[hg] galaxy 3313: Added UI support for annotating histories, HDA...

2 Feb 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/068d572a2bf8
changeset: 3313:068d572a2bf8
user:      jeremy goecks <jeremy.goecks@emory.edu>
date:      Mon Feb 01 16:30:18 2010 -0500
description:
Added UI support for annotating histories, HDAs, workflows, and workflow steps. Numerous small changes as well: (a) added an 'edit workflow attributes' to workflow editor; (b) added 'Edit tags and Annotation' area to history panel; (c) added generic javascript method to ajax text updates. Also fixed public URL column bug.

diffstat:

 lib/galaxy/web/base/controller.py                      |  57 ++++++++++-
 lib/galaxy/web/controllers/history.py                  |  13 ++-
 lib/galaxy/web/controllers/root.py                     |   4 +
 lib/galaxy/web/controllers/workflow.py                 |  67 +++++++++++-
 static/june_2007_style/base.css.tmpl                   |  42 +++++++
 static/june_2007_style/blue/base.css                   |   7 +
 static/june_2007_style/blue/history.css                |   7 -
 static/june_2007_style/history.css.tmpl                |  40 -------
 static/scripts/galaxy.base.js                          |  44 ++++++++
 static/scripts/galaxy.workflow_editor.canvas.js        |   5 +-
 static/scripts/packed/galaxy.base.js                   |   2 +-
 static/scripts/packed/galaxy.workflow_editor.canvas.js |   2 +-
 templates/dataset/edit_attributes.mako                 |  39 ++++--
 templates/grid_base.mako                               |   2 +-
 templates/root/history.mako                            |  80 ++++++++------
 templates/sharing_base.mako                            |   8 +-
 templates/tagging_common.mako                          |  10 +-
 templates/workflow/edit_attributes.mako                |  66 ++++++++++++
 templates/workflow/editor.mako                         |  96 +++++++++++++++--
 19 files changed, 461 insertions(+), 130 deletions(-)

diffs (993 lines):

diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/base/controller.py

--- a/lib/galaxy/web/base/controller.py	Mon Feb 01 13:34:44 2010 -0500
+++ b/lib/galaxy/web/base/controller.py	Mon Feb 01 16:30:18 2010 -0500
@@ -25,9 +25,13 @@
 # Item's public URL based on username and slug.
 class PublicURLColumn( grids.TextColumn ):
     def get_link( self, trans, grid, item ):
-        if item.user.username:
+        if item.user.username and item.slug:
             return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug )
-        else:
+        elif not item.user.username:
+            # TODO: provide link to set username.
+            return None
+        elif not item.user.slug:
+            # TODO: provide link to set slg
             return None
         
 class BaseController( object ):
@@ -73,6 +77,55 @@
             item_class = None
         return item_class
         
+    def get_item_annotation_str( self, db_session, user, item ):
+        """ Returns a user's annotation string for an item. """
+        annotation_obj = self.get_item_annotation_obj( db_session, user, item )
+        if annotation_obj:
+            return annotation_obj.annotation
+        return None
+        
+    def get_item_annotation_obj( self, db_session, user, item ):
+        """ Returns a user's annotation object for an item. """
+        # Get annotation association. TODO: we could replace this eval() with a long if/else stmt, but this is more general without sacrificing
+        try:
+            annotation_assoc_class = eval( "model.%sAnnotationAssociation" % item.__class__.__name__ )
+        except:
+            # Item doesn't have an annotation association class and cannot be annotated.
+            return False
+        
+        # Get annotation association object.
+        annotation_assoc = db_session.query( annotation_assoc_class ).filter_by( user=user )
+        if item.__class__ == model.History:
+            annotation_assoc = annotation_assoc.filter_by( history=item )
+        elif item.__class__ == model.HistoryDatasetAssociation:
+            annotation_assoc = annotation_assoc.filter_by( hda=item )
+        elif item.__class__ == model.StoredWorkflow:
+            annotation_assoc = annotation_assoc.filter_by( stored_workflow=item )
+        elif item.__class__ == model.WorkflowStep:
+            annotation_assoc = annotation_assoc.filter_by( workflow_step=item )
+        return annotation_assoc.first()
+        
+    def add_item_annotation( self, trans, item, annotation ):
+        """ Add or update an item's annotation; a user can only have a single annotation for an item. """
+
+        # Get/create annotation association object.
+        annotation_assoc = self.get_item_annotation_obj( trans.sa_session, trans.get_user(), item )
+        if not annotation_assoc:
+            # Create association.
+            # TODO: we could replace this eval() with a long if/else stmt, but this is more general without sacrificing
+            try:
+                annotation_assoc_class = eval( "model.%sAnnotationAssociation" % item.__class__.__name__ )
+            except:
+                # Item doesn't have an annotation association class and cannot be annotated.
+                return False
+            annotation_assoc = annotation_assoc_class()
+            item.annotations.append( annotation_assoc )
+            annotation_assoc.user = trans.get_user()
+
+        # Set annotation.
+        annotation_assoc.annotation = annotation
+        return True
+        
 Root = BaseController
 
