commit/galaxy-central: 5 new changesets - galaxy-commits

28 Jul 2011

5 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/7507b7be224c/
changeset:   7507b7be224c
user:        dannon
date:        2011-07-21 20:22:23
summary:     Trailing whitespace cleanup workflow editor.
affected #:  1 file (612 bytes)

--- a/templates/workflow/editor.mako	Thu Jul 21 13:55:24 2011 -0400
+++ b/templates/workflow/editor.mako	Thu Jul 21 14:22:23 2011 -0400
@@ -18,17 +18,17 @@
 </%def><%def name="javascripts()">
-    
+
     ${parent.javascripts()}
-    
+
     <!--[if lt IE 9]><script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]-->
${h.js( "jquery",
             "jquery.tipsy",
-            "jquery.event.drag", 
-            "jquery.event.drop", 
+            "jquery.event.drag",
+            "jquery.event.drop",
             "jquery.event.hover",
             "jquery.form",
             "json2",
@@ -43,7 +43,7 @@
     window.lt_ie_7 = true;
     </script><![endif]-->
-    
+
     <script type='text/javascript'>
     // Globals
     workflow = null;
@@ -51,10 +51,10 @@
     active_ajax_call = false;
     var galaxy_async = new GalaxyAsync();
     galaxy_async.set_func_url(galaxy_async.set_user_pref, "${h.url_for( controller='user', action='set_user_pref_async' )}");
-    
+
     // jQuery onReady
     $( function() {
-        
+
         if ( window.lt_ie_7 ) {
             show_modal(
                 "Browser not supported",
@@ -62,7 +62,7 @@
             );
             return;
         }
-        
+
         // Init tool options.
         %if trans.app.toolbox_search.enabled:
         make_popupmenu( $("#tools-options-button"), {
@@ -71,7 +71,7 @@
                 show_tool_search = False
                 if trans.user:
                     show_tool_search = trans.user.preferences.get( "workflow.show_tool_search", "True" )
-                    
+
                 if show_tool_search == "True":
                     initial_text = "Hide Search"
                 else:
@@ -85,7 +85,6 @@
                     pref_value = "False";
                     menu_option_text = "Search Tools";
                     menu.toggle();
-                    
                     // Reset search.
                     reset_tool_search(true);
                 } else {
@@ -94,14 +93,12 @@
                     menu_option_text = "Hide Search";
                     menu.toggle();
                 }
-        
                 // Update menu option.
                 $("#tools-options-button-menu").find("li").eq(0).text(menu_option_text);
-        
                 galaxy_async.set_user_pref("workflow.show_tool_search", pref_value);
             }
         });
-        
+
         // Init searching.
         $("#tool-search-query").click( function (){
             $(this).focus();
@@ -110,7 +107,6 @@
         .keyup( function () {
             // Remove italics.
             $(this).css("font-style", "normal");
-            
             // Don't update if same value as last time
             if ( this.value.length < 3 ) {
                 reset_tool_search(false);
@@ -127,7 +123,6 @@
                 // Start a new ajax-request in X ms
                 $("#search-spinner").show();
                 this.timer = setTimeout(function () {
-                    
                     $.get("${h.url_for( controller='root', action='tool_search' )}", { query: q }, function (data) {
                         // input.removeClass(config.loadingClass);
                         // Show live-search if results and search-term aren't empty
@@ -139,17 +134,15 @@
                         if ( data.length != 0 ) {
                             // Map tool ids to element ids and join them.
                             var s = $.map( data, function( n, i ) { return "#link-" + n; } ).join( ", " );
-                            
                             // First pass to show matching tools and their parents.
                             $(s).each( function() {
                                 // Add class to denote match.
                                 $(this).parent().addClass("search_match");
                                 $(this).parent().show().parent().parent().show().parent().show();
                             });
-                            
                             // Hide labels that have no visible children.
                             $(".toolPanelLabel").each( function() {
-                               var this_label = $(this);                                   
+                               var this_label = $(this);
                                var next = this_label.next();
                                var no_visible_tools = true;
                                // Look through tools following label and, if none are visible, hide label.
@@ -174,11 +167,11 @@
             }
             this.lastValue = this.value;
         });
-        %endif          
-        
+        %endif
+
         // Canvas overview management
         canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") );
-        
+
         // Initialize workflow state
         reset();
         // Load the datatype info
@@ -225,7 +218,7 @@
                 });
             }
         });
-        
+
         // For autosave purposes
         $(document).ajaxStart( function() {
             active_ajax_call = true;
@@ -233,14 +226,14 @@
                 active_ajax_call = false;
             });
         });
-        
+
         $(document).ajaxError( function ( e, x ) {
             // console.log( e, x );
             var message = x.responseText || x.statusText || "Could not connect to server";
             show_modal( "Server error", message, { "Ignore error" : hide_modal } );
             return false;
         });
-         
+
         make_popupmenu( $("#workflow-options-button"), {
             "Save" : save_current_workflow,
             ##"Create New" : create_new_workflow_dialog,
@@ -250,7 +243,7 @@
             ##"Load a Workflow" : load_workflow,
             "Close": close_editor
         });
-        
+
         function edit_workflow_outputs(){
             workflow.clear_active_node();
             $('.right-content').hide();
@@ -297,14 +290,14 @@
             scroll_to_nodes();
             canvas_manager.draw_overview();
         }
-        
+
         function edit_workflow_attributes() {
             workflow.clear_active_node();
             $('.right-content').hide();
             $('#edit-attributes').show();
}
-        
+
         // On load, set the size to the pref stored in local storage if it exists
         overview_size = $.jStorage.get("overview-size");
         if (overview_size !== undefined) {
@@ -313,14 +306,14 @@
                 height: overview_size
             });
         }
-        
+
         // Show viewport on load unless pref says it's off
         if ($.jStorage.get("overview-off")) {
             hide_overview();
         } else {
             show_overview();
         }
-        
+
         // Stores the size of the overview into local storage when it's resized
         $("#overview-border").bind( "dragend", function( e, d ) {
             var op = $(this).offsetParent();
@@ -329,19 +322,19 @@
                                      op.height() - ( d.offsetY - opo.top ) );
             $.jStorage.set("overview-size", new_size + "px");
         });
-        
+
         function show_overview() {
             $.jStorage.set("overview-off", false);
             $("#overview-border").css("right", "0px");
             $("#close-viewport").css("background-position", "0px 0px");
         }
-        
+
         function hide_overview() {
             $.jStorage.set("overview-off", true);
             $("#overview-border").css("right", "20000px");
             $("#close-viewport").css("background-position", "12px 0px");
         }
-        
+
         // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly
         $("#close-viewport").click( function() {
             if ( $("#overview-border").css("right") === "0px" ) {
@@ -350,19 +343,19 @@
                 show_overview();
             }
         });
-        
+
         // Unload handler
         window.onbeforeunload = function() {
             if ( workflow && workflow.has_changes ) {
                 return "There are unsaved changes to your workflow which will be lost.";
             }
         };
-        
+
         // Tool menu
         $( "div.toolSectionBody" ).hide();
         $( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" );
         var last_expanded = null;
-        $( "div.toolSectionTitle" ).each( function() { 
+        $( "div.toolSectionTitle" ).each( function() {
            var body = $(this).next( "div.toolSectionBody" );
            $(this).click( function() {
                if ( body.is( ":hidden" ) ) {
@@ -379,7 +372,7 @@
// Rename async.
         async_save_text("workflow-name", "workflow-name", "${h.url_for( action='rename_async', id=trans.security.encode_id(stored.id) )}", "new_name");
-        
+
         // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging.
         $('#workflow-tag').click( function() {
             $('.tag-area').click();
@@ -396,7 +389,7 @@
         }
         workflow = new Workflow( $("#canvas-container") );
     }
-        
+
     function scroll_to_nodes() {
         var cv = $("#canvas-viewport");
         var cc = $("#canvas-container");
@@ -413,7 +406,7 @@
         }
         cc.css( { left: left, top: top } );
     }
-    
+
     // Add a new step to the workflow by tool id
     function add_node_for_tool( id, title ) {
         var node = prebuild_node( 'tool', title, id );
@@ -422,7 +415,7 @@
         canvas_manager.draw_overview();
         workflow.activate_node( node );
         $.ajax( {
-            url: "${h.url_for( action='get_new_module_info' )}", 
+            url: "${h.url_for( action='get_new_module_info' )}",
             data: { type: "tool", tool_id: id, "_": "true" },
             global: false,
             dataType: "json",
@@ -438,7 +431,7 @@
             }
         });
     }
-    
+
     function add_node_for_module( type, title ) {
         node = prebuild_node( type, title );
         workflow.add_node( node );
@@ -446,8 +439,8 @@
         canvas_manager.draw_overview();
         workflow.activate_node( node );
         $.ajax( {
-            url: "${h.url_for( action='get_new_module_info' )}", 
-            data: { type: type, "_": "true" }, 
+            url: "${h.url_for( action='get_new_module_info' )}",
+            data: { type: type, "_": "true" },
             dataType: "json",
             success: function( data ) {
                 node.init_field_data( data );
@@ -479,11 +472,11 @@
             workflow.active_form_has_changes = true;
         });
     }
-    
+
     function display_pja_list(){
         return "${ActionBox.get_add_list()}";
     }
-    
+
     function display_file_list(node){
         addlist = "<select id='node_data_list' name='node_data_list'>";
         for (var out_terminal in node.output_terminals){
@@ -492,7 +485,7 @@
         addlist += "</select>";
         return addlist;
     }
-    
+
     function new_pja(action_type, target, node){
         if (node.post_job_actions === undefined){
             //New tool node, set up dict.
@@ -511,7 +504,7 @@
             return false;
         }
     }
-    
+
     function show_workflow_parameters(){
         var parameter_re = /${.+?}/g;
         var workflow_parameters = [];
@@ -532,7 +525,7 @@
                             if (arg_matches){
                                 matches = matches.concat(arg_matches);
                             }
-                        });                        
+                        });
                     }
                 });
                 if (matches){
@@ -541,7 +534,7 @@
                             workflow_parameters.push(element);
                         }
                     });
-                }                
+                }
             }
         });
         if (workflow_parameters && workflow_parameters.length !== 0){
@@ -555,7 +548,7 @@
             wf_parm_box.hide();
         }
     }
-    
+
     function show_form_for_tool( text, node ) {
         $('.right-content').hide();
         $("#right-content").show().html( text );
@@ -632,7 +625,7 @@
             });
         });
     }
-    
+
     var close_editor = function() {
         <% next_url = h.url_for( controller='workflow', action='index' ) %>
         workflow.check_changes_in_active_form();
@@ -655,7 +648,7 @@
             window.document.location = "${next_url}";
         }
     };
-    
+
     var save_current_workflow = function ( eventObj, success_callback ) {
         show_modal( "Saving workflow", "progress" );
         workflow.check_changes_in_active_form();
@@ -677,7 +670,7 @@
                     "_": "true"
                 },
                 dataType: 'json',
-                success: function( data ) { 
+                success: function( data ) {
                     var body = $("<div></div>").text( data.message );
                     if ( data.errors ) {
                         body.addClass( "warningmark" );
@@ -704,7 +697,7 @@
                 }
             });
         };
-        
+
         // We bind to ajaxStop because of auto-saving, since the form submission ajax
         // call needs to be completed so that the new data is saved
         if (active_ajax_call) {
@@ -718,7 +711,7 @@
             savefn(success_callback);
         }
     };
-    
+
     </script></%def>
@@ -732,7 +725,7 @@
<style type="text/css">
     body { margin: 0; padding: 0; overflow: hidden; }
-    
+
     /* Wider right panel */
     #center       { right: 309px; }
     #right-border { right: 300px; }
@@ -744,11 +737,11 @@
     ##     top: 2.5em;
     ##     margin-top: 7px;
     ## }
-    
+
     #left {
         background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x;
     }
-    
+
     div.toolMenu {
         margin: 5px;
         margin-left: 10px;
@@ -785,8 +778,8 @@
     .right-content {
         margin: 5px;
     }
-    
-    canvas { position: absolute; z-index: 10; } 
+
+    canvas { position: absolute; z-index: 10; }
     canvas.dragging { position: absolute; z-index: 1000; }
     .input-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; top: 50%; margin-top: -6px; left: -6px; z-index: 1500; }
     .output-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; top: 50%; margin-top: -6px; right: -6px; z-index: 1500; }
@@ -795,12 +788,12 @@
     ## .input-terminal-hover { background: yellow; border: solid black 1px; }
     .unselectable { -moz-user-select: none; -khtml-user-select: none; user-select: none; }
     img { border: 0; }
-    
+
     div.buttons img {
     width: 16px; height: 16px;
     cursor: pointer;
     }
-    
+
     ## Extra styles for the representation of a tool on the canvas (looks like
     ## a tiny tool form)
     div.toolFormInCanvas {
@@ -809,18 +802,18 @@
         ## min-width: 130px;
         margin: 6px;
     }
-    
+
     div.toolForm-active {
         z-index: 1001;
         border: solid #8080FF 4px;
         margin: 3px;
     }
-    
+
     div.toolFormTitle {
         cursor: move;
         min-height: 16px;
     }
-    
+
     div.titleRow {
         font-weight: bold;
         border-bottom: dotted gray 1px;
@@ -830,7 +823,7 @@
     div.form-row {
       position: relative;
     }
-    
+
     div.tool-node-error div.toolFormTitle {
         background: #FFCCCC;
         border-color: #AA6666;
@@ -838,14 +831,14 @@
     div.tool-node-error {
         border-color: #AA6666;
     }
-    
+
     #canvas-area {
         position: absolute;
         top: 0; left: 305px; bottom: 0; right: 0;
         border: solid red 1px;
         overflow: none;
     }
-    
+
     .form-row {
     }
@@ -855,14 +848,14 @@
     .form-row-clear {
         clear: both;
     }
-    
+
     div.rule {
         height: 0;
         border: none;
         border-bottom: dotted black 1px;
         margin: 0 5px;
     }
-    
+
     .callout {
         position: absolute;
         z-index: 10000;
@@ -871,21 +864,21 @@
     .pjaForm {
         margin-bottom:10px;
     }
-    
+
     .pjaForm .toolFormBody{
         padding:10px;
     }
-    
+
     .pjaForm .toolParamHelp{
         padding:5px;
     }
-    
+
     .panel-header-button-group {
         margin-right: 5px;
         padding-right: 5px;
         border-right: solid gray 1px;
     }
-        
+
     </style></%def>
@@ -945,7 +938,7 @@
             ${n_('Tools')}
         </div></div>
-    
+
     <div class="unified-panel-body" style="overflow: auto;"><div class="toolMenu">
             ## Tool search.
@@ -953,7 +946,6 @@
                 show_tool_search = False
                 if trans.user:
                     show_tool_search = trans.user.preferences.get( "workflow.show_tool_search", "True" )
-            
                 if show_tool_search == "True":
                     display = "block"
                 else:
@@ -963,7 +955,6 @@
                 <input type="text" name="query" value="search tools" id="tool-search-query" style="width: 100%; font-style:italic; font-size: inherit" autocomplete="off"/><img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" style="display: none; position: absolute; right: 0; top: 5px;"/></div>
-        
             <div class="toolSectionList">
                 %for key, val in app.toolbox.tool_panel.items():
                     <div class="toolSectionWrapper">
@@ -1007,10 +998,10 @@
                         <a href="#" onclick="add_node_for_module( 'data_input', 'Input Dataset' )">Input dataset</a></div></div>
-            </div>                    
+            </div></div></div>
-    
+
 </%def><%def name="center_panel()">
@@ -1023,7 +1014,6 @@
             Workflow Canvas | ${h.to_unicode( stored.name ) | h}
         </div></div>
-
     <div class="unified-panel-body"><div id="canvas-viewport" style="width: 100%; height: 100%; position: absolute; overflow: hidden; background: #EEEEEE; background: white url(${h.url_for('/static/images/light_gray_grid.gif')}) repeat;"><div id="canvas-container" style="position: absolute; width: 100%; height: 100%;"></div>
@@ -1079,7 +1069,7 @@
                     <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div></div>
                 ## Workflow annotation.
-                ## Annotation elt.                
+                ## Annotation elt.
                 <div id="workflow-annotation-area" class="form-row"><label>Annotation / Notes:</label><div id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation">
http://bitbucket.org/galaxy/galaxy-central/changeset/2687588bca04/
changeset:   2687588bca04
user:        dannon
date:        2011-07-26 19:18:22
summary:     merge
affected #:  17 files (15.8 KB)
--- a/datatypes_conf.xml.sample	Thu Jul 21 14:22:23 2011 -0400
+++ b/datatypes_conf.xml.sample	Tue Jul 26 13:18:22 2011 -0400
@@ -123,7 +123,7 @@
         <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"><converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-            <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>    
+            <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/></datatype><datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
@@ -274,10 +274,10 @@
     </registration><sniffers><!--
-          The order in which Galaxy attempts to determine data types is 
-          important because some formats are much more loosely defined 
-          than others.  The following list should be the most rigidly 
-          defined format first, followed by next-most rigidly defined, 
+          The order in which Galaxy attempts to determine data types is
+          important because some formats are much more loosely defined
+          than others.  The following list should be the most rigidly
+          defined format first, followed by next-most rigidly defined,
           and so on.
