 
+sub add_tracks {
+    my $self        = shift;
+    my $track_names = shift;
+
+    my %track_data;
+
+    foreach my $track_name ( @$track_names ) {
+
+	warn "add_track_to_state($track_name)" if DEBUG;
+
+	$self->add_track_to_state($track_name);
+	next unless $self->segment;
+
+	my @track_ids = $self->expand_track_names($track_name);
+
+	for my $track_id (@track_ids) {
+
+	    warn "rendering track $track_id" if DEBUG;
+
+	    my ( $track_keys, $display_details, $details_msg )
+		= $self->background_individual_track_render($track_id);
+	    
+	    my $track_key        = $track_keys->{$track_id};
+	    my $track_section    = $self->get_section_from_label($track_id);
+	    my $image_width      = $self->get_image_width;
+	    my $image_element_id = $track_name . "_image";
+
+	    my $track_html;
+	    if ( $track_section eq 'detail' and not $display_details ) {
+		my $image_width = $self->get_image_width;
+		$track_html .= $self->render_grey_track(
+		    track_id         => $track_name,
+		    image_width      => $image_width,
+		    image_height     => EMPTY_IMAGE_HEIGHT,
+		    image_element_id => $track_name . "_image",
+		    );
+	    }
+	    else {
+		$track_html = $self->render_deferred_track(
+		    cache_key  => $track_key,
+		    track_id   => $track_id,
+		    ) || '';
+	    }
+	    $track_html = $self->wrap_track_in_track_div(
+		track_id   => $track_id,
+		track_name => $track_name,
+		track_html => $track_html,
+		);
+	    
+	    my $panel_id = 'detail_panels';
+	    if ( $track_id =~ /:overview$/ ) {
+		$panel_id = 'overview_panels';
+	    }
+	    elsif ( $track_id =~ /:region$/ ) {
+		$panel_id = 'region_panels';
+	    }
+	    warn "add_track() returning track_id=$track_id, key=$track_key, name=$track_name, panel_id=$panel_id" if DEBUG;
+	    
+	    $track_data{$track_id} = {
+		track_key        => $track_key,
+		track_id         => $track_id,
+		track_name       => $track_name,
+		track_html       => $track_html,
+		track_section    => $track_section,
+		image_element_id => $image_element_id,
+		panel_id         => $panel_id,
+		display_details  => $display_details,
+		details_msg      => $details_msg,
+	    };
+	}
+    }
+
+    return \%track_data;
+}
+
 sub create_cache_extra {
     my $self     = shift;
     my $settings = $self->state();
@@ -1723,7 +1474,11 @@
 							 $self->state,
 							 $self->language);
     $uploads->add_file($uploads->name_file($file));
-    my @sections = eval {$self->_featurefile_sections($uploads->feature_file($file))};
+
+    my $ff = eval {$uploads->feature_file($file)};
+    return (0,[],$@) unless $ff;
+
+    my @sections = $self->_featurefile_sections($ff);
     my @tracks   = map {"$file:$_"} @sections;
 
     warn "will return tracks @tracks" if DEBUG;
@@ -3476,9 +3231,11 @@
 	    warn "FEATURESET = $featureset, sources = ",join ' ',eval{$featureset->sources} if DEBUG;
 	    next unless $featureset;
 
-	    $featureset->annotate($meta_segment,$f,
-				  $rel2abs,$rel2abs_slow,$max_segment,
-				  $self->whole_segment,$self->region_segment);
+	    eval {
+		$featureset->annotate($meta_segment,$f,
+				      $rel2abs,$rel2abs_slow,$max_segment,
+				      $self->whole_segment,$self->region_segment);
+	    };
 	}
     }
 
@@ -3546,9 +3303,6 @@
   $q->param(-name=>'h_region',-value=>$settings->{h_region}) if $settings->{h_region};
   my @h_feat= map {"$_\@$settings->{h_feat}{$_}"} keys %{$settings->{h_feat}};
   $q->param(-name=>'h_feat',  -value=>\@h_feat) if @h_feat;
-
-  warn 'query string = ',$q->query_string();
-
   return "?".$q->query_string();
 }
 

Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/RenderPanels.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/RenderPanels.pm	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/RenderPanels.pm	2009-09-28 20:25:38 UTC (rev 22122)
@@ -459,7 +459,7 @@
                 -onMouseOver =>
                     "$balloon_style.showTooltip(event,'$share_this_track')",
 		    -onMousedown =>
-                    "GBox.showTooltip(event,'url:?share_track=$escaped_label',1,500,500)",
+                    "GBox.showTooltip(event,'url:?action=share_track;track=$escaped_label',1,500,500)",
             }
         ),
 

Modified: Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/UploadSet.pm
===================================================================
--- Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/UploadSet.pm	2009-09-28 15:23:59 UTC (rev 22121)
+++ Generic-Genome-Browser/trunk/lib/Bio/Graphics/Browser2/UploadSet.pm	2009-09-28 20:25:38 UTC (rev 22122)
@@ -152,14 +152,13 @@
   my $fh   = $self->open_file($url) or return;
   my $safe = $self->config->setting('allow remote callbacks') || 0;
   warn "creating $url feature_file" if DEBUG;
-  my $feature_file = eval {
+  my $feature_file = 
       Bio::Graphics::FeatureFile->new(-file             => $fh,
 				      -smart_features   => 1,
 				      -allow_whitespace => 1,
 				      -safe_world       => $safe,
 				      @args,
-	  );
-  };
+      );
   close $fh;
 
   # BUG: breaking encapsulation here


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