 class SharingStatusColumn( grids.GridColumn ):
diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py	Mon Feb 01 13:34:44 2010 -0500
+++ b/lib/galaxy/web/controllers/history.py	Mon Feb 01 16:30:18 2010 -0500
@@ -353,7 +353,7 @@
         return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] )
     @web.expose
     def rename_async( self, trans, id=None, new_name=None ):
-        history = trans.sa_session.query( model.History ).get( id )
+        history = self.get_history( trans, id )
         # Check that the history exists, and is either owned by the current
         # user (if logged in) or the current history
         assert history is not None
@@ -365,6 +365,17 @@
         history.name = new_name
         trans.sa_session.add( history )
         trans.sa_session.flush()
+        
+    @web.expose
+    @web.require_login( "use Galaxy histories" )
+    def annotate_async( self, trans, id, new_annotation=None, **kwargs ):
+        history = self.get_history( trans, id )
+        if new_annotation:
+            self.add_item_annotation( trans, history, new_annotation )
+            trans.sa_session.flush()
+            return
+        else:
+            return "failed"
     
     @web.expose
     @web.json
diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/controllers/root.py
--- a/lib/galaxy/web/controllers/root.py	Mon Feb 01 13:34:44 2010 -0500
+++ b/lib/galaxy/web/controllers/root.py	Mon Feb 01 16:30:18 2010 -0500
@@ -78,6 +78,7 @@
                 query = query.filter( model.HistoryDatasetAssociation.deleted == False )
             return trans.stream_template_mako( "root/history.mako",
                                                history = history,
+                                               annotation = self.get_item_annotation_str( trans.sa_session, trans.get_user(), history ),
                                                datasets = query.all(),
                                                hda_id = hda_id,
                                                show_deleted = show_deleted )
@@ -304,6 +305,8 @@
                             else:
                                 setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
                     data.datatype.after_setting_metadata( data )
+                    self.add_item_annotation( trans, data, params.annotation )
+                    
                 else:
                     msg = ' (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.)'
                 trans.sa_session.flush()
@@ -383,6 +386,7 @@
                 messagetype = 'done'
             return trans.fill_template( "/dataset/edit_attributes.mako",
                                         data=data,
+                                        data_annotation=self.get_item_annotation_str( trans.sa_session, trans.get_user(), data ),
                                         datatypes=ldatatypes,
                                         current_user_roles=current_user_roles,
                                         all_roles=all_roles,
diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py	Mon Feb 01 13:34:44 2010 -0500
+++ b/lib/galaxy/web/controllers/workflow.py	Mon Feb 01 16:30:18 2010 -0500
@@ -303,6 +303,28 @@
             session.flush()
             # Redirect to load galaxy frames.
             return trans.response.send_redirect( url_for( controller='workflow' ) )
+            
+    @web.expose
+    @web.require_login( "use Galaxy workflows" )
+    def edit_attributes( self, trans, id, **kwargs ):
+        # Get workflow and do error checking.
+        stored = get_stored_workflow( trans, id )
+        if not stored:
+            error( "You do not own this workflow or workflow ID is invalid." )
+            
+        # Update workflow attributes if new values submitted.
+        if 'name' in kwargs:
+            # Rename workflow.
+            stored.name = kwargs[ 'name' ]
+        if 'annotation' in kwargs:
+            # Set workflow annotation.
+            self.add_item_annotation( trans, stored, kwargs[ 'annotation' ] )
+        trans.sa_session.flush()
+        
+        return trans.fill_template( 'workflow/edit_attributes.mako', 
+                                    stored=stored, 
+                                    annotation=self.get_item_annotation_str( trans.sa_session, trans.get_user(), stored ) 
+                                    )
     