         --><sniffer type="galaxy.datatypes.tabular:Vcf"/>
--- a/lib/galaxy/web/controllers/tracks.py	Thu Jul 21 14:22:23 2011 -0400
+++ b/lib/galaxy/web/controllers/tracks.py	Tue Jul 26 13:18:22 2011 -0400
@@ -90,10 +90,14 @@
 class DbKeyColumn( grids.GridColumn ):
     """ Column for filtering by and displaying dataset dbkey. """
     def filter( self, trans, user, query, dbkey ):
-        """ Filter by dbkey. """
+        """ Filter by dbkey; datasets without a dbkey are returned as well. """
         # use raw SQL b/c metadata is a BLOB
         dbkey = dbkey.replace("'", "\'")
-        return query.filter( or_( "metadata like '%%"dbkey": ["%s"]%%'" % dbkey, "metadata like '%%"dbkey": "%s"%%'" % dbkey ) )
+        return query.filter( or_( \
+                                or_( "metadata like '%%"dbkey": ["%s"]%%'" % dbkey, "metadata like '%%"dbkey": "%s"%%'" % dbkey ), \
+                                or_( "metadata like '%%"dbkey": ["?"]%%'", "metadata like '%%"dbkey": "?"%%'" ) \
+                                )
+                            )
class HistoryColumn( grids.GridColumn ):
     """ Column for filtering by history id. """
--- a/lib/galaxy/webapps/community/controllers/repository.py	Thu Jul 21 14:22:23 2011 -0400
+++ b/lib/galaxy/webapps/community/controllers/repository.py	Tue Jul 26 13:18:22 2011 -0400
@@ -935,14 +935,22 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         repository = get_repository( trans, repository_id )
-        tool = load_tool( trans, os.path.abspath( tool_config ) )
-        tool_state = self.__new_state( trans )
-        return trans.fill_template( "/webapps/community/repository/tool_form.mako",
-                                    repository=repository,
-                                    tool=tool,
-                                    tool_state=tool_state,
-                                    message=message,
-                                    status=status )
+        try:
+            tool = load_tool( trans, os.path.abspath( tool_config ) )
+            tool_state = self.__new_state( trans )
+            return trans.fill_template( "/webapps/community/repository/tool_form.mako",
+                                        repository=repository,
+                                        tool=tool,
+                                        tool_state=tool_state,
+                                        message=message,
+                                        status=status )
+        except Exception, e:
+            message = 'Error loading tool: %s.  Click <b>Reset metadata</b> to correct this error.' % str( e )
+            return trans.response.send_redirect( web.url_for( controller='repository',
+                                                              action='manage_repository',
+                                                              id=repository_id,
+                                                              message=message,
+                                                              status='error' ) )
     def __new_state( self, trans, all_pages=False ):
         """
         Create a new `DefaultToolState` for this tool. It will not be initialized
@@ -955,6 +963,27 @@
         state.inputs = {}
         return state
     @web.expose
+    def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        repository = get_repository( trans, repository_id )
+        metadata = {}
+        tool = None
+        repository_metadata = get_repository_metadata( trans, repository_id, changeset_revision ).metadata
+        if 'tools' in repository_metadata:
+            for tool_metadata_dict in repository_metadata[ 'tools' ]:
+                if tool_metadata_dict[ 'id' ] == tool_id:
+                    metadata = tool_metadata_dict
+                    tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) )
+                    break
+        return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako",
+                                    repository=repository,
+                                    tool=tool,
+                                    metadata=metadata,
+                                    message=message,
+                                    status=status )
+    @web.expose
     def download( self, trans, repository_id, file_type, **kwd ):
         # Download an archive of the repository files compressed as zip, gz or bz2.
         params = util.Params( kwd )
--- a/static/june_2007_style/blue/panel_layout.css	Thu Jul 21 14:22:23 2011 -0400
+++ b/static/june_2007_style/blue/panel_layout.css	Tue Jul 26 13:18:22 2011 -0400
@@ -1,4 +1,3 @@
-body,html{overflow:hidden;margin:0;padding:0;width:100%;height:100%;}
 body{font:75% "Lucida Grande",verdana,arial,helvetica,sans-serif;background:#eee;}
 .unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;}
 #background{position:absolute;background:#eee;z-index:-1;top:0;left:0;margin:0;padding:0;width:100%;height:100%;}
--- a/static/june_2007_style/blue/trackster.css	Thu Jul 21 14:22:23 2011 -0400
+++ b/static/june_2007_style/blue/trackster.css	Tue Jul 26 13:18:22 2011 -0400
@@ -55,4 +55,4 @@
 .icon.more-down{background:url('../images/fugue/arrow-transition-270-bw.png') no-repeat 0px 0px;}
 .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;}
 .intro{padding:1em;}
-.intro>.action-button{background-color:#CCC;padding:1em;}
\ No newline at end of file
+.intro > .action-button{background-color:#CCC;padding:1em;}
--- a/static/june_2007_style/panel_layout.css.tmpl	Thu Jul 21 14:22:23 2011 -0400
+++ b/static/june_2007_style/panel_layout.css.tmpl	Tue Jul 26 13:18:22 2011 -0400
@@ -1,11 +1,3 @@
-body, html {
-    overflow: hidden;
-    margin: 0;
-    padding: 0;
-    width: 100%;
-    height: 100%;
-}
-
 body {
     font: 75% "Lucida Grande",verdana,arial,helvetica,sans-serif; 
     background: ${layout_bg};
--- a/static/scripts/trackster.js	Thu Jul 21 14:22:23 2011 -0400
+++ b/static/scripts/trackster.js	Tue Jul 26 13:18:22 2011 -0400
@@ -807,6 +807,9 @@
         }
         view.redraw();
     },
+    /**
+     * Add a track to the view.
+     */
     add_track: function(track) {
         track.view = this;
         track.track_id = this.track_id_counter;
@@ -822,6 +825,9 @@
         label_track.view = this;
         this.label_tracks.push(label_track);
     },
+    /**
+     * Remove a track from the view.
+     */
     remove_track: function(track) {
         this.has_changes = true;
         delete this.tracks[this.tracks.indexOf(track)];
@@ -1588,23 +1594,24 @@
 /**
  * Tiles drawn by tracks.
  */
-var Tile = function(index, resolution, canvas) {
+var Tile = function(index, resolution, canvas, data) {
     this.index = index;
     this.low = index * DENSITY * resolution;
     this.high = (index + 1) * DENSITY * resolution;
     this.resolution = resolution;
     // Wrap element in div for background.
     this.canvas = $("<div class='track-tile'/>").append(canvas);
+    this.data = data;
     this.stale = false;
 };
-var SummaryTreeTile = function(index, resolution, canvas, max_val) {
-    Tile.call(this, index, resolution, canvas);
+var SummaryTreeTile = function(index, resolution, canvas, data, max_val) {
+    Tile.call(this, index, resolution, canvas, data);
     this.max_val = max_val;
 };
-var FeatureTrackTile = function(index, resolution, canvas, message) {
-    Tile.call(this, index, resolution, canvas);
+var FeatureTrackTile = function(index, resolution, canvas, data, message) {
+    Tile.call(this, index, resolution, canvas, data);
     this.message = message;
 };
@@ -2096,13 +2103,17 @@
                         filters[f].update_ui_elt();
                     }
-                    // Determine if filters are available; this is based on the example feature.
-                    var filters_available = false;
-                    if (track.example_feature) {
-                        for (var f = 0; f < filters.length; f++) {
-                            if (filters[f].applies_to(track.example_feature)) {
-                                filters_available = true;
-                                break;
+                    // Determine if filters are available; this is based on the tiles' data.
+                    var filters_available = false,
+                        example_feature;
+                    for (var i = 0; i < drawn_tiles.length; i++) {
+                        if (drawn_tiles[i].data.length) {
+                            example_feature = drawn_tiles[i].data[0];
+                            for (var f = 0; f < filters.length; f++) {
+                                if (filters[f].applies_to(example_feature)) {
+                                    filters_available = true;
+                                    break;
+                                }
                             }
                         }
                     }
@@ -2385,7 +2396,7 @@
                 var c_start = Math.round(c * w_scale);
                 ctx.fillText(seq[c], c_start + track.left_offset, 10);
             }
-            return new Tile(tile_index, resolution, canvas);
+            return new Tile(tile_index, resolution, canvas, seq);
         }
         this.content_div.css("height", "0px");
     }
@@ -2523,7 +2534,7 @@
         var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, this.mode);
         painter.draw(ctx, width, height);
-        return new Tile(tile_index, resolution, canvas);
+        return new Tile(tile_index, resolution, canvas, result.data);
     } 
 });
@@ -2737,7 +2748,7 @@
             // TODO: this shouldn't be done at the tile level
             this.container_div.find(".yaxislabel").remove();
             var max_label = $("<div />").addClass('yaxislabel');
-            max_label.text( result.max );
+            max_label.text(result.max);
             max_label.css({ position: "absolute", top: "24px", left: "10px", color: this.prefs.label_color });
             max_label.prependTo(this.container_div);
             // Create canvas
@@ -2760,7 +2771,7 @@
             // Deal with left_offset by translating
             ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
             painter.draw(ctx, width, required_height);
-            return new SummaryTreeTile(tile_index, resolution, canvas, result.max);
+            return new SummaryTreeTile(tile_index, resolution, canvas, result.data, result.max);
         }
// Start dealing with row-by-row tracks
@@ -2811,16 +2822,12 @@
         this.container_div.find(".yaxislabel").remove();
if (result.data) {
-            // Set example feature. This is needed so that track can update its UI based on feature attributes.
-            // TODO: use tile data rather than example feature?
-            this.example_feature = (result.data.length ? result.data[0] : undefined);
-
             // Draw features.
             ctx.translate(left_offset, 0);
             painter.draw(ctx, width, required_height, slots);
         }
-        return new FeatureTrackTile(tile_index, resolution, canvas, result.message);        
+        return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message);        
     }
 });
--- a/templates/base_panels.mako	Thu Jul 21 14:22:23 2011 -0400
+++ b/templates/base_panels.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -19,6 +19,13 @@
 <%def name="stylesheets()">
     ${h.css('base','panel_layout','jquery.rating')}
     <style type="text/css">
+    body, html {
+        overflow: hidden;
+        margin: 0;
+        padding: 0;
+        width: 100%;
+        height: 100%;
+    }
     #center {
         %if not self.has_left_panel:
             left: 0;
--- a/templates/tool_form.mako	Thu Jul 21 14:22:23 2011 -0400
+++ b/templates/tool_form.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -2,7 +2,12 @@
 <%namespace file="/base_panels.mako" import="overlay" /><%def name="stylesheets()">
-    ${h.css( "autocomplete_tagging", "panel_layout", "base", "library" )}
+    ${h.css( "autocomplete_tagging", "base", "panel_layout", "library" )}
+    <style type="text/css">
+        html, body {
+            background-color: #fff;
+        }
+    </style></%def><%def name="javascripts()">
--- a/templates/tracks/browser.mako	Thu Jul 21 14:22:23 2011 -0400
+++ b/templates/tracks/browser.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -273,7 +273,7 @@
                         }
// Add track.
-                        tracks.push( {
+                        tracks.push({
                             "track_type": track.get_type(),
                             "name": track.name,
                             "hda_ldda": track.hda_ldda,
--- a/templates/visualization/display.mako	Thu Jul 21 14:22:23 2011 -0400
+++ b/templates/visualization/display.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -122,6 +122,11 @@
             // Keyboard navigation. Scroll ~7% of height when scrolling up/down.
             //
             $(document).keydown(function(e) {
+                // Do not navigate if arrow keys used in input element.
+                if ($(e.srcElement).is(':input')) {
+                    return;
+                }
+                
                 // Key codes: left == 37, up == 38, right == 39, down == 40
                 switch(e.which) {
                     case 37:
--- a/templates/webapps/community/repository/manage_repository.mako	Thu Jul 21 14:22:23 2011 -0400
+++ b/templates/webapps/community/repository/manage_repository.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -120,7 +120,7 @@
                 <div style="clear: both"></div></div><div class="form-row">
-                <label>Version:</label>
+                <label>Revision:</label>
                 %if can_view_change_log:
                     <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a>
                 %else:
@@ -151,34 +151,6 @@
         </form></div></div>
-<p/>
-<div class="toolForm">
-    <div class="toolFormTitle">Manage categories</div>
-    <div class="toolFormBody">
-        <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
-            <div class="form-row">
-                <label>Categories</label>
-                <select name="category_id" multiple>
-                    %for category in categories:
-                        %if category.id in selected_categories:
-                            <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option>
-                        %else:
-                            <option value="${trans.security.encode_id( category.id )}">${category.name}</option>
-                        %endif
-                    %endfor
-                </select>
-                <div class="toolParamHelp" style="clear: both;">
-                    Multi-select list - hold the appropriate key while clicking to select multiple categories.
-                </div>
-                <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <input type="submit" name="manage_categories_button" value="Save"/>
-            </div>
-        </form>
-    </div>
-</div>
-<p/>
 %if can_set_metadata:
     <p/><div class="toolForm">
@@ -204,7 +176,16 @@
                             </tr>
                             %for tool_dict in tool_dicts:
                                 <tr>
-                                    <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td>
+                                    <td>
+                                        <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ]}-popup">
+                                            <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">
+                                                ${tool_dict[ 'name' ]}
+                                            </a>
+                                        </div>
+                                        <div popupmenu="tool-${tool_dict[ 'id' ]}-popup">
+                                            <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a>
+                                        </div>
+                                    </td><td>${tool_dict[ 'description' ]}</td><td>${tool_dict[ 'version' ]}</td><td>
@@ -274,6 +255,33 @@
         </div></div>
 %endif
+<p/>
+<div class="toolForm">
+    <div class="toolFormTitle">Manage categories</div>
+    <div class="toolFormBody">
+        <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
+            <div class="form-row">
+                <label>Categories</label>
+                <select name="category_id" multiple>
+                    %for category in categories:
+                        %if category.id in selected_categories:
+                            <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option>
+                        %else:
+                            <option value="${trans.security.encode_id( category.id )}">${category.name}</option>
+                        %endif
+                    %endfor
+                </select>
+                <div class="toolParamHelp" style="clear: both;">
+                    Multi-select list - hold the appropriate key while clicking to select multiple categories.