     @web.expose
     @web.require_login( "use Galaxy workflows" )
@@ -320,7 +342,29 @@
         else:
             return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \
                 .add_text( "new_name", "Workflow Name", value=stored.name )
-    
+                
+    @web.expose
+    @web.require_login( "use Galaxy workflows" )
+    def rename_async( self, trans, id, new_name=None, **kwargs ):
+        stored = get_stored_workflow( trans, id )
+        if new_name:
+            stored.name = new_name
+            trans.sa_session.flush()
+            return
+        else:
+            return "failed"
+            
+    @web.expose
+    @web.require_login( "use Galaxy workflows" )
+    def annotate_async( self, trans, id, new_annotation=None, **kwargs ):
+        stored = get_stored_workflow( trans, id )
+        if new_annotation:
+            self.add_item_annotation( trans, stored, new_annotation )
+            trans.sa_session.flush()
+            return
+        else:
+            return "failed"
+            
     @web.expose
     @web.require_login( "use Galaxy workflows" )
     def clone( self, trans, id ):
@@ -400,11 +444,11 @@
         """
         if not id:
             error( "Invalid workflow id" )
-        id = trans.security.decode_id( id )
-        return trans.fill_template( "workflow/editor.mako", workflow_id=id )
+        stored = get_stored_workflow( trans, id )
+        return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.get_user(), stored ) )
         
     @web.json
-    def editor_form_post( self, trans, type='tool', tool_id=None, **incoming ):
+    def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ):
         """
         Accepts a tool state and incoming values, and generates a new tool
         form and some additional information, packed into a json dictionary.
@@ -423,7 +467,8 @@
             'data_inputs': module.get_data_inputs(),
             'data_outputs': module.get_data_outputs(),
             'tool_errors': module.get_errors(),
-            'form_html': module.get_config_form()
+            'form_html': module.get_config_form(),
+            'annotation': annotation
         }
         
     @web.json
@@ -445,7 +490,8 @@
             'tooltip': module.get_tooltip(),
             'data_inputs': module.get_data_inputs(),
             'data_outputs': module.get_data_outputs(),
-            'form_html': module.get_config_form()
+            'form_html': module.get_config_form(),
+            'annotation': ""
         }
                 
     @web.json
@@ -477,6 +523,11 @@
                 # FIXME: Frontend should be able to handle workflow messages
                 #        as a dictionary not just the values
                 data['upgrade_messages'][step.order_index] = upgrade_message.values()
+            # Get user annotation.
+            step_annotation = self.get_item_annotation_obj ( trans.sa_session, trans.get_user(), step )
+            annotation_str = ""
+            if step_annotation:
+                annotation_str = step_annotation.annotation
             # Pack attributes into plain dictionary
             step_dict = {
                 'id': step.order_index,
@@ -489,6 +540,7 @@
                 'data_inputs': module.get_data_inputs(),
                 'data_outputs': module.get_data_outputs(),
                 'form_html': module.get_config_form(),
+                'annotation' : annotation_str
             }
             # Connections
             input_connections = step.input_connections
@@ -551,6 +603,9 @@
                 workflow.has_errors = True
             # Stick this in the step temporarily
             step.temp_input_connections = step_dict['input_connections']
+            
+            # Save step annotation.
+            self.add_item_annotation( trans, step, step_dict[ 'annotation' ] )
         # Second pass to deal with connections between steps
         for step in steps:
             # Input connections
diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/base.css.tmpl
--- a/static/june_2007_style/base.css.tmpl	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/june_2007_style/base.css.tmpl	Mon Feb 01 16:30:18 2010 -0500
@@ -656,3 +656,45 @@
     }
 