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="manage_categories_button" value="Save"/>
+            </div>
+        </form>
+    </div>
+</div>
 %if trans.app.config.smtp_server:
     <p/><div class="toolForm">
@@ -330,8 +338,8 @@
         </form></div></div>
-<p/>
 %if repository.ratings:
+    <p/><div class="toolForm"><div class="toolFormTitle">Rating</div><div class="toolFormBody">
--- a/templates/webapps/community/repository/view_repository.mako	Thu Jul 21 14:22:23 2011 -0400
+++ b/templates/webapps/community/repository/view_repository.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -118,7 +118,7 @@
             </div>
         %endif
         <div class="form-row">
-            <label>Version:</label>
+            <label>Revision:</label>
             %if can_view_change_log:
                 <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a>
             %else:
@@ -145,20 +145,6 @@
         %endif
     </div></div>
-%if repository.categories:
-    <p/>
-    <div class="toolForm">
-        <div class="toolFormTitle">Categories</div>
-        <div class="toolFormBody">
-            %for rca in repository.categories:
-                <div class="form-row">
-                    ${rca.category.name}
-                </div>
-            %endfor
-            <div style="clear: both"></div>
-        </div>
-    </div>
-%endif
 %if metadata:
     <p/><div class="toolForm">
@@ -183,9 +169,18 @@
                         </tr>
                         %for tool_dict in tool_dicts:
                             <tr>
-                                <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td>
+                                <td>
+                                    <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${repository.id}-popup">
+                                        <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">
+                                            ${tool_dict[ 'name' ]}
+                                        </a>
+                                    </div>
+                                    <div popupmenu="tool-${repository.id}-popup">
+                                        <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a>
+                                    </div>
+                                </td><td>${tool_dict[ 'description' ]}</td>
-                                <td>version: ${tool_dict[ 'version' ]}</td>
+                                <td>${tool_dict[ 'version' ]}</td><td><%
                                         if 'requirements' in tool_dict:
@@ -242,6 +237,20 @@
         </div></div>
 %endif
+%if repository.categories:
+    <p/>
+    <div class="toolForm">
+        <div class="toolFormTitle">Categories</div>
+        <div class="toolFormBody">
+            %for rca in repository.categories:
+                <div class="form-row">
+                    ${rca.category.name}
+                </div>
+            %endfor
+            <div style="clear: both"></div>
+        </div>
+    </div>
+%endif
 %if trans.user and trans.app.config.smtp_server:
     <p/><div class="toolForm">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/webapps/community/repository/view_tool_metadata.mako	Tue Jul 26 13:18:22 2011 -0400
@@ -0,0 +1,202 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/webapps/community/common/common.mako" import="*" />
+<%namespace file="/webapps/community/repository/common.mako" import="*" />
+
+<%
+    from galaxy.web.framework.helpers import time_ago
+    from urllib import quote_plus
+    is_admin = trans.user_is_admin()
+    is_new = repository.is_new
+    can_push = trans.app.security_agent.can_push( trans.user, repository )
+    can_upload = can_push
+    can_browse_contents = not is_new
+    can_rate = repository.user != trans.user
+    can_manage = is_admin or repository.user == trans.user
+    can_view_change_log = not is_new
+    if can_push:
+        browse_label = 'Browse or delete repository files'
+    else:
+        browse_label = 'Browse repository files'
+%>
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/community/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+<br/><br/>
+<ul class="manage-table-actions">
+    %if is_new:
+        <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+    %else:
+        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+        <div popupmenu="repository-${repository.id}-popup">
+            %if can_manage:
+                <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a>
+            %else:
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a>
+            %endif
+            %if can_upload:
+                <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+            %endif
+            %if can_view_change_log:
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+            %endif
+            %if can_browse_contents:
+                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+            %endif
+            <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a>
+        </div>
+    %endif
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">${repository.name}</div>
+    <div class="toolFormBody">
+        <div class="form-row">
+            <label>Clone this repository:</label>
+            ${render_clone_str( repository )}
+        </div>
+    </div>
+</div>
+%if metadata:
+## "{"tools": 
+## [{"description": "data on any column using simple expressions", 
+##   "id": "Filter1", 
+##   "name": "Filter", 
+##   "requirements": [], 
+##   "tests": [{
+##               "inputs": [["input", "1.bed", {"children": [], "value": "1.bed"}], ["cond", "c1=='chr22'", {"children": [], "value": "c1=='chr22'"}]], "name": "Test-1", 
+##               "outputs": [["out_file1", "filter1_test1.bed", {"compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], 
+##               "required_files": [["1.bed", {"children": [], "value": "1.bed"}]]}, {"inputs": [["input", "7.bed", {"children": [], "value": "7.bed"}], ["cond", "c1=='chr1' and c3-c2>=2000 and c6=='+'", {"children": [], "value": "c1=='chr1' and c3-c2>=2000 and c6=='+'"}]], "name": "Test-2", "outputs": [["out_file1", "filter1_test2.bed", {"compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], "required_files": [["7.bed", {"children": [], "value": "7.bed"}]]}], "tool_config": "database/community_files/000/repo_1/filtering.xml", "version": "1.0.1", "version_string_cmd": null}], "workflows": [{"a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Workflow constructed from history 'Unnamed history'", "steps": {"0": {"annotation": "", "id": 0, "input_connections": {}, "inputs": [{"description": "", "name": "Input Dataset"}], "name": "Input dataset", "outputs": [], "position": {"left": 10, "top": 10}, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "user_outputs": []}, "1": {"annotation": "", "id": 1, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "name": "Filter", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 230, "top": 10}, "post_job_actions": {}, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c1=='chr1'\\\"\", \"chromInfo\": \"\\\"/Users/gvk/workspaces_2008/central_051111/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", "tool_version": null, "type": "tool", "user_outputs": []}, "2": {"annotation": "", "id": 2, "input_connections": {"input1": {"id": 0, "output_name": "output"}, "input2": {"id": 1, "output_name": "out_file1"}}, "inputs": [], "name": "Subtract Whole Dataset", "outputs": [{"name": "output", "type": "input"}], "position": {"left": 450, "top": 10}, "post_job_actions": {}, "tool_errors": null, "tool_id": "subtract_query1", "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"end_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"None\\\"}\", \"begin_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"None\\\"}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/Users/gvk/workspaces_2008/central_051111/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": null, "type": "tool", "user_outputs": []}}}]}"
+    <p/>
+    <div class="toolForm">
+        <div class="toolFormTitle">${metadata[ 'name' ]} tool metadata</div>
+        <div class="toolFormBody">
+            <div class="form-row">
+                <label>Name:</label>
+                <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ] )}">${metadata[ 'name' ]}</a>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Description:</label>
+                ${metadata[ 'description' ]}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Id:</label>
+                ${metadata[ 'id' ]}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Version:</label>
+                ${metadata[ 'version' ]}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Version command string:</label>
+                ${metadata[ 'version_string_cmd' ]}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Command:</label>
+                ${tool.command}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Interpreter:</label>
+                ${tool.interpreter}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Is multi-byte:</label>
+                ${tool.is_multi_byte}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Forces a history refresh:</label>
+                ${tool.force_history_refresh}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Parallelism:</label>
+                ${tool.parallelism}
+                <div style="clear: both"></div>
+            </div>
+            <%
+                if 'requirements' in metadata:
+                    requirements = metadata[ 'requirements' ]
+                else:
+                    requirements = None
+            %>
+            %if requirements:
+                <%
+                    requirements_str = ''
+                    for requirement_dict in metadata[ 'requirements' ]:
+                        requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] )
+                    requirements_str = requirements_str.rstrip( ', ' )
+                %>
+                <div class="form-row">
+                    <label>Requirements:</label>
+                    ${requirements_str}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            <%
+                if 'tests' in metadata:
+                    tests = metadata[ 'tests' ]
+                else:
+                    tests = None
+            %>
+            %if tests:
+                <div class="form-row">
+                    <label>Functional tests:</label></td>
+                    <table class="grid">
+                        <tr>
+                            <td><b>name</b></td>
+                            <td><b>inputs</b></td>
+                            <td><b>outputs</b></td>
+                            <td><b>required files</b></td>
+                        </tr>
+                        %for test_dict in tests:
+                            <%
+                                inputs = test_dict[ 'inputs' ]
+                                outputs = test_dict[ 'outputs' ]
+                                required_files = test_dict[ 'required_files' ]
+                            %>
+                            <tr>
+                                <td>${test_dict[ 'name' ]}</td>
+                                <td>
+                                    %for input in inputs:
+                                        <b>${input[0]}:</b> ${input[1]}<br/>
+                                    %endfor
+                                </td>
+                                <td>
+                                    %for output in outputs:
+                                        <b>${output[0]}:</b> ${output[1]}<br/>
+                                    %endfor
+                                </td>
+                                <td>
+                                    %for required_file in required_files:
+                                        ${required_file[0]}<br/>
+                                    %endfor
+                                </td>
+                            </tr>
+                        %endfor
+                    </table>
+                </div>
+            %endif
+        </div>
+    </div>
+%endif
--- a/tool_conf.xml.main	Thu Jul 21 14:22:23 2011 -0400
+++ b/tool_conf.xml.main	Tue Jul 26 13:18:22 2011 -0400
@@ -51,7 +51,7 @@
     <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" />
-    <tool file="maf/maf_to_interval.xml" /> 
+    <tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="fastq/fastq_to_fasta.xml" />
@@ -78,13 +78,13 @@
         <tool file="filters/gff/extract_GFF_Features.xml" /><tool file="filters/gff/gff_filter_by_attribute.xml" /><tool file="filters/gff/gff_filter_by_feature_count.xml" />
-		<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
+        <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /></section><section name="Join, Subtract and Group" id="group"><tool file="filters/joiner.xml" /><tool file="filters/compare.xml"/><tool file="new_operations/subtract_query.xml"/>
-    <tool file="stats/grouping.xml" />   
+    <tool file="stats/grouping.xml" /><tool file="new_operations/column_join.xml"/></section><section name="Extract Features" id="features">
@@ -112,7 +112,7 @@
     <tool file="extract/phastOdds/phastOdds_tool.xml" /></section><section name="Operate on Genomic Intervals" id="bxops">
-    <tool file="new_operations/intersect.xml" />  
+    <tool file="new_operations/intersect.xml" /><tool file="new_operations/subtract.xml" /><tool file="new_operations/merge.xml" /><tool file="new_operations/concat.xml" />
@@ -127,7 +127,7 @@
   </section><section name="Statistics" id="stats"><tool file="stats/gsummary.xml" />
-    <tool file="filters/uniq.xml" /> 
+    <tool file="filters/uniq.xml" /><tool file="stats/cor.xml" /><tool file="stats/generate_matrix_for_pca_lda.xml" /><tool file="stats/lda_analy.xml" />
@@ -223,13 +223,13 @@
     <tool file="emboss_5/emboss_chips.xml" /><tool file="emboss_5/emboss_cirdna.xml" /><tool file="emboss_5/emboss_codcmp.xml" />
-    <tool file="emboss_5/emboss_coderet.xml" /> 
+    <tool file="emboss_5/emboss_coderet.xml" /><tool file="emboss_5/emboss_compseq.xml" />
-    <tool file="emboss_5/emboss_cpgplot.xml" /> 
+    <tool file="emboss_5/emboss_cpgplot.xml" /><tool file="emboss_5/emboss_cpgreport.xml" /><tool file="emboss_5/emboss_cusp.xml" /><tool file="emboss_5/emboss_cutseq.xml" />
-    <tool file="emboss_5/emboss_dan.xml" /> 
+    <tool file="emboss_5/emboss_dan.xml" /><tool file="emboss_5/emboss_degapseq.xml" /><tool file="emboss_5/emboss_descseq.xml" /><tool file="emboss_5/emboss_diffseq.xml" />
@@ -245,7 +245,7 @@
     <tool file="emboss_5/emboss_etandem.xml" /><tool file="emboss_5/emboss_extractfeat.xml" /><tool file="emboss_5/emboss_extractseq.xml" />
-    <tool file="emboss_5/emboss_freak.xml" /> 
+    <tool file="emboss_5/emboss_freak.xml" /><tool file="emboss_5/emboss_fuzznuc.xml" /><tool file="emboss_5/emboss_fuzzpro.xml" /><tool file="emboss_5/emboss_fuzztran.xml" />
@@ -266,7 +266,7 @@
     <tool file="emboss_5/emboss_merger.xml" /><tool file="emboss_5/emboss_msbar.xml" /><tool file="emboss_5/emboss_needle.xml" />
-    <tool file="emboss_5/emboss_newcpgreport.xml" /> 
+    <tool file="emboss_5/emboss_newcpgreport.xml" /><tool file="emboss_5/emboss_newcpgseek.xml" /><tool file="emboss_5/emboss_newseq.xml" /><tool file="emboss_5/emboss_noreturn.xml" />
@@ -294,7 +294,7 @@
     <tool file="emboss_5/emboss_revseq.xml" /><tool file="emboss_5/emboss_seqmatchall.xml" /><tool file="emboss_5/emboss_seqret.xml" />
-    <tool file="emboss_5/emboss_showfeat.xml" /> 
+    <tool file="emboss_5/emboss_showfeat.xml" /><tool file="emboss_5/emboss_shuffleseq.xml" /><tool file="emboss_5/emboss_sigcleave.xml" /><tool file="emboss_5/emboss_sirna.xml" />
@@ -316,7 +316,7 @@
     <tool file="emboss_5/emboss_water.xml" /><tool file="emboss_5/emboss_wobble.xml" /><tool file="emboss_5/emboss_wordcount.xml" />
-    <tool file="emboss_5/emboss_wordmatch.xml" /> 
+    <tool file="emboss_5/emboss_wordmatch.xml" /></section><label text="NGS Toolbox Beta" id="ngs" /><section name="NGS: QC and manipulation" id="cshl_library_information">
--- a/tool_conf.xml.sample	Thu Jul 21 14:22:23 2011 -0400
+++ b/tool_conf.xml.sample	Tue Jul 26 13:18:22 2011 -0400
@@ -144,14 +144,14 @@
     <tool file="regVariation/t_test_two_samples.xml" /><tool file="regVariation/compute_q_values.xml" /><label text="GFF" id="gff" />
-		<tool file="stats/count_gff_features.xml" />
+      <tool file="stats/count_gff_features.xml" /></section><!--
   Keep this section commented until all of the tools have functional tests
   <section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_IvC_all.xml" /><tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
-    <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /> 
+    <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /><tool file="discreteWavelet/execute_dwt_var_perClass.xml" /></section>
  -->
@@ -184,8 +184,8 @@
     <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /><tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
     <tool file="regVariation/draw_stacked_barplots.xml" />
-    <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />    
-    <tool file="regVariation/microsatellite_birthdeath.xml" />        
+    <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
+    <tool file="regVariation/microsatellite_birthdeath.xml" /></section><section name="Multiple regression" id="multReg"><tool file="regVariation/linear_regression.xml" />
@@ -241,7 +241,7 @@
   </section><section name="NGS: QC and manipulation" id="NGS_QC"><label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
-    <tool file="rgenetics/rgFastQC.xml" />         
+    <tool file="rgenetics/rgFastQC.xml" /><label text="Illumina fastq" id="illumina" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" />
@@ -280,21 +280,21 @@
     <tool file="fastx_toolkit/fastx_collapser.xml" /><tool file="fastx_toolkit/fastx_renamer.xml" /><tool file="fastx_toolkit/fastx_reverse_complement.xml" />
-     <tool file="fastx_toolkit/fastx_trimmer.xml" />  
+     <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><section name="NGS: Picard (beta)" id="picard_beta"><label text="QC/Metrics for sam/bam" id="qcsambam"/><tool file="picard/picard_BamIndexStats.xml" />
-    <tool file="picard/rgPicardASMetrics.xml" />    
-    <tool file="picard/rgPicardGCBiasMetrics.xml" />     
-    <tool file="picard/rgPicardLibComplexity.xml" />     
+    <tool file="picard/rgPicardASMetrics.xml" />
+    <tool file="picard/rgPicardGCBiasMetrics.xml" />
+    <tool file="picard/rgPicardLibComplexity.xml" /><tool file="picard/rgPicardInsertSize.xml" /><tool file="picard/rgPicardHsMetrics.xml" /><label text="bam/sam Cleaning" id="picard-clean" /><tool file="picard/picard_AddOrReplaceReadGroups.xml" /><tool file="picard/picard_ReorderSam.xml" /><tool file="picard/picard_ReplaceSamHeader.xml" />
-    <tool file="picard/rgPicardFixMate.xml" />          
+    <tool file="picard/rgPicardFixMate.xml" /><tool file="picard/rgPicardMarkDups.xml" /></section><!--
--- a/tool_list.py	Thu Jul 21 14:22:23 2011 -0400
+++ b/tool_list.py	Tue Jul 26 13:18:22 2011 -0400
@@ -4,19 +4,19 @@
 onoff = 1
 tool_list = []
 for line in open("tool_conf.xml.sample", "r"):
-   if line.find("<!--") != -1: 
+   if line.find("<!--") != -1:
       onoff = 0
-   if line.find("file") != -1 and onoff==1: 
-      strs = line.split('\"') 
+   if line.find("file") != -1 and onoff==1:
+      strs = line.split('\"')
       tool_list.append(strs[1])
-   if line.find("<section") != -1 and onoff==1: 
+   if line.find("<section") != -1 and onoff==1:
       keys = line.strip().split('\"')
       n = 0
       strtmp = "section::"
-      while n < len(keys) : 
-         if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1]  
-         if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-" 
-	 n = n + 1
+      while n < len(keys) :
+         if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1]
+         if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-"
+         n = n + 1
       tool_list.append(strtmp.replace(' ', '_'))
    if line.find("-->") != -1:
       onoff =1
@@ -26,42 +26,42 @@
 id = []
 desc = []
 tool_infos = []
-for tool in tool_list : 
-   if tool.find("section")!=-1 : 
+for tool in tool_list :
+   if tool.find("section")!=-1 :
       tool_info = dict()
       tool_info["id"] = tool
       tool_infos.append(tool_info)
-   if os.path.exists("tools/"+tool) : 
-      for line in open("tools/"+tool) : 
-	  if line.find("<tool ") != -1 and line.find("id") != -1 : 
-	     keys = line.strip().split('"')
-	     n = 0
-	     tool_info = dict()
-	     tool_info["desc"] = ''
-	     while n < len(keys) : 
-	        if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_') 
-	        if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1] 
-	        if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1] 
-		n = n + 1
-	     tool_infos.append(tool_info)
-	     break
+   if os.path.exists("tools/"+tool) :
+      for line in open("tools/"+tool) :
+         if line.find("<tool ") != -1 and line.find("id") != -1 :
+            keys = line.strip().split('"')
+            n = 0
+            tool_info = dict()
+            tool_info["desc"] = ''
+            while n < len(keys) :
+               if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_')
+               if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1]
+               if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1]
+               n = n + 1
+            tool_infos.append(tool_info)
+            break
flag=0
-if len(sys.argv) == 1 : 
-   for tool_info in tool_infos: 
-      if tool_info["id"].find("section") != -1 : 
+if len(sys.argv) == 1 :
+   for tool_info in tool_infos:
+      if tool_info["id"].find("section") != -1 :
          print "==========================================================================================================================================="
          print "%-45s\t%-40s\t%s" % ("id", "name", tool_info["id"])
          print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -"
       else :
          print "%-45s\t%-40s" % (tool_info["id"], tool_info["name"])
-else: 
-   for tool_info in tool_infos: 
+else:
+   for tool_info in tool_infos:
       if tool_info["id"].find("section") != -1 :
          flag=0
       elif flag==1:
          print " functional.test_toolbox:TestForTool_%s" % tool_info["id"],
-      if tool_info["id"].replace('section::', '')==sys.argv[1]:  
+      if tool_info["id"].replace('section::', '')==sys.argv[1]:
          flag=1
#for key in tool_infos.keys():
http://bitbucket.org/galaxy/galaxy-central/changeset/e055ca3efb5c/
changeset:   e055ca3efb5c
user:        dannon
date:        2011-07-26 19:56:16
summary:     merge
affected #:  13 files (41.1 KB)
--- a/lib/galaxy/jobs/__init__.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/lib/galaxy/jobs/__init__.py	Tue Jul 26 13:56:16 2011 -0400
@@ -646,9 +646,14 @@
                              tool=self.tool, stdout=stdout, stderr=stderr )
         job.command_line = self.command_line
+        bytes = 0
         # Once datasets are collected, set the total dataset size (includes extra files)
         for dataset_assoc in job.output_datasets + job.output_library_datasets:
             dataset_assoc.dataset.dataset.set_total_size()
+            bytes += dataset_assoc.dataset.dataset.get_total_size()
+
+        if job.user:
+            job.user.total_disk_usage += bytes
# fix permissions
         for path in [ dp.real_path for dp in self.get_output_fnames() ]:
--- a/lib/galaxy/model/__init__.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/lib/galaxy/model/__init__.py	Tue Jul 26 13:56:16 2011 -0400
@@ -70,6 +70,27 @@
                 if role not in roles:
                     roles.append( role )
         return roles
+    def get_disk_usage( self, nice_size=False ):
+        rval = 0
+        if self.disk_usage is not None:
+            rval = self.disk_usage
+        if nice_size:
+            rval = galaxy.datatypes.data.nice_size( rval )
+        return rval
+    def set_disk_usage( self, bytes ):
+        self.disk_usage = bytes
+    total_disk_usage = property( get_disk_usage, set_disk_usage )
+    def calculate_disk_usage( self ):
+        dataset_ids = []
+        total = 0
+        # this can be a huge number and can run out of memory, so we avoid the mappers
+        db_session = object_session( self )
+        for history in db_session.query( History ).enable_eagerloads( False ).filter_by( user_id=self.id ).yield_per( 1000 ):
+            for hda in db_session.query( HistoryDatasetAssociation ).enable_eagerloads( False ).filter_by( history_id=history.id, purged=False ).yield_per( 1000 ):
+                if not hda.dataset.id in dataset_ids and not hda.dataset.purged and not hda.dataset.library_associations:
+                    dataset_ids.append( hda.dataset.id )
+                    total += hda.dataset.get_total_size()
+        return total
class Job( object ):
     """
@@ -349,7 +370,7 @@
             self.galaxy_sessions.append( GalaxySessionToHistoryAssociation( galaxy_session, self ) )
         else:
             self.galaxy_sessions.append( association )
-    def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid = True ):
+    def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid=True, quota=True ):
         if isinstance( dataset, Dataset ):
             dataset = HistoryDatasetAssociation(dataset=dataset)
             object_session( self ).add( dataset )
@@ -367,6 +388,8 @@
         else:
             if set_hid:
                 dataset.hid = self._next_hid()
+        if quota and self.user:
+            self.user.total_disk_usage += dataset.quota_amount( self.user )
         dataset.history = self
         if genome_build not in [None, '?']:
             self.genome_build = genome_build
@@ -378,6 +401,9 @@
             name = self.name
         if not target_user:
             target_user = self.user
+        quota = True
+        if target_user == self.user:
+            quota = False
         new_history = History( name=name, user=target_user )
         db_session = object_session( self )
         db_session.add( new_history )
@@ -393,8 +419,8 @@
             hdas = self.active_datasets
         for hda in hdas:
             # Copy HDA.
-            new_hda = hda.copy( copy_children=True, target_history=new_history )
-            new_history.add_dataset( new_hda, set_hid = False )
+            new_hda = hda.copy( copy_children=True )
+            new_history.add_dataset( new_hda, set_hid = False, quota=quota )
             db_session.add( new_hda )
             db_session.flush()            
             # Copy annotation.
@@ -741,6 +767,10 @@
     def set_size( self ):
         """Returns the size of the data on disk"""
         return self.dataset.set_size()
+    def get_total_size( self ):
+        return self.dataset.get_total_size()
+    def set_total_size( self ):
+        return self.dataset.set_total_size()
     def has_data( self ):
         """Detects whether there is any data"""
         return self.dataset.has_data()
@@ -922,7 +952,7 @@
         self.history = history
         self.copied_from_history_dataset_association = copied_from_history_dataset_association
         self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association
-    def copy( self, copy_children = False, parent_id = None, target_history = None ):
+    def copy( self, copy_children = False, parent_id = None ):
         hda = HistoryDatasetAssociation( hid=self.hid, 
                                          name=self.name, 
                                          info=self.info, 
@@ -934,8 +964,7 @@
                                          visible=self.visible, 
                                          deleted=self.deleted, 
                                          parent_id=parent_id, 
-                                         copied_from_history_dataset_association=self,
-                                         history = target_history )
+                                         copied_from_history_dataset_association=self )
         object_session( self ).add( hda )
         object_session( self ).flush()
         hda.set_size()
@@ -1017,6 +1046,26 @@
         return hda_name
     def get_access_roles( self, trans ):
         return self.dataset.get_access_roles( trans )
+    def quota_amount( self, user ):
+        """
+        If the user has multiple instances of this dataset, it will not affect their disk usage statistic.
+        """
+        rval = 0
+        # Anon users are handled just by their single history size.
+        if not user:
+            return rval
+        # Gets an HDA and its children's disk usage, if the user does not already have an association of the same dataset
+        if not self.dataset.library_associations and not self.purged and not self.dataset.purged:
+            for hda in self.dataset.history_associations:
+                if hda.id == self.id:
+                    continue
+                if not hda.purged and hda.history and hda.history.user and hda.history.user == user:
+                    break
+            else:
+                rval += self.get_total_size()
+        for child in self.children:
+            rval += child.get_disk_usage( user )
+        return rval
class HistoryDatasetAssociationDisplayAtAuthorization( object ):
     def __init__( self, hda=None, user=None, site=None ):
@@ -1467,6 +1516,13 @@
             self.histories.append( GalaxySessionToHistoryAssociation( self, history ) )
         else:
             self.histories.append( association )
+    def get_disk_usage( self ):
+        if self.disk_usage is None:
+            return 0
+        return self.disk_usage
+    def set_disk_usage( self, bytes ):
+        self.disk_usage = bytes
+    total_disk_usage = property( get_disk_usage, set_disk_usage )
class GalaxySessionToHistoryAssociation( object ):
     def __init__( self, galaxy_session, history ):
--- a/lib/galaxy/web/controllers/dataset.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/lib/galaxy/web/controllers/dataset.py	Tue Jul 26 13:56:16 2011 -0400
@@ -9,6 +9,7 @@
 from galaxy.util import inflector
 from galaxy.model.item_attrs import *
 from galaxy.model import LibraryDatasetDatasetAssociation, HistoryDatasetAssociation
+from galaxy.web.framework.helpers import to_unicode
import pkg_resources; 
 pkg_resources.require( "Paste" )
@@ -383,6 +384,188 @@
             return trans.stream_template_mako( "/dataset/large_file.mako",
                                             truncated_data = open( data.file_name ).read(max_peek_size),
                                             data = data )
+
+    @web.expose
+    def edit(self, trans, dataset_id=None, filename=None, hid=None, **kwd):
+        """Allows user to modify parameters of an HDA."""
+        message = None
+        status = 'done'
+        refresh_frames = []
+        error = False
+        def __ok_to_edit_metadata( dataset_id ):
+            #prevent modifying metadata when dataset is queued or running as input/output
+            #This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now
+            for job_to_dataset_association in trans.sa_session.query( self.app.model.JobToInputDatasetAssociation ) \
+                                                              .filter_by( dataset_id=dataset_id ) \
+                                                              .all() \
+                                            + trans.sa_session.query( self.app.model.JobToOutputDatasetAssociation ) \
+                                                              .filter_by( dataset_id=dataset_id ) \
+                                                              .all():
+                if job_to_dataset_association.job.state not in [ job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED ]:
+                    return False
+            return True
+        if hid is not None:
+            history = trans.get_history()
+            # TODO: hid handling
+            data = history.datasets[ int( hid ) - 1 ]
+            id = None
+        elif dataset_id is not None: 
+            id = trans.app.security.decode_id( dataset_id )
+            data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
+        else:
+            trans.log_event( "dataset_id and hid are both None, cannot load a dataset to edit" )
+            return trans.show_error_message( "You must provide a history dataset id to edit" )
+        if data is None:
+            trans.log_event( "Problem retrieving dataset (encoded: %s, decoded: %s) with history id %s." % ( str( dataset_id ), str( id ), str( hid ) ) )
+            return trans.show_error_message( "History dataset id is invalid" )
+        if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:
+            trans.log_event( "User attempted to edit an HDA they do not own (encoded: %s, decoded: %s)" % ( dataset_id, id ) )
+            # Do not reveal the dataset's existence
+            return trans.show_error_message( "History dataset id is invalid" )
+        current_user_roles = trans.get_current_user_roles()
+        if data.history.user and not data.dataset.has_manage_permissions_roles( trans ):
+            # Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
+            # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
+            # permission.  In this case, we'll reset this permission to the hda user's private role.
+            manage_permissions_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action )
+            permissions = { manage_permissions_action : [ trans.app.security_agent.get_private_user_role( data.history.user ) ] }
+            trans.app.security_agent.set_dataset_permission( data.dataset, permissions )        
+        if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
+            if data.state == trans.model.Dataset.states.UPLOAD:
+                return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." )
+            params = util.Params( kwd, sanitize=False )
+            if params.change:
+                # The user clicked the Save button on the 'Change data type' form
+                if data.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
+                    #prevent modifying datatype when dataset is queued or running as input/output
+                    if not __ok_to_edit_metadata( data.id ):
+                        message = "This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them."
+                        error = True
+                    else:
+                        trans.app.datatypes_registry.change_datatype( data, params.datatype, set_meta = not trans.app.config.set_metadata_externally )
+                        trans.sa_session.flush()
+                        if trans.app.config.set_metadata_externally:
+                            trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data }, overwrite = False ) #overwrite is False as per existing behavior
+                        message = "Changed the type of dataset '%s' to %s" % ( to_unicode( data.name ), params.datatype )
+                        refresh_frames=['history']
+                else:
+                    message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype )
+                    error = True
+            elif params.save:
+                # The user clicked the Save button on the 'Edit Attributes' form
+                data.name  = params.name
+                data.info  = params.info
+                message = ''
+                if __ok_to_edit_metadata( data.id ):
+                    # The following for loop will save all metadata_spec items
+                    for name, spec in data.datatype.metadata_spec.items():
+                        if spec.get("readonly"):
+                            continue
+                        optional = params.get("is_"+name, None)
+                        other = params.get("or_"+name, None)
+                        if optional and optional == 'true':
+                            # optional element... == 'true' actually means it is NOT checked (and therefore omitted)
+                            setattr(data.metadata, name, None)
+                        else:
+                            if other:
+                                setattr( data.metadata, name, other )
+                            else:
+                                setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
+                    data.datatype.after_setting_metadata( data )
+                    # Sanitize annotation before adding it.
+                    if params.annotation:
+                        annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' )
+                        self.add_item_annotation( trans.sa_session, trans.get_user(), data, annotation )
+                    # If setting metadata previously failed and all required elements have now been set, clear the failed state.
+                    if data._state == trans.model.Dataset.states.FAILED_METADATA and not data.missing_meta():
+                        data._state = None
+                    trans.sa_session.flush()
+                    message = "Attributes updated%s" % message
+                    refresh_frames=['history']
+                else:
+                    trans.sa_session.flush()
+                    message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata."
+                    status = "warning"
+                    refresh_frames=['history']
+            elif params.detect:
+                # The user clicked the Auto-detect button on the 'Edit Attributes' form
+                #prevent modifying metadata when dataset is queued or running as input/output
+                if not __ok_to_edit_metadata( data.id ):
+                    message = "This dataset is currently being used as input or output.  You cannot change metadata until the jobs have completed or you have canceled them."
+                    error = True
+                else:
+                    for name, spec in data.metadata.spec.items():
+                        # We need to be careful about the attributes we are resetting
+                        if name not in [ 'name', 'info', 'dbkey', 'base_name' ]:
+                            if spec.get( 'default' ):
+                                setattr( data.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
+                    if trans.app.config.set_metadata_externally:
+                        message = 'Attributes have been queued to be updated'
+                        trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data } )
+                    else:
+                        message = 'Attributes updated'
+                        data.set_meta()
+                        data.datatype.after_setting_metadata( data )
+                    trans.sa_session.flush()
+                    refresh_frames=['history']
+            elif params.convert_data:
+                target_type = kwd.get("target_type", None)
+                if target_type:
+                    message = data.datatype.convert_dataset(trans, data, target_type)
+                    refresh_frames=['history']
+            elif params.update_roles_button:
+                if not trans.user:
+                    return trans.show_error_message( "You must be logged in if you want to change permissions." )
+                if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ):
+                    access_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action )
+                    manage_permissions_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action )
+                    # The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles.  We
+                    # need to ensure that they did not associate roles that would cause accessibility problems.
+                    permissions, in_roles, error, message = \
+                    trans.app.security_agent.derive_roles_from_access( trans, data.dataset.id, 'root', **kwd )
+                    if error:
+                        # Keep the original role associations for the DATASET_ACCESS permission on the dataset.
+                        permissions[ access_action ] = data.dataset.get_access_roles( trans )
+                        status = 'error'
+                    else:
+                        error = trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions )
+                        if error:
+                            message += error
+                            status = 'error'
+                        else:
+                            message = 'Your changes completed successfully.'
+                    trans.sa_session.refresh( data.dataset )
+                else:
+                    message = "You are not authorized to change this dataset's permissions"
+                    error = True
+            else:
+                if "dbkey" in data.datatype.metadata_spec and not data.metadata.dbkey:
+                    # Copy dbkey into metadata, for backwards compatability
+                    # This looks like it does nothing, but getting the dbkey
+                    # returns the metadata dbkey unless it is None, in which
+                    # case it resorts to the old dbkey.  Setting the dbkey
+                    # sets it properly in the metadata
+                    #### This is likely no longer required, since the dbkey exists entirely within metadata (the old_dbkey field is gone): REMOVE ME?
+                    data.metadata.dbkey = data.dbkey
+            # let's not overwrite the imported datatypes module with the variable datatypes?
+            # the built-in 'id' is overwritten in lots of places as well
+            ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
+            ldatatypes.sort()
+            all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' )
+            if error:
+                status = 'error'
+            return trans.fill_template( "/dataset/edit_attributes.mako",
+                                        data=data,
+                                        data_annotation=self.get_item_annotation_str( trans.sa_session, trans.user, data ),
+                                        datatypes=ldatatypes,
+                                        current_user_roles=current_user_roles,
+                                        all_roles=all_roles,
+                                        message=message,
+                                        status=status,
+                                        dataset_id=dataset_id,
+                                        refresh_frames=refresh_frames )
+        else:
+            return trans.show_error_message( "You do not have permission to edit this dataset's ( id: %s ) information." % str( dataset_id ) )
@web.expose
     @web.require_login( "see all available datasets" )
@@ -654,111 +837,190 @@
             return trans.fill_template_mako( "dataset/display_application/display.mako", msg = msg, display_app = display_app, display_link = display_link, refresh = refresh )
         return trans.show_error_message( 'You do not have permission to view this dataset at an external display application.' )
-    def _undelete( self, trans, id ):
+    def _delete( self, trans, dataset_id ):
+        message = None
+        status = 'done'
+        id = None
         try:
-            id = int( id )
-        except ValueError, e:
-            return False
-        history = trans.get_history()
-        data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
-        if data and data.undeletable:
+            id = trans.app.security.decode_id( dataset_id )
+            history = trans.get_history()
+            hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
+            assert hda, 'Invalid HDA: %s' % id
             # Walk up parent datasets to find the containing history
-            topmost_parent = data
+            topmost_parent = hda
+            while topmost_parent.parent:
+                topmost_parent = topmost_parent.parent
+            assert topmost_parent in trans.history.datasets, "Data does not belong to current history"
+            # Mark deleted and cleanup
+            hda.mark_deleted()
+            hda.clear_associated_files()
+            trans.log_event( "Dataset id %s marked as deleted" % str(id) )
+            if hda.parent_id is None and len( hda.creating_job_associations ) > 0:
+                # Mark associated job for deletion
+                job = hda.creating_job_associations[0].job
+                if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]:
+                    # Are *all* of the job's other output datasets deleted?
+                    if job.check_if_output_datasets_deleted():
+                        job.mark_deleted( self.app.config.get_bool( 'enable_job_running', True ),
+                                          self.app.config.get_bool( 'track_jobs_in_database', False ) )
+                        self.app.job_manager.job_stop_queue.put( job.id )
+            trans.sa_session.flush()
+        except Exception, e:
+            msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id )
+            log.exception( msg )
+            trans.log_event( msg )
+            message = 'Dataset deletion failed'
+            status = 'error'
+        return ( message, status )
+
+    def _undelete( self, trans, dataset_id ):
+        message = None
+        status = 'done'
+        id = None
+        try:
+            id = trans.app.security.decode_id( dataset_id )
+            history = trans.get_history()
+            hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
+            assert hda and hda.undeletable, 'Invalid HDA: %s' % id
+            # Walk up parent datasets to find the containing history
+            topmost_parent = hda
             while topmost_parent.parent:
                 topmost_parent = topmost_parent.parent
             assert topmost_parent in history.datasets, "Data does not belong to current history"
             # Mark undeleted
-            data.mark_undeleted()
+            hda.mark_undeleted()
             trans.sa_session.flush()
             trans.log_event( "Dataset id %s has been undeleted" % str(id) )
-            return True
-        return False
+        except Exception, e:
+            msg = 'HDA undeletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id )
+            log.exception( msg )
+            trans.log_event( msg )
+            message = 'Dataset undeletion failed'
+            status = 'error'
+        return ( message, status )
-    def _unhide( self, trans, id ):
+    def _unhide( self, trans, dataset_id ):
         try:
-            id = int( id )
-        except ValueError, e:
+            id = trans.app.security.decode_id( dataset_id )
+        except:
             return False
         history = trans.get_history()
-        data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
-        if data:
+        hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
+        if hda:
             # Walk up parent datasets to find the containing history
-            topmost_parent = data
+            topmost_parent = hda
             while topmost_parent.parent:
                 topmost_parent = topmost_parent.parent
             assert topmost_parent in history.datasets, "Data does not belong to current history"
             # Mark undeleted
-            data.mark_unhidden()
+            hda.mark_unhidden()
             trans.sa_session.flush()
             trans.log_event( "Dataset id %s has been unhidden" % str(id) )
             return True
         return False
-    def _purge( self, trans, id ):
+    def _purge( self, trans, dataset_id ):
+        message = None
+        status = 'done'
         try:
-            id = int( id )
-        except ValueError, e:
-            return False
-        hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
-        # Invalid HDA or not deleted
-        if not hda or not hda.history or not hda.deleted:
-            return False
-        # If the user is anonymous, make sure the HDA is owned by the current session.