 }
+
+## Icon buttons.
+
+.icon-button  {
+    width: 16px;
+    height: 16px;
+    display: block;
+    float: left;
+    margin-left: 2px;
+    ## Allow alt text for screen readers
+    text-indent: 20px;
+}
+
+.icon-button.display {
+    -sprite-group: history-buttons;
+    -sprite-image: eye_icon.png;
+}
+
+.icon-button.display:hover {
+    -sprite-group: history-buttons;
+    -sprite-image: eye_icon_dark.png;
+}
+
+.icon-button.delete {
+    -sprite-group: history-buttons;
+    -sprite-image: delete_icon.png;
+}
+
+.icon-button.delete:hover {
+    -sprite-group: history-buttons;
+    -sprite-image: delete_icon_dark.png;
+}
+
+.icon-button.edit {
+    -sprite-group: history-buttons;
+    -sprite-image: pencil_icon.png;
+}
+
+.icon-button.edit:hover {
+    -sprite-group: history-buttons;
+    -sprite-image: pencil_icon_dark.png;
+}
\ No newline at end of file
diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/blue/base.css
--- a/static/june_2007_style/blue/base.css	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/june_2007_style/blue/base.css	Mon Feb 01 16:30:18 2010 -0500
@@ -110,3 +110,10 @@
 .text-content fieldset{border-color:#ccc;border:1px solid #ccc;}
 .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;}
 .text-content th,.text-content td{padding:.8em;}
+.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;}
+.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -52px;}
+.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -78px;}
+.icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;}
+.icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;}
+.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;}
+.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;}
\ No newline at end of file
diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/blue/history.css
--- a/static/june_2007_style/blue/history.css	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/june_2007_style/blue/history.css	Mon Feb 01 16:30:18 2010 -0500
@@ -22,13 +22,6 @@
 div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;}
 div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;}
 div.historyItemButtons{float:right;}
-.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;}
-.icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;}
-.icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;}
-.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -52px;}
-.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -78px;}
-.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;}
-.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;}
 div.historyItemBody div{padding-top:2px;}
 pre.peek{background:white;color:black;width:100%;overflow:auto;}
 pre.peek th{color:white;background:#023858;}
diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/history.css.tmpl
--- a/static/june_2007_style/history.css.tmpl	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/june_2007_style/history.css.tmpl	Mon Feb 01 16:30:18 2010 -0500
@@ -120,46 +120,6 @@
     float: right;
 }
 
-.icon-button  {
-    width: 16px;
-    height: 16px;
-    display: block;
-    float: left;
-    margin-left: 2px;
-    ## Allow alt text for screen readers
-    text-indent: 20px;
-}
-
-.icon-button.display {
-    -sprite-group: history-buttons;
-    -sprite-image: eye_icon.png;
-}
-
-.icon-button.display:hover {
-    -sprite-group: history-buttons;
-    -sprite-image: eye_icon_dark.png;
-}
-
-.icon-button.edit {
-    -sprite-group: history-buttons;
-    -sprite-image: pencil_icon.png;
-}
-
-.icon-button.edit:hover {
-    -sprite-group: history-buttons;
-    -sprite-image: pencil_icon_dark.png;
-}
-
-.icon-button.delete {
-    -sprite-group: history-buttons;
-    -sprite-image: delete_icon.png;
-}
-
-.icon-button.delete:hover {
-    -sprite-group: history-buttons;
-    -sprite-image: delete_