-        if not hda.history.user and trans.galaxy_session.id not in [ s.id for s in hda.history.galaxy_sessions ]:
-            return False
-        # If the user is known, make sure the HDA is owned by the current user.
-        if hda.history.user and hda.history.user != trans.user:
-            return False
-        # HDA is purgeable
-        hda.purged = True
-        trans.sa_session.add( hda )
-        trans.log_event( "HDA id %s has been purged" % hda.id )
-        # Don't delete anything if there are active HDAs or any LDDAs, even if
-        # the LDDAs are deleted.  Let the cleanup scripts get it in the latter
-        # case.
-        if hda.dataset.user_can_purge:
-            try:
-                hda.dataset.full_delete()
-                trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) )
-                trans.sa_session.add( hda.dataset )
-            except:
-                log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) )
-        trans.sa_session.flush()
-        return True
+            id = trans.app.security.decode_id( dataset_id )
+            history = trans.get_history()
+            user = trans.get_user()
+            hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
+            # Invalid HDA
+            assert hda, 'Invalid history dataset ID'
+            # Walk up parent datasets to find the containing history
+            topmost_parent = hda
+            while topmost_parent.parent:
+                topmost_parent = topmost_parent.parent
+            assert topmost_parent in history.datasets, "Data does not belong to current history"
+            # If the user is anonymous, make sure the HDA is owned by the current session.
+            if not user:
+                assert trans.galaxy_session.id in [ s.id for s in hda.history.galaxy_sessions ], 'Invalid history dataset ID'
+            # If the user is known, make sure the HDA is owned by the current user.
+            else:
+                assert topmost_parent.history.user == trans.user, 'Invalid history dataset ID'
+            # HDA is not deleted
+            assert hda.deleted, 'History dataset is not marked as deleted'
+            # HDA is purgeable
+            # Decrease disk usage first
+            if user:
+                user.total_disk_usage -= hda.quota_amount( user )
+            # Mark purged
+            hda.purged = True
+            trans.sa_session.add( hda )
+            trans.log_event( "HDA id %s has been purged" % hda.id )
+            # Don't delete anything if there are active HDAs or any LDDAs, even if
+            # the LDDAs are deleted.  Let the cleanup scripts get it in the latter
+            # case.
+            if hda.dataset.user_can_purge:
+                try:
+                    hda.dataset.full_delete()
+                    trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) )
+                    trans.sa_session.add( hda.dataset )
+                except:
+                    log.exception( 'Unable to purge dataset (%s) on purge of HDA (%s):' % ( hda.dataset.id, hda.id ) )
+            trans.sa_session.flush()
+        except Exception, e:
+            msg = 'HDA purge failed (encoded: %s, decoded: %s)' % ( dataset_id, id )
+            log.exception( msg )
+            trans.log_event( msg )
+            message = 'Dataset removal from disk failed'
+            status = 'error'
+        return ( message, status )
@web.expose
-    def undelete( self, trans, id ):
-        if self._undelete( trans, id ):
-            return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) )
-        raise Exception( "Error undeleting" )
+    def delete( self, trans, dataset_id, filename, show_deleted_on_refresh = False ):
+        message, status = self._delete( trans, dataset_id )
+        return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted=show_deleted_on_refresh, message=message, status=status ) )
@web.expose
-    def unhide( self, trans, id ):
-        if self._unhide( trans, id ):
+    def delete_async( self, trans, dataset_id, filename ):
+        message, status = self._delete( trans, dataset_id )
+        if status == 'done':
+            return "OK"
+        else:
+            raise Exception( message )
+
+    @web.expose
+    def undelete( self, trans, dataset_id, filename ):
+        message, status = self._undelete( trans, dataset_id )
+        return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True, message=message, status=status ) )
+
+    @web.expose
+    def undelete_async( self, trans, dataset_id, filename ):
+        message, status =self._undelete( trans, dataset_id )
+        if status == 'done':
+            return "OK"
+        else:
+            raise Exception( message )
+    
+    @web.expose
+    def unhide( self, trans, dataset_id, filename ):
+        if self._unhide( trans, dataset_id ):
             return trans.response.send_redirect( web.url_for( controller='root', action='history', show_hidden = True ) )
         raise Exception( "Error unhiding" )
@web.expose
-    def undelete_async( self, trans, id ):
-        if self._undelete( trans, id ):
-            return "OK"
-        raise Exception( "Error undeleting" )
-    
-    @web.expose
-    def purge( self, trans, id ):
-        if not trans.app.config.allow_user_dataset_purge:
-            raise Exception( "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator." )
-        if self._purge( trans, id ):
-            return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) )
-        raise Exception( "Error removing disk file" )
+    def purge( self, trans, dataset_id, filename, show_deleted_on_refresh = False ):
+        if trans.app.config.allow_user_dataset_purge:
+            message, status = self._purge( trans, dataset_id )
+        else:
+            message = "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator."
+            status = 'error'
+        return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted=show_deleted_on_refresh, message=message, status=status ) )
@web.expose
-    def purge_async( self, trans, id ):
-        if not trans.app.config.allow_user_dataset_purge:
-            raise Exception( "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator." )
-        if self._purge( trans, id ):
+    def purge_async( self, trans, dataset_id, filename ):
+        if trans.app.config.allow_user_dataset_purge:
+            message, status = self._purge( trans, dataset_id )
+        else:
+            message = "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator."
+            status = 'error'
+        if status == 'done':
             return "OK"
-        raise Exception( "Error removing disk file" )
+        else:
+            raise Exception( message )
@web.expose
     def show_params( self, trans, dataset_id=None, from_noframe=None, **kwd ):
--- a/lib/galaxy/web/controllers/root.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/lib/galaxy/web/controllers/root.py	Tue Jul 26 13:56:16 2011 -0400
@@ -8,7 +8,6 @@
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.model.orm import *
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.web.framework.helpers import to_unicode
log = logging.getLogger( __name__ )
@@ -99,11 +98,14 @@
         return trans.fill_template_mako( "/my_data.mako" )
@web.expose
-    def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None ):
+    def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ):
         """
         Display the current history, creating a new history if necessary.
         NOTE: No longer accepts "id" or "template" options for security reasons.
         """
+        params = util.Params( kwd )
+        message = params.get( 'message', None )
+        status = params.get( 'status', 'done' )
         if trans.app.config.require_login and not trans.user:
             return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' )
         history = trans.get_history( create=True )
@@ -123,7 +125,9 @@
                                                datasets = datasets,
                                                hda_id = hda_id,
                                                show_deleted = show_deleted,
-                                               show_hidden=show_hidden )
+                                               show_hidden=show_hidden,
+                                               message=message,
+                                               status=status )
@web.expose
     def dataset_state ( self, trans, id=None, stamp=None ):
@@ -160,9 +164,13 @@
         # Create new HTML for any that have changed
         rval = {}
         if ids is not None and states is not None:
-            ids = map( int, ids.split( "," ) )
+            ids = ids.split( "," )
             states = states.split( "," )
-            for id, state in zip( ids, states ):
+            for encoded_id, state in zip( ids, states ):
+                try:
+                    id = int( trans.app.security.decode_id( encoded_id ) )
+                except:
+                    id = int( encoded_id )
                 data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
                 if data.state != state:
                     job_hda = data
@@ -175,7 +183,7 @@
                             force_history_refresh = tool.force_history_refresh
                     if not job_hda.visible:
                         force_history_refresh = True 
-                    rval[id] = {
+                    rval[encoded_id] = {
                         "state": data.state,
                         "html": unicode( trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ), 'utf-8' ),
                         "force_history_refresh": force_history_refresh
@@ -288,237 +296,6 @@
         else:
             yield "No data with id=%d" % id
-    @web.expose
-    def edit(self, trans, id=None, hid=None, **kwd):
-        """Allows user to modify parameters of an HDA."""
-        message = ''
-        error = False
-        def __ok_to_edit_metadata( dataset_id ):
-            #prevent modifying metadata when dataset is queued or running as input/output
-            #This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now
-            for job_to_dataset_association in trans.sa_session.query( self.app.model.JobToInputDatasetAssociation ) \
-                                                              .filter_by( dataset_id=dataset_id ) \
-                                                              .all() \
-                                            + trans.sa_session.query( self.app.model.JobToOutputDatasetAssociation ) \
-                                                              .filter_by( dataset_id=dataset_id ) \
-                                                              .all():
-                if job_to_dataset_association.job.state not in [ job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED ]:
-                    return False
-            return True
-        if hid is not None:
-            history = trans.get_history()
-            # TODO: hid handling
-            data = history.datasets[ int( hid ) - 1 ]
-        elif id is not None: 
-            data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
-        else:
-            trans.log_event( "Problem loading dataset id %s with history id %s." % ( str( id ), str( hid ) ) )
-            return trans.show_error_message( "Problem loading dataset." )
-        if data is None:
-            trans.log_event( "Problem retrieving dataset id %s with history id." % ( str( id ), str( hid ) ) )
-            return trans.show_error_message( "Problem retrieving dataset." )
-        if id is not None and data.history.user is not None and data.history.user != trans.user:
-            return trans.show_error_message( "This instance of a dataset (%s) in a history does not belong to you." % ( data.id ) )
-        current_user_roles = trans.get_current_user_roles()
-        if data.history.user and not data.dataset.has_manage_permissions_roles( trans ):
-            # Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
-            # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
-            # permission.  In this case, we'll reset this permission to the hda user's private role.
-            manage_permissions_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action )
-            permissions = { manage_permissions_action : [ trans.app.security_agent.get_private_user_role( data.history.user ) ] }
-            trans.app.security_agent.set_dataset_permission( data.dataset, permissions )        
-        if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
-            if data.state == trans.model.Dataset.states.UPLOAD:
-                return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." )
-            params = util.Params( kwd, sanitize=False )
-            if params.change:
-                # The user clicked the Save button on the 'Change data type' form
-                if data.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
-                    #prevent modifying datatype when dataset is queued or running as input/output
-                    if not __ok_to_edit_metadata( data.id ):
-                        return trans.show_error_message( "This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them." )
-                    trans.app.datatypes_registry.change_datatype( data, params.datatype, set_meta = not trans.app.config.set_metadata_externally )
-                    trans.sa_session.flush()
-                    if trans.app.config.set_metadata_externally:
-                        trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data }, overwrite = False ) #overwrite is False as per existing behavior
-                    return trans.show_ok_message( "Changed the type of dataset '%s' to %s" % ( to_unicode( data.name ), params.datatype ), refresh_frames=['history'] )
-                else:
-                    return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) )
-            elif params.save:
-                # The user clicked the Save button on the 'Edit Attributes' form
-                data.name  = params.name
-                data.info  = params.info
-                message = ''
-                if __ok_to_edit_metadata( data.id ):
-                    # The following for loop will save all metadata_spec items
-                    for name, spec in data.datatype.metadata_spec.items():
-                        if spec.get("readonly"):
-                            continue
-                        optional = params.get("is_"+name, None)
-                        other = params.get("or_"+name, None)
-                        if optional and optional == 'true':
-                            # optional element... == 'true' actually means it is NOT checked (and therefore omitted)
-                            setattr(data.metadata, name, None)
-                        else:
-                            if other:
-                                setattr( data.metadata, name, other )
-                            else:
-                                setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
-                    data.datatype.after_setting_metadata( data )
-                    # Sanitize annotation before adding it.
-                    if params.annotation:
-                        annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' )
-                        self.add_item_annotation( trans.sa_session, trans.get_user(), data, annotation )
-                    # If setting metadata previously failed and all required elements have now been set, clear the failed state.
-                    if data._state == trans.model.Dataset.states.FAILED_METADATA and not data.missing_meta():
-                        data._state = None
-                    trans.sa_session.flush()
-                    return trans.show_ok_message( "Attributes updated%s" % message, refresh_frames=['history'] )
-                else:
-                    trans.sa_session.flush()
-                    return trans.show_warn_message( "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.", refresh_frames=['history'] )
-            elif params.detect:
-                # The user clicked the Auto-detect button on the 'Edit Attributes' form
-                #prevent modifying metadata when dataset is queued or running as input/output
-                if not __ok_to_edit_metadata( data.id ):
-                    return trans.show_error_message( "This dataset is currently being used as input or output.  You cannot change metadata until the jobs have completed or you have canceled them." )
-                for name, spec in data.metadata.spec.items():
-                    # We need to be careful about the attributes we are resetting
-                    if name not in [ 'name', 'info', 'dbkey', 'base_name' ]:
-                        if spec.get( 'default' ):
-                            setattr( data.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
-                if trans.app.config.set_metadata_externally:
-                    message = 'Attributes have been queued to be updated'
-                    trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data } )
-                else:
-                    message = 'Attributes updated'
-                    data.set_meta()
-                    data.datatype.after_setting_metadata( data )
-                trans.sa_session.flush()
-                return trans.show_ok_message( message, refresh_frames=['history'] )
-            elif params.convert_data:
-                target_type = kwd.get("target_type", None)
-                if target_type:
-                    message = data.datatype.convert_dataset(trans, data, target_type)
-                    return trans.show_ok_message( message, refresh_frames=['history'] )
-            elif params.update_roles_button:
-                if not trans.user:
-                    return trans.show_error_message( "You must be logged in if you want to change permissions." )
-                if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ):
-                    access_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action )
-                    manage_permissions_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action )
-                    # The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles.  We
-                    # need to ensure that they did not associate roles that would cause accessibility problems.
-                    permissions, in_roles, error, message = \
-                    trans.app.security_agent.derive_roles_from_access( trans, data.dataset.id, 'root', **kwd )
-                    if error:
-                        # Keep the original role associations for the DATASET_ACCESS permission on the dataset.
-                        permissions[ access_action ] = data.dataset.get_access_roles( trans )
-                        status = 'error'
-                    else:
-                        error = trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions )
-                        if error:
-                            message += error
-                            status = 'error'
-                        else:
-                            message = 'Your changes completed successfully.'
-                    trans.sa_session.refresh( data.dataset )
-                else:
-                    return trans.show_error_message( "You are not authorized to change this dataset's permissions" )
-            if "dbkey" in data.datatype.metadata_spec and not data.metadata.dbkey:
-                # Copy dbkey into metadata, for backwards compatability
-                # This looks like it does nothing, but getting the dbkey
-                # returns the metadata dbkey unless it is None, in which
-                # case it resorts to the old dbkey.  Setting the dbkey
-                # sets it properly in the metadata
-                #### This is likely no longer required, since the dbkey exists entirely within metadata (the old_dbkey field is gone): REMOVE ME?
-                data.metadata.dbkey = data.dbkey
-            # let's not overwrite the imported datatypes module with the variable datatypes?
-            # the built-in 'id' is overwritten in lots of places as well
-            ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
-            ldatatypes.sort()
-            all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' )
-            if error:
-                status = 'error'
-            else:
-                status = 'done'
-            return trans.fill_template( "/dataset/edit_attributes.mako",
-                                        data=data,
-                                        data_annotation=self.get_item_annotation_str( trans.sa_session, trans.user, data ),
-                                        datatypes=ldatatypes,
-                                        current_user_roles=current_user_roles,
-                                        all_roles=all_roles,
-                                        message=message,
-                                        status=status )
-        else:
-            return trans.show_error_message( "You do not have permission to edit this dataset's ( id: %s ) information." % str( id ) )
-
-    def __delete_dataset( self, trans, id ):
-        data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
-        if data:
-            # Walk up parent datasets to find the containing history
-            topmost_parent = data
-            while topmost_parent.parent:
-                topmost_parent = topmost_parent.parent
-            assert topmost_parent in trans.history.datasets, "Data does not belong to current history"
-            # Mark deleted and cleanup
-            data.mark_deleted()
-            data.clear_associated_files()
-            trans.log_event( "Dataset id %s marked as deleted" % str(id) )
-            if data.parent_id is None and len( data.creating_job_associations ) > 0:
-                # Mark associated job for deletion
-                job = data.creating_job_associations[0].job
-                if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]:
-                    # Are *all* of the job's other output datasets deleted?
-                    if job.check_if_output_datasets_deleted():
-                        job.mark_deleted( self.app.config.get_bool( 'enable_job_running', True ),
-                                          self.app.config.get_bool( 'track_jobs_in_database', False ) )
-                        self.app.job_manager.job_stop_queue.put( job.id )
-            trans.sa_session.flush()
-
-    @web.expose
-    def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd):
-        if id:
-            if isinstance( id, list ):
-                dataset_ids = id
-            else:
-                dataset_ids = [ id ]
-            history = trans.get_history()
-            for id in dataset_ids:
-                try:
-                    id = int( id )
-                except:
-                    continue
-                self.__delete_dataset( trans, id )
-        return self.history( trans, show_deleted = show_deleted_on_refresh )
-        
-    @web.expose
-    def delete_async( self, trans, id = None, **kwd):
-        if id:
-            try:
-                id = int( id )
-            except:
-                return "Dataset id '%s' is invalid" %str( id )
-            self.__delete_dataset( trans, id )
-        return "OK"
-
-    @web.expose
-    def purge( self, trans, id = None, show_deleted_on_refresh = False, **kwd ):
-        if not trans.app.config.allow_user_dataset_purge:
-            return trans.show_error_message( "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator." )
-        hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( int( id ) )
-        if bool( hda.dataset.active_history_associations or hda.dataset.library_associations ):
-            return trans.show_error_message( "Unable to purge: LDDA(s) or active HDA(s) exist" )
-        elif hda.dataset.purged:
-            return trans.show_error_message( "Unable to purge: dataset is already purged" )
-        os.unlink( hda.dataset.file_name )
-        if os.path.exists( hda.extra_files_path ):
-            shutil.rmtree( hda.extra_files_path )
-        hda.dataset.purged = True
-        trans.sa_session.add( hda.dataset )
-        trans.sa_session.flush()
-        return self.history( trans, show_deleted = show_deleted_on_refresh )
-
     ## ---- History management -----------------------------------------------
@web.expose
--- a/lib/galaxy/web/framework/__init__.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/lib/galaxy/web/framework/__init__.py	Tue Jul 26 13:56:16 2011 -0400
@@ -471,6 +471,7 @@
            - associate new session with user
            - if old session had a history and it was not associated with a user, associate it with the new session, 
              otherwise associate the current session's history with the user
+           - add the disk usage of the current session to the user's total disk usage
         """
         # Set the previous session
         prev_galaxy_session = self.galaxy_session
@@ -494,6 +495,10 @@
                     # If the previous galaxy session had a history, associate it with the new
                     # session, but only if it didn't belong to a different user.
                     history = prev_galaxy_session.current_history
+                    if prev_galaxy_session.user is None:
+                        # Increase the user's disk usage by the amount of the previous history's datasets if they didn't already own it.
+                        for hda in history.datasets:
+                            user.total_disk_usage += hda.quota_amount( user )
             elif self.galaxy_session.current_history:
                 history = self.galaxy_session.current_history
             if not history and \
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/set_user_disk_usage.py	Tue Jul 26 13:56:16 2011 -0400
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+import os, sys
+from ConfigParser import ConfigParser
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' )
+parser.add_option( '-u', '--username', dest='username', help='Username of user to update', default='all' )
+parser.add_option( '-e', '--email', dest='email', help='Email address of user to update', default='all' )
+parser.add_option( '--dry-run', dest='dryrun', help='Dry run (show changes but do not save to database)', action='store_true', default=False )
+( options, args ) = parser.parse_args()
+
+def init():
+
+    options.config = os.path.abspath( options.config )
+    if options.username == 'all':
+        options.username = None
+    if options.email == 'all':
+        options.email = None
+
+    os.chdir( os.path.dirname( options.config ) )
+    sys.path.append( 'lib' )
+
+    from galaxy import eggs
+    import pkg_resources
+
+    config = ConfigParser( dict( file_path = 'database/files',
+                                 database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) )
+    config.read( os.path.basename( options.config ) )
+
+    from galaxy.model import mapping
+
+    return mapping.init( config.get( 'app:main', 'file_path' ), config.get( 'app:main', 'database_connection' ), create_tables = False )
+
+def quotacheck( sa_session, users ):
+    sa_session.refresh( user )
+    current = user.get_disk_usage()
+    print user.username, '<' + user.email + '> current usage:', str( current ) + ',',
+    new = user.calculate_disk_usage()
+    sa_session.refresh( user )
+    # usage changed while calculating, do it again
+    if user.get_disk_usage() != current:
+        print 'usage changed while calculating, trying again...'
+        return quotacheck( sa_session, user )
+    # yes, still a small race condition between here and the flush
+    if new == current:
+        print 'no change'
+    else:
+        print 'new:', new
+        if not options.dryrun:
+            user.set_disk_usage( new )
+            sa_session.add( user )
+            sa_session.flush()
+
+if __name__ == '__main__':
+    print 'Loading Galaxy model...'
+    model = init()
+    sa_session = model.context.current
+
+    if not options.username and not options.email:
+        user_count = sa_session.query( model.User ).count()
+        print 'Processing %i users...' % user_count
+        for i, user in enumerate( sa_session.query( model.User ).enable_eagerloads( False ).yield_per( 1000 ) ):
+            print '%3i%%' % int( float(i) / user_count * 100 ),
+            quotacheck( sa_session, user )
+        print '100% complete'
+        sys.exit( 0 )
+    elif options.username:
+        user = sa_session.query( model.User ).enable_eagerloads( False ).filter_by( username=options.username ).first()
+    elif options.email:
+        user = sa_session.query( model.User ).enable_eagerloads( False ).filter_by( email=options.email ).first()
+    if not user:
+        print 'User not found'
+        sys.exit( 1 )
+    quotacheck( sa_session, user )
--- a/templates/dataset/edit_attributes.mako	Tue Jul 26 13:18:22 2011 -0400
+++ b/templates/dataset/edit_attributes.mako	Tue Jul 26 13:56:16 2011 -0400
@@ -1,5 +1,6 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/message.mako" name="message_ns" import="javascripts" /><%def name="title()">${_('Edit Dataset Attributes')}</%def>
@@ -10,6 +11,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+    ${message_ns.javascripts()}
 </%def><%def name="datatype( dataset, datatypes )">
@@ -31,8 +33,7 @@
 <div class="toolForm"><div class="toolFormTitle">${_('Edit Attributes')}</div><div class="toolFormBody">
-        <form name="edit_attributes" action="${h.url_for( controller='root', action='edit' )}" method="post">
-            <input type="hidden" name="id" value="${data.id}"/>
+        <form name="edit_attributes" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"><div class="form-row"><label>
                     Name:
@@ -80,8 +81,7 @@
                 <input type="submit" name="save" value="${_('Save')}"/></div></form>
-        <form name="auto_detect" action="${h.url_for( controller='root', action='edit' )}" method="post">
-            <input type="hidden" name="id" value="${data.id}"/>
+        <form name="auto_detect" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"><div class="form-row"><div style="float: left; width: 250px; margin-right: 10px;"><input type="submit" name="detect" value="${_('Auto-detect')}"/>
@@ -104,8 +104,7 @@
     <div class="toolForm"><div class="toolFormTitle">${_('Convert to new format')}</div><div class="toolFormBody">
-            <form name="convert_data" action="${h.url_for( controller='root', action='edit' )}" method="post">
-                <input type="hidden" name="id" value="${data.id}"/>
+            <form name="convert_data" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"><div class="form-row"><div style="float: left; width: 250px; margin-right: 10px;"><select name="target_type">
@@ -132,8 +131,7 @@
     <div class="toolFormTitle">${_('Change data type')}</div><div class="toolFormBody">
         %if data.datatype.allow_datatype_change:
-            <form name="change_datatype" action="${h.url_for( controller='root', action='edit' )}" method="post">
-                <input type="hidden" name="id" value="${data.id}"/>
+            <form name="change_datatype" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"><div class="form-row"><label>
                         ${_('New Type')}:
@@ -161,7 +159,7 @@
%if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ):
     <%namespace file="/dataset/security_common.mako" import="render_permission_form" />
-    ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='root', action='edit', id=data.id ), all_roles )}
+    ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='dataset', action='edit', dataset_id=dataset_id ), all_roles )}
 %elif trans.user:
     <div class="toolForm"><div class="toolFormTitle">View Permissions</div>
--- a/templates/root/history.mako	Tue Jul 26 13:18:22 2011 -0400
+++ b/templates/root/history.mako	Tue Jul 26 13:56:16 2011 -0400
@@ -1,3 +1,5 @@
+<%namespace file="/message.mako" import="render_msg" />
+
 <% _=n_ %><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
@@ -105,6 +107,11 @@
     });
 };
+// Update the message for async operations
+function render_message(message, status) {
+    $("div#message-container").html( "<div class="" + status + "message">" + message + "</div><br/>" );
+}
+
 $(function() {
     var historywrapper = $("div.historyItemWrapper");
     init_history_items(historywrapper);
@@ -115,8 +122,8 @@
             $(this).click( function() {
                 $( '#historyItem-' + data_id + "> div.historyItemTitleBar" ).addClass( "spinner" );
                 $.ajax({
-                    url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ),
-                    error: function() { alert( "Delete failed" ); },
+                    url: "${h.url_for( controller='dataset', action='delete_async', dataset_id='XXX' )}".replace( 'XXX', data_id ),
+                    error: function() { render_message( "Dataset deletion failed", "error" ); },
                     success: function(msg) {
                         if (msg === "OK") {
                             %if show_deleted:
@@ -133,7 +140,7 @@
                             %endif
                             $(".tipsy").remove();
                         } else {
-                            alert( "Delete failed" );
+                            render_message( "Dataset deletion failed", "error" );
                         }
                     }
                 });
@@ -147,8 +154,8 @@
             $(this).click( function() {
                 $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" );
                 $.ajax({
-                    url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ),
-                    error: function() { alert( "Undelete failed" ) },
+                    url: "${h.url_for( controller='dataset', action='undelete_async', dataset_id='XXX' )}".replace( 'XXX', data_id ),
+                    error: function() { render_message( "Dataset undeletion failed", "error" ); },
                     success: function() {
                         var to_update = {};
                         to_update[data_id] = "none";
@@ -165,8 +172,8 @@
             $(this).click( function() {
                 $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" );
                 $.ajax({
-                    url: "${h.url_for( controller='dataset', action='purge_async', id='XXX' )}".replace( 'XXX', data_id ),
-                    error: function() { alert( "Removal from disk failed" ) },
+                    url: "${h.url_for( controller='dataset', action='purge_async', dataset_id='XXX' )}".replace( 'XXX', data_id ),
+                    error: function() { render_message( "Dataset removal from disk failed", "error" ) },
                     success: function() {
                         var to_update = {};
                         to_update[data_id] = "none";
@@ -258,7 +265,7 @@
// Updater
     updater(
-        ${ h.to_json_string( dict([(data.id, data.state) for data in reversed( datasets ) if data.visible and data.state not in TERMINAL_STATES]) ) }
+        ${ h.to_json_string( dict([(trans.app.security.encode_id(data.id), data.state) for data in reversed( datasets ) if data.visible and data.state not in TERMINAL_STATES]) ) }
     );
// Navigate to a dataset.
@@ -311,11 +318,11 @@
                     if ( val.force_history_refresh ){
                         force_history_refresh = true;
                     }
-                    delete tracked_datasets[ parseInt(id) ];
+                    delete tracked_datasets[id];
                     // When a dataset becomes terminal, check for changes in history disk size
                     check_history_size = true;
                 } else {
-                    tracked_datasets[ parseInt(id) ] = val.state;
+                    tracked_datasets[id] = val.state;
                 }
             });
             if ( force_history_refresh ) {
@@ -458,6 +465,12 @@
     </div>
 %endif
+<div id="message-container">
+    %if message:
+        ${render_msg( message, status )}
+    %endif
+</div>
+
 %if not datasets:
<div class="infomessagesmall" id="emptyHistoryMessage">
@@ -467,7 +480,7 @@
     ## Render requested datasets, ordered from newest to oldest
     %for data in reversed( datasets ):
         %if data.visible or show_hidden:
-            <div class="historyItemContainer" id="historyItemContainer-${data.id}">
+            <div class="historyItemContainer" id="historyItemContainer-${trans.app.security.encode_id(data.id)}">
                 ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = True )}
             </div>
         %endif
--- a/templates/root/history_common.mako	Tue Jul 26 13:18:22 2011 -0400
+++ b/templates/root/history_common.mako	Tue Jul 26 13:56:16 2011 -0400
@@ -39,9 +39,9 @@
         can_edit = not ( data.deleted or data.purged )
     %>
     %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
-        <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${data.id}">
+        <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${dataset_id}">
     %else:
-        <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${data.id}">
+        <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${dataset_id}">
     %endif
%if data.deleted or data.purged or data.dataset.purged:
@@ -51,9 +51,9 @@
             %else:
                 This dataset has been deleted. 
                 %if for_editing:
-                    Click <a href="${h.url_for( controller='dataset', action='undelete', id=data.id )}" class="historyItemUndelete" id="historyItemUndeleter-${data.id}" target="galaxy_history">here</a> to undelete
+                    Click <a href="${h.url_for( controller='dataset', action='undelete', dataset_id=dataset_id )}" class="historyItemUndelete" id="historyItemUndeleter-${dataset_id}" target="galaxy_history">here</a> to undelete
                     %if trans.app.config.allow_user_dataset_purge:
-                        or <a href="${h.url_for( controller='dataset', action='purge', id=data.id )}" class="historyItemPurge" id="historyItemPurger-${data.id}" target="galaxy_history">here</a> to immediately remove it from disk.
+                        or <a href="${h.url_for( controller='dataset', action='purge', dataset_id=dataset_id )}" class="historyItemPurge" id="historyItemPurger-${dataset_id}" target="galaxy_history">here</a> to immediately remove it from disk.
                     %else:
                         it.
                     %endif
@@ -64,7 +64,7 @@
%if data.visible is False:
         <div class="warningmessagesmall">
-            <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', id=data.id )}" class="historyItemUnhide" id="historyItemUnhider-${data.id}" target="galaxy_history">here</a> to unhide.</strong>
+            <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', dataset_id=dataset_id )}" class="historyItemUnhide" id="historyItemUnhider-${dataset_id}" target="galaxy_history">here</a> to unhide.</strong></div>
     %endif
@@ -110,13 +110,13 @@
                     %elif data.purged:
                         <span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled tooltip"></span>
                     %else:
-                        <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a>
+                        <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a>
                     %endif
                 %endif
             %endif
             %if for_editing:
                 %if can_edit:
-                    <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a>
+                    <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a>
                 %else:
                     <span title="Dataset is already deleted" class="icon-button delete_disabled tooltip"></span>
                 %endif
@@ -184,7 +184,7 @@
                 <div class="warningmessagesmall" style="margin: 4px 0 4px 0">
                     An error occurred setting the metadata for this dataset.
                     %if can_edit:
-                        You may be able to <a href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main">set it manually or retry auto-detection</a>.
+                        You may be able to <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">set it manually or retry auto-detection</a>.
                     %endif
                 </div>
             %endif
@@ -193,7 +193,7 @@
                 format: <span class="${data.ext}">${data.ext}</span>, 
                 database:
                 %if data.dbkey == '?' and can_edit:
-                    <a href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main">${_(data.dbkey)}</a>
+                    <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">${_(data.dbkey)}</a>
                 %else:
                     <span class="${data.dbkey}">${_(data.dbkey)}</span>
                 %endif
--- a/templates/user/index.mako	Tue Jul 26 13:18:22 2011 -0400
+++ b/templates/user/index.mako	Tue Jul 26 13:56:16 2011 -0400
@@ -22,6 +22,7 @@
             <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller,  webapp='community' )}">${_('Manage your information')}</a></li>
         %endif
     </ul>
+    <p>You are currently using <strong>${trans.user.get_disk_usage( nice_size=True )}</strong> of disk space in this Galaxy instance.</p>
 %else:
     %if not message:
         <p>${n_('You are currently not logged in.')}</p>
--- a/templates/webapps/community/repository/common.mako	Tue Jul 26 13:18:22 2011 -0400
+++ b/templates/webapps/community/repository/common.mako	Tue Jul 26 13:56:16 2011 -0400
@@ -50,39 +50,4 @@
                 onActivate: function(dtnode) {
                     var cell = $("#file_contents");
                     var selected_value;
-                    if (dtnode.data.key == 'root') {
-                        selected_value = "${repository.repo_path}/";
-                    } else {
-                        selected_value = dtnode.data.key;
-                    };
-                    if (selected_value.charAt(selected_value.length-1) != '/') {
-                        // Make ajax call
-                        $.ajax( {
-                            type: "POST",
-                            url: "${h.url_for( controller='repository', action='get_file_contents' )}",
-                            dataType: "json",
-                            data: { file_path: selected_value },
-                            success : function ( data ) {
-                                cell.html( '<label>'+data+'</label>' )
-                            }
-                        });
-                    } else {
-                        cell.html( '' );
-                    };
-                },
-            });
-        });
-    </script>
-</%def>
-
-<%def name="render_clone_str( repository )">
-    <%
-        protocol, base = trans.request.base.split( '://' )
-        if trans.user:
-            username = '%s@' % trans.user.username
-        else:
-            username = ''
-        clone_str = '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name )
-    %>
-    hg clone <a href="${clone_str}">${clone_str}</a>
-</%def>
\ No newline at end of file
+ 
\ No newline at end of file
--- a/test/base/twilltestcase.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/test/base/twilltestcase.py	Tue Jul 26 13:56:16 2011 -0400
@@ -474,7 +474,7 @@
             elem = data_list[-1]
             hid = int( elem.get('hid') )
         self.assertTrue( hid )
-        self.visit_page( "edit?hid=%s" % hid )
+        self.visit_page( "dataset/edit?hid=%s" % hid )
         for subpatt in patt.split():
             tc.find(subpatt)
     def delete_history_item( self, hda_id, strings_displayed=[] ):
@@ -483,7 +483,7 @@
             hda_id = int( hda_id )
         except:
             raise AssertionError, "Invalid hda_id '%s' - must be int" % hda_id
-        self.visit_url( "%s/root/delete?show_deleted_on_refresh=False&id=%s" % ( self.url, hda_id ) )
+        self.visit_url( "%s/datasets/%s/delete?show_deleted_on_refresh=False" % ( self.url, self.security.encode_id( hda_id ) ) )
         for check_str in strings_displayed:
             self.check_page_for_string( check_str )
     def undelete_history_item( self, hda_id, strings_displayed=[] ):
@@ -492,7 +492,7 @@
             hda_id = int( hda_id )
         except:
             raise AssertionError, "Invalid hda_id '%s' - must be int" % hda_id
-        self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, hda_id ) )
+        self.visit_url( "%s/datasets/%s/undelete" % ( self.url, self.security.encode_id( hda_id ) ) )
         for check_str in strings_displayed:
             self.check_page_for_string( check_str )
     def display_history_item( self, hda_id, strings_displayed=[] ):
@@ -511,7 +511,7 @@
                                  strings_displayed=[], strings_not_displayed=[] ):
         """Edit history_dataset_association attribute information"""
         self.home()
-        self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
+        self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) )
         submit_required = False
         self.check_page_for_string( 'Edit Attributes' )
         if new_name:
@@ -545,9 +545,9 @@
     def auto_detect_metadata( self, hda_id ):
         """Auto-detect history_dataset_association metadata"""
         self.home()
-        self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
+        self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) )
         self.check_page_for_string( 'This will inspect the dataset and attempt' )
-        tc.fv( 'auto_detect', 'id', hda_id )
+        tc.fv( 'auto_detect', 'detect', 'Auto-detect' )
         tc.submit( 'detect' )
         try:
             self.check_page_for_string( 'Attributes have been queued to be updated' )
@@ -559,7 +559,7 @@
     def convert_format( self, hda_id, target_type ):
         """Convert format of history_dataset_association"""
         self.home()
-        self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
+        self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) )
         self.check_page_for_string( 'This will inspect the dataset and attempt' )
         tc.fv( 'convert_data', 'target_type', target_type )
         tc.submit( 'convert_data' )
@@ -569,7 +569,7 @@
     def change_datatype( self, hda_id, datatype ):
         """Change format of history_dataset_association"""
         self.home()
-        self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
+        self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) )
         self.check_page_for_string( 'This will change the datatype of the existing dataset but' )
         tc.fv( 'change_datatype', 'datatype', datatype )
         tc.submit( 'change' )
--- a/test/functional/test_history_functions.py	Tue Jul 26 13:18:22 2011 -0400
+++ b/test/functional/test_history_functions.py	Tue Jul 26 13:56:16 2011 -0400
@@ -664,7 +664,7 @@
                                .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
                                .first()
         self.home()
-        self.visit_url( "%s/root/delete?show_deleted_on_refresh=False&id=%s" % ( self.url, str( latest_hda.id ) ) )
+        self.delete_history_item( str( latest_hda.id ) )
         self.check_history_for_string( 'Your history is empty' )
         self.home()
         self.visit_url( "%s/history/?show_deleted=True" % self.url )
http://bitbucket.org/galaxy/galaxy-central/changeset/57c8053675b6/
changeset:   57c8053675b6
user:        dannon
date:        2011-07-28 14:22:07
summary:     Expose workflows shared with the user in /workflows list of the API.
affected #:  1 file (597 bytes)
--- a/lib/galaxy/web/api/workflows.py	Tue Jul 26 13:56:16 2011 -0400
+++ b/lib/galaxy/web/api/workflows.py	Thu Jul 28 08:22:07 2011 -0400
@@ -29,6 +29,14 @@
             encoded_id = trans.security.encode_id(wf.id)
             item['url'] = url_for('workflow', id=encoded_id)
             rval.append(item)
+        for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by(
+                user=trans.user ).join( 'stored_workflow' ).filter(
+                trans.app.model.StoredWorkflow.deleted == False ).order_by(
+                desc( trans.app.model.StoredWorkflow.update_time ) ).all():
+            item = wf_sa.stored_workflow.get_api_value(value_mapper={'id':trans.security.encode_id})
+            encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
+            item['url'] = url_for('workflow', id=encoded_id)
+            rval.append(item)
         return rval
     @web.expose_api
     def show(self, trans, id, **kwd):
http://bitbucket.org/galaxy/galaxy-central/changeset/f0c4e3efcb99/
changeset:   f0c4e3efcb99
user:        dannon
date:        2011-07-28 14:22:22
summary:     Merge.
affected #:  15 files (61.1 KB)
--- a/datatypes_conf.xml.sample	Thu Jul 28 08:22:07 2011 -0400
+++ b/datatypes_conf.xml.sample	Thu Jul 28 08:22:22 2011 -0400
@@ -72,9 +72,10 @@
             <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> --></datatype><datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
-        <datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
+        <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/><datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/><datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/>
+        <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/><datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/><datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"><converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
@@ -90,7 +91,21 @@
         <datatype extension="picard_interval_list" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/><datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/><datatype extension="gatk_dbsnp" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
-        <datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
+        <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
+        <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/>
+        <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/>
+        <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/>
+        <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/>
+        <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/>
+        <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/>
+        <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/>
+        <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/>
+        <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/>
+        <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
+        <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
+        <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
+        <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
+        <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/><datatype extension="laj" type="galaxy.datatypes.images:Laj"/><datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/><datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
@@ -102,7 +117,7 @@
         </datatype><datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/><datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
-        <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
+        <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /><datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/><datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
@@ -116,7 +131,7 @@
         <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/><datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
-	<datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+        <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
@@ -304,6 +319,24 @@
         <sniffer type="galaxy.datatypes.tabular:Pileup"/><sniffer type="galaxy.datatypes.interval:Interval"/><sniffer type="galaxy.datatypes.tabular:Sam"/>
+        <sniffer type="galaxy.datatypes.images:Jpg"/>
+        <sniffer type="galaxy.datatypes.images:Png"/>
+        <sniffer type="galaxy.datatypes.images:Tiff"/>
+        <sniffer type="galaxy.datatypes.images:Bmp"/>
+        <sniffer type="galaxy.datatypes.images:Gif"/>
+        <sniffer type="galaxy.datatypes.images:Im"/>
+        <sniffer type="galaxy.datatypes.images:Pcd"/>
+        <sniffer type="galaxy.datatypes.images:Pcx"/>
+        <sniffer type="galaxy.datatypes.images:Ppm"/>
+        <sniffer type="galaxy.datatypes.images:Psd"/>
+        <sniffer type="galaxy.datatypes.images:Xbm"/>
+        <sniffer type="galaxy.datatypes.images:Xpm"/>
+        <sniffer type="galaxy.datatypes.images:Rgb"/>
+        <sniffer type="galaxy.datatypes.images:Pbm"/>
+        <sniffer type="galaxy.datatypes.images:Pgm"/>
+        <sniffer type="galaxy.datatypes.images:Xpm"/>
+        <sniffer type="galaxy.datatypes.images:Eps"/>
+        <sniffer type="galaxy.datatypes.images:Rast"/><!--
         Keep this commented until the sniff method in the assembly.py
         module is fixed to not read the entire file.
--- a/lib/galaxy/datatypes/binary.py	Thu Jul 28 08:22:07 2011 -0400
+++ b/lib/galaxy/datatypes/binary.py	Thu Jul 28 08:22:22 2011 -0400
@@ -18,7 +18,7 @@
 log = logging.getLogger(__name__)
# Currently these supported binary data types must be manually set on upload
-unsniffable_binary_formats = [ 'ab1', 'scf' ]
+unsniffable_binary_formats = [ 'ab1', 'scf', 'h5' ]
class Binary( data.Data ):
     """Binary data"""
@@ -206,7 +206,24 @@
             return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) )
     def get_track_type( self ):
         return "ReadTrack", {"data": "bai", "index": "summary_tree"}
-    
+
+class H5( Binary ):
+    """Class describing an HDF5 file"""
+    file_ext = "h5"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek  = "Binary h5 file" 
+            dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Binary h5 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) )
+
 class Scf( Binary ):
     """Class describing an scf binary sequence file"""
     file_ext = "scf"
@@ -292,7 +309,6 @@
         Binary.__init__( self, **kwd )
         self._magic = 0x8789F2EB
         self._name = "BigBed"
-        
     def get_track_type( self ):
         return "LineTrack", {"data_standalone": "bigbed"}
@@ -309,14 +325,12 @@
                 return True
         except IOError:
             return False
-        
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
             dataset.peek = "Binary TwoBit format nucleotide file"
             dataset.blurb = data.nice_size(dataset.get_size())
         else:
             return super(TwoBit, self).set_peek(dataset, is_multi_byte)
-    
     def display_peek(self, dataset):
         try:
             return dataset.peek
--- a/lib/galaxy/datatypes/checkers.py	Thu Jul 28 08:22:07 2011 -0400
+++ b/lib/galaxy/datatypes/checkers.py	Thu Jul 28 08:22:22 2011 -0400
@@ -1,6 +1,28 @@
 import os, gzip, re, gzip, zipfile, binascii, bz2
 from galaxy import util
+try:
+    import Image as PIL
+except ImportError:
+    try:
+        from PIL import Image as PIL
+    except:
+        PIL = None
+
+def check_image( file_path ):
+    if PIL != None:
+        try:
+            im = PIL.open( file_path )
+        except:
+            return False
+        if im:
+            return im
+        return False
+    else:
+        if imghdr.what( file_path ) != None:
+            return True
+        return False
+
 def check_html( file_path, chunk=None ):
     if chunk is None:
         temp = open( file_path, "U" )
--- a/lib/galaxy/datatypes/images.py	Thu Jul 28 08:22:07 2011 -0400
+++ b/lib/galaxy/datatypes/images.py	Thu Jul 28 08:22:22 2011 -0400
@@ -7,12 +7,31 @@
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes import metadata
 from galaxy.datatypes.sniff import *
+from galaxy.datatypes.util.image_util import *
 from urllib import urlencode, quote_plus
 import zipfile
-import os, subprocess, tempfile
+import os, subprocess, tempfile, imghdr
+
+try:
+    import Image as PIL
+except ImportError:
+    try:
+        from PIL import Image as PIL
+    except:
+        PIL = None
log = logging.getLogger(__name__)
+# TODO: Uploading image files of various types is supported in Galaxy, but on
+# the main public instance, the display_in_upload is not set for these data
+# types in datatypes_conf.xml because we do not allow image files to be uploaded
+# there.  There is currently no API feature that allows uploading files outside 
+# of a data library ( where it requires either the upload_paths or upload_directory
+# option to be enabled, which is not the case on the main public instance ).  Because
+# of this, we're currently safe, but when the api is enhanced to allow other uploads,
+# we need to ensure that the implementation is such that image files cannot be uploaded
+# to our main public instance.
+
 class Image( data.Data ):
     """Class describing an image"""
     def set_peek( self, dataset, is_multi_byte=False ):
@@ -22,11 +41,110 @@
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
+    def sniff( self, filename ):
+        # First check if we can  use PIL
+        if PIL is not None:
+            try:
+                im = PIL.open( filename )
+                im.close()
+                return True
+            except:
+                return False
+        else:
+            if imghdr.what( filename ) is not None:
+                return True
+            else:
+                return False
+    
+class Jpg( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in jpg format."""
+        return check_image_type( filename, ['JPEG'], image )
+
+class Png( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in png format."""
+        return check_image_type( filename, ['PNG'], image )
+    
+class Tiff( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in tiff format."""
+        return check_image_type( filename, ['TIFF'], image )
+    
+class Bmp( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in bmp format."""
+        return check_image_type( filename, ['BMP'], image )
+
+class Gif( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in gif format."""
+        return check_image_type( filename, ['GIF'], image )
+
+class Im( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in im format."""
+        return check_image_type( filename, ['IM'], image )
+
+class Pcd( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in pcd format."""
+        return check_image_type( filename, ['PCD'], image )        
+
+class Pcx( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in pcx format."""
+        return check_image_type( filename, ['PCX'], image )
+
+class Ppm( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in ppm format."""
+        return check_image_type( filename, ['PPM'], image )        
+
+class Psd( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in psd format."""
+        return check_image_type( filename, ['PSD'], image )        
+
+class Xbm( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in XBM format."""
+        return check_image_type( filename, ['XBM'], image )        
+
+class Xpm( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in XPM format."""
+        return check_image_type( filename, ['XPM'], image )        
+
+class Rgb( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in RGB format."""
+        return check_image_type( filename, ['RGB'], image )
+
+class Pbm( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in PBM format"""
+        return check_image_type( filename, ['PBM'], image )
+
+class Pgm( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in PGM format"""
+        return check_image_type( filename, ['PGM'], image )
+
+class Eps( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in eps format."""
+        return check_image_type( filename, ['EPS'], image )        
+
+
+class Rast( Image ):
+    def sniff(self, filename, image=None):
+        """Determine if the file is in rast format"""
+        return check_image_type( filename, ['RAST'], image )
class Pdf( Image ):
     def sniff(self, filename):
-        """Determine if the file is in pdf format.
-        """
+        """Determine if the file is in pdf format."""
         headers = get_headers(filename, None, 1)
         try:
             if headers[0][0].startswith("%PDF"):
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/util/image_util.py	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,76 @@
+"""
+Provides utilities for working with image files.
+"""
+import logging, imghdr
+
+try:
+    import Image as PIL
+except ImportError:
+    try:
+        from PIL import Image as PIL
+    except:
+        PIL = None
+
+log = logging.getLogger(__name__)
+
+def image_type( filename, image=None ):
+    format = ''
+    if PIL is not None:
+        if image is not None:
+            format = image.format
+        else:
+            try:
+                im = PIL.open( filename )
+                format = im.format
+                im.close()
+            except:
+                return False
+    else:
+        format = imghdr.what( filename )
+        if format is not None:
+            format = format.upper()
+        else:
+            return False
+    return format
+def check_image_type( filename, types, image=None ):
+    format = image_type( filename, image )
+    # First check if we can  use PIL        
+    if format in types:
+        return True
+    return False
+def get_image_ext ( file_path, image ):
+    #determine ext
+    format = image_type( file_path, image )    
+    if format in [ 'JPG','JPEG' ]:
+        return 'jpg'
+    if format == 'PNG':
+        return 'png'
+    if format == 'TIFF':
+        return 'tiff'
+    if format == 'BMP':
+        return 'bmp'
+    if format == 'GIF':
+        return 'gif'
+    if format == 'IM':
+        return 'im'
+    if format == 'PCD':
+        return 'pcd'
+    if format == 'PCX':
+        return 'pcx'
+    if format == 'PPM':
+        return 'ppm'
+    if format == 'PSD':
+        return 'psd'
+    if format == 'XBM':
+        return 'xbm'
+    if format == 'XPM':
+        return 'xpm'
+    if format == 'RGB':
+        return 'rgb'
+    if format == 'PBM':
+        return 'pbm'
+    if format == 'PGM':
+        return 'pgm'
+    if format == 'EPS':
+        return 'eps'
+    return None
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5_mult_liftover_mapped.bed	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,132 @@
+chr7	116197893	116197920	CCDS5763.1_cds_0_0_chr7_115444713_f	1	+
+chr7	116222929	116223015	CCDS5763.1_cds_1_0_chr7_115468539_f	1	+
+chr7	116237938	116238188	CCDS5763.1_cds_2_0_chr7_115483025_f	1	+
+chr7	116239076	116239412	CCDS5763.1_cds_3_0_chr7_115484166_f	1	+
+chr7	116240675	116240891	CCDS5763.1_cds_4_0_chr7_115485765_f	1	+
+chr7	116241233	116241396	CCDS5763.1_cds_5_0_chr7_115486323_f	1	+
+chr7	116246193	116246382	CCDS5763.1_cds_6_0_chr7_115491299_f	1	+
+chr7	116222929	116223015	CCDS5764.1_cds_0_0_chr7_115468539_f	1	+
+chr7	116237938	116238188	CCDS5764.1_cds_1_0_chr7_115483025_f	1	+
+chr7	116239076	116239412	CCDS5764.1_cds_2_0_chr7_115484166_f	1	+
+chr7	116240675	116240891	CCDS5764.1_cds_3_0_chr7_115485765_f	1	+
+chr7	116241233	116241396	CCDS5764.1_cds_4_0_chr7_115486323_f	1	+
+chr7	116246193	116246382	CCDS5764.1_cds_5_0_chr7_115491299_f	1	+
+chr7	116495075	116495225	CCDS5766.1_cds_0_0_chr7_115733787_f	1	+
+chr7	116495546	116495734	CCDS5766.1_cds_1_0_chr7_115734265_f	1	+
+chr7	116501260	116501411	CCDS5766.1_cds_2_0_chr7_115739976_f	1	+
+chr7	116495075	116495225	CCDS5765.1_cds_0_0_chr7_115733787_f	1	+
+chr7	116501260	116501449	CCDS5765.1_cds_1_0_chr7_115739976_f	1	+
+chr7	116522088	116522118	CCDS5767.1_cds_0_0_chr7_115759068_f	1	+
+chr7	116523550	116523715	CCDS5767.1_cds_1_0_chr7_115760530_f	1	+
+chr7	116562770	116563112	CCDS5767.1_cds_2_0_chr7_115792951_f	1	+
+chr7	116872904	116872943	CCDS5768.1_cds_0_0_chr7_116096617_f	1	+
+chr7	116899050	116899114	CCDS5768.1_cds_1_0_chr7_116122132_f	1	+
+chr7	116903933	116903985	CCDS5768.1_cds_2_0_chr7_116126999_f	1	+
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+chr7	116915110	116915317	CCDS5768.1_cds_4_0_chr7_116138182_f	1	+
+chr7	116917198	116917278	CCDS5768.1_cds_5_0_chr7_116140268_f	1	+
+chr7	116921242	116921321	CCDS5768.1_cds_6_0_chr7_116144238_f	1	+
+chr7	116923078	116923150	CCDS5768.1_cds_7_0_chr7_116146074_f	1	+
+chr7	116927214	116927277	CCDS5768.1_cds_8_0_chr7_116150065_f	1	+
+chr7	116928880	116929021	CCDS5768.1_cds_9_0_chr7_116151732_f	1	+
+chr7	116964784	116964932	CCDS5770.1_cds_0_0_chr7_116187546_f	1	+
+chr7	117108894	117108977	CCDS5770.1_cds_1_0_chr7_116333767_f	1	+
+chr7	117128694	117128854	CCDS5770.1_cds_2_0_chr7_116353566_f	1	+
+chr7	117138899	117138954	CCDS5770.1_cds_3_0_chr7_116363798_f	1	+
+chr7	117139597	117139713	CCDS5770.1_cds_4_0_chr7_116364496_f	1	+
+chr7	117140988	117141064	CCDS5770.1_cds_5_0_chr7_116365890_f	1	+
+chr7	117143259	117143328	CCDS5770.1_cds_6_0_chr7_116368129_f	1	+
+chr7	117145226	117145381	CCDS5770.1_cds_7_0_chr7_116370086_f	1	+
+chr7	117147574	117147672	CCDS5770.1_cds_8_0_chr7_116372440_f	1	+
+chr7_random	2679423	2679538	CCDS5770.1_cds_9_0_chr7_116404867_f	1	+
+chr7	117201671	117201751	CCDS5770.1_cds_10_0_chr7_116423326_f	1	+
+chr7	117203227	117203330	CCDS5770.1_cds_11_0_chr7_116424839_f	1	+
+chr7	117222109	117222260	CCDS5770.1_cds_12_0_chr7_116443792_f	1	+
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+chr7	116964784	116964932	CCDS5769.1_cds_0_0_chr7_116187546_f	1	+
+chr7	117108894	117108977	CCDS5769.1_cds_1_0_chr7_116333767_f	1	+
+chr7	117128694	117128854	CCDS5769.1_cds_2_0_chr7_116353566_f	1	+
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+chr7	117147574	117147672	CCDS5769.1_cds_7_0_chr7_116372440_f	1	+
+chr7_random	2679423	2679538	CCDS5769.1_cds_8_0_chr7_116404867_f	1	+
+chr7	117201671	117201751	CCDS5769.1_cds_9_0_chr7_116423326_f	1	+
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+chr7	117241962	117242058	CCDS5769.1_cds_14_0_chr7_116463767_f	1	+
+chr7	117291331	117291561	CCDS5771.1_cds_0_0_chr7_116512160_r	1	-
+chr7	117310742	117311007	CCDS5771.1_cds_1_0_chr7_116531617_r	1	-
+chr7	117328536	117328629	CCDS5771.1_cds_2_0_chr7_116549076_r	1	-
+chr7	117333743	117333970	CCDS5771.1_cds_3_0_chr7_116554572_r	1	-
+chr7	117336084	117336167	CCDS5771.1_cds_4_0_chr7_116556912_r	1	-
+chr7	117382797	117382950	CCDS5772.1_cds_0_0_chr7_116597601_r	1	-
+chr7	117386552	117386666	CCDS5772.1_cds_1_0_chr7_116601357_r	1	-
+chr7	117387812	117387919	CCDS5772.1_cds_2_0_chr7_116602617_r	1	-
+chr7	117397672	117397782	CCDS5772.1_cds_3_0_chr7_116613943_r	1	-
+chr7	117398745	117398802	CCDS5772.1_cds_4_0_chr7_116615016_r	1	-
+chr7	117399808	117399884	CCDS5772.1_cds_5_0_chr7_116616074_r	1	-
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+chr7	117403442	117403554	CCDS5772.1_cds_8_0_chr7_116619703_r	1	-
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+chr7	117444948	117445048	CCDS5772.1_cds_11_0_chr7_116660841_r	1	-
+chr7	117445468	117445573	CCDS5772.1_cds_12_0_chr7_116661361_r	1	-
+chr7	117499706	117499759	CCDS5773.1_cds_0_0_chr7_116714100_f	1	+
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+chr7	117556111	117556237	CCDS5773.1_cds_6_0_chr7_116770553_f	1	+
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+chr7	117674548	117674638	CCDS5773.1_cds_23_0_chr7_116886847_f	1	+
+chr7	117686685	117686858	CCDS5773.1_cds_24_0_chr7_116898693_f	1	+
+chr7	117687456	117687562	CCDS5773.1_cds_25_0_chr7_116899464_f	1	+
+chr7	117688902	117689103	CCDS5773.1_cds_26_0_chr7_116900913_f	1	+
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+chr7	117741224	117741326	CCDS5774.1_cds_1_0_chr7_116952023_r	1	-
+chr7	117743450	117743638	CCDS5774.1_cds_4_0_chr7_116958552_r	1	-
+chr7	117743957	117744164	CCDS5774.1_cds_5_0_chr7_116959057_r	1	-
+chr7	117746996	117747175	CCDS5774.1_cds_6_0_chr7_116962094_r	1	-
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+chr7	117764699	117764799	CCDS5774.1_cds_9_0_chr7_116979836_r	1	-
+chr7	117764881	117764968	CCDS5774.1_cds_10_0_chr7_116980018_r	1	-
+chr7	117775103	117775183	CCDS5774.1_cds_11_0_chr7_116990560_r	1	-
+chr7	117776423	117776519	CCDS5774.1_cds_12_0_chr7_116991880_r	1	-
+chr7	117779436	117779712	CCDS5774.1_cds_13_0_chr7_116994440_r	1	-
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+chr7	117799369	117799520	CCDS5774.1_cds_16_0_chr7_117014446_r	1	-
+chr7	117801790	117801890	CCDS5774.1_cds_17_0_chr7_117016867_r	1	-
+chr7	117803186	117803390	CCDS5774.1_cds_18_0_chr7_117018256_r	1	-
+chr7	117810065	117811719	CCDS5774.1_cds_19_0_chr7_117025133_r	1	-
+chr7	117829639	117829865	CCDS5774.1_cds_20_0_chr7_117044770_r	1	-
+chr7	117880732	117880840	CCDS5774.1_cds_21_0_chr7_117095214_r	1	-
+chr7	117893163	117893244	CCDS5774.1_cds_22_0_chr7_117107340_r	1	-
+chr5	133682646	133682808	CCDS4149.1_cds_0_0_chr5_131424299_f	1	+
+chr5	133682906	133682948	CCDS4149.1_cds_1_0_chr5_131424559_f	1	+
+chr5	133684249	133684339	CCDS4149.1_cds_2_0_chr5_131425904_f	1	+
+chr5	133684463	133684505	CCDS4149.1_cds_3_0_chr5_131426118_f	1	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5_mult_liftover_unmapped.bed	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,4 @@
+#Deleted in new
+chr7	116953508	116953641	CCDS5774.1_cds_2_0_chr7_116953509_r	0	-
+#Deleted in new
+chr7	116955071	116955135	CCDS5774.1_cds_3_0_chr7_116955072_r	0	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_liftover_mapped.bed	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,86 @@
+chr1	Cufflinks	transcript	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_liftover_unmapped.bed	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,28 @@
+# Deleted in new
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1	Cufflinks	exon	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1	Cufflinks	exon	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1	Cufflinks	exon	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_mult_liftover_mapped.bed	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,92 @@
+chr1	Cufflinks	transcript	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3162123	3162179	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	exon	3162123	3162179	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	transcript	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3161752	3162025	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	exon	3161752	3162025	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	transcript	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3109449	3109512	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	exon	3109449	3109512	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	transcript	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_mult_liftover_unmapped.bed	Thu Jul 28 08:22:22 2011 -0400
@@ -0,0 +1,16 @@
+# Deleted in new
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
--- a/test/functional/test_get_data.py	Thu Jul 28 08:22:07 2011 -0400
+++ b/test/functional/test_get_data.py	Thu Jul 28 08:22:22 2011 -0400
@@ -124,7 +124,7 @@
         self.upload_file( '454Score.png' )
         hda = get_latest_hda()
         assert hda is not None, "Problem retrieving hda from database"
-        self.check_history_for_string( "The uploaded file contains inappropriate content" )
+        self.check_history_for_string( "454Score.png" )
     def test_0055_upload_file( self ):
         """Test uploading lped composite datatype file, manually setting the file format"""
         # Logged in as admin_user
--- a/tools/data_source/upload.py	Thu Jul 28 08:22:07 2011 -0400
+++ b/tools/data_source/upload.py	Thu Jul 28 08:22:22 2011 -0400
@@ -14,9 +14,18 @@
 from galaxy.datatypes.images import Pdf
 from galaxy.datatypes.registry import Registry
 from galaxy import util
+from galaxy.datatypes.util.image_util import *
 from galaxy.util.json import *
try:
+    import Image as PIL
+except ImportError:
+    try:
+        from PIL import Image as PIL
+    except:
+        PIL = None
+
+try:
     import bz2
 except:
     bz2 = None
@@ -51,16 +60,12 @@
         return d
 def check_bam( file_path ):
     return Bam().sniff( file_path )
-
 def check_sff( file_path ):
     return Sff().sniff( file_path )
-
 def check_pdf( file_path ):
     return Pdf().sniff( file_path )
-
 def check_bigwig( file_path ):
     return BigWig().sniff( file_path )
-
 def check_bigbed( file_path ):
     return BigBed().sniff( file_path )
 def parse_outputs( args ):
@@ -102,8 +107,16 @@
             dataset.is_multi_byte = util.is_multi_byte( codecs.open( dataset.path, 'r', 'utf-8' ).read( 100 ) )
         except UnicodeDecodeError, e:
             dataset.is_multi_byte = False
+    # Is dataset an image?
+    image = check_image( dataset.path )
+    if image:
+        if not PIL:
+            image = None
+        # get_image_ext() returns None if nor a supported Image type
+        ext = get_image_ext( dataset.path, image )
+        data_type = ext
     # Is dataset content multi-byte?
-    if dataset.is_multi_byte:
+    elif dataset.is_multi_byte:
         data_type = 'multi-byte char'
         ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
     # Is dataset content supported sniffable binary?
@@ -122,7 +135,7 @@
     elif check_bigbed( dataset.path ):
         ext = 'bigbed'
         data_type = 'bigbed'
-    else:
+    if not data_type:
         # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
         is_gzipped, is_valid = check_gzip( dataset.path )
         if is_gzipped and not is_valid:
@@ -314,7 +327,6 @@
     if datatype.dataset_content_needs_grooming( output_path ):
         # Groom the dataset content if necessary
         datatype.groom_dataset_content( output_path )
-
 def add_composite_file( dataset, registry, json_file, output_path, files_path ):
         if dataset.composite_files:
             os.mkdir( files_path )
--- a/tools/extract/liftOver_wrapper.py	Thu Jul 28 08:22:07 2011 -0400
+++ b/tools/extract/liftOver_wrapper.py	Thu Jul 28 08:22:22 2011 -0400
@@ -34,15 +34,27 @@
     out_handle.close()
     return fname
-if len( sys.argv ) != 7:
-    stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey minMatch" )
+if len( sys.argv ) < 9:
+    stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey infile_type minMatch multiple <minChainT><minChainQ><minSizeQ>" )
infile = sys.argv[1]
 outfile1 = sys.argv[2]
 outfile2 = sys.argv[3]
 in_dbkey = sys.argv[4]
 mapfilepath = sys.argv[5]
-minMatch = sys.argv[6]
+infile_type = sys.argv[6]
+gff_option = ""
+if infile_type == "gff":
+    gff_option = "-gff "
+minMatch = sys.argv[7]
+multiple = int(sys.argv[8])
+multiple_option = ""
+if multiple:
+    minChainT = sys.argv[9]
+    minChainQ = sys.argv[10]
+    minSizeQ = sys.argv[11]
+    multiple_option = " -multiple -minChainT=%s -minChainQ=%s -minSizeQ=%s " %(minChainT,minChainQ,minSizeQ)
+
 try:
     assert float(minMatch)
 except:
@@ -55,7 +67,8 @@
     stop_err( "%s mapping is not currently available."  % ( mapfilepath.split('/')[-1].split('.')[0] ) )
safe_infile = safe_bed_file(infile)
-cmd_line = "liftOver -minMatch=" + str(minMatch) + " " + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null"
+cmd_line = "liftOver " + gff_option + "-minMatch=" + str(minMatch) + multiple_option + " "  + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null"
+
 try:
     # have to nest try-except in try-finally to handle 2.4
     try:
--- a/tools/extract/liftOver_wrapper.xml	Thu Jul 28 08:22:07 2011 -0400
+++ b/tools/extract/liftOver_wrapper.xml	Thu Jul 28 08:22:22 2011 -0400
@@ -1,8 +1,21 @@
-<tool id="liftOver1" name="Convert genome coordinates" version="1.0.2">
+<tool id="liftOver1" name="Convert genome coordinates" version="1.0.3"><description> between assemblies and genomes</description>
-  <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>
+  <command interpreter="python">
+  liftOver_wrapper.py 
+  $input 
+  "$out_file1" 
+  "$out_file2" 
+  $dbkey 
+  $to_dbkey 
+  #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__) or isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gtf').__class__):
+        "gff"
+  #else:
+        "interval"
+  #end if
+  $minMatch ${multiple.choice} ${multiple.minChainT} ${multiple.minChainQ} ${multiple.minSizeQ}
+  </command><inputs>
-    <param format="interval" name="input" type="data" label="Convert coordinates of">
+    <param format="interval,gff,gtf" name="input" type="data" label="Convert coordinates of"><validator type="unspecified_build" /><validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." /></param>
@@ -14,7 +27,23 @@
         <filter type="data_meta" ref="input" key="dbkey" column="0" /></options></param> 
-    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" />
+    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" />
+    <conditional name="multiple">
+	    <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes">
+	    	<option value="0" selected="true">No</option>
+	    	<option value="1">Yes</option>
+		</param>
+		<when value="0">
+		    <param name="minSizeQ" type="hidden" value="0" />
+    		<param name="minChainQ" type="hidden" value="0" />
+    		<param name="minChainT" type="hidden" value="0" />
+    	</when>
+    	<when value="1">
+    	    <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/>
+    		<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/>
+    		<param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
+    	</when>
+	</conditional></inputs><outputs><data format="input" name="out_file1" label="${tool.name} on ${on_string} [ MAPPED COORDINATES ]">
@@ -37,9 +66,40 @@
       <param name="input" value="5.bed" dbkey="hg18" ftype="bed" /><param name="to_dbkey" value="panTro2" /><param name="minMatch" value="0.95" />
+      <param name="choice" value="0" /><output name="out_file1" file="5_liftover_mapped.bed"/><output name="out_file2" file="5_liftover_unmapped.bed"/></test>
+    <test>
+      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
+      <param name="to_dbkey" value="panTro2" />
+      <param name="minMatch" value="0.10" />
+      <param name="choice" value="1" />
+      <param name="minSizeQ" value="0" />
+      <param name="minChainQ" value="500" />
+      <param name="minChainT" value="500" />
+      <output name="out_file1" file="5_mult_liftover_mapped.bed"/>
+      <output name="out_file2" file="5_mult_liftover_unmapped.bed"/>
+    </test>
+    <test>
+      <param name="input" value="cuffcompare_in1.gtf" dbkey="hg18" ftype="gtf" />
+      <param name="to_dbkey" value="panTro2" />
+      <param name="minMatch" value="0.95" />
+      <param name="choice" value="0" />
+      <output name="out_file1" file="cuffcompare_in1_liftover_mapped.bed"/>
+      <output name="out_file2" file="cuffcompare_in1_liftover_unmapped.bed"/>
+    </test>
+    <test>
+      <param name="input" value="cuffcompare_in1.gtf" dbkey="hg18" ftype="gtf" />
+      <param name="to_dbkey" value="panTro2" />
+      <param name="minMatch" value="0.10" />
+      <param name="choice" value="1" />
+      <param name="minSizeQ" value="0" />
+      <param name="minChainQ" value="500" />
+      <param name="minChainT" value="500" />
+      <output name="out_file1" file="cuffcompare_in1_mult_liftover_mapped.bed"/>
+      <output name="out_file2" file="cuffcompare_in1_mult_liftover_unmapped.bed"/>
+    </test></tests><help>
 .. class:: warningmark
@@ -48,7 +108,7 @@
.. class:: warningmark
-This tool will only work on interval datasets with chromosome in column 1,
+This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,
 start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
 and track and browser lines will be ignored, but if other non-interval lines
 are present the tool will return empty output datasets.
@@ -59,7 +119,11 @@
**What it does**
-This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. 
+This tool is based on the LiftOver utility and Chain track from `the UC Santa Cruz Genome Browser`__.
+
+It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. 
+
+ .. __: http://genome.ucsc.edu/
-----
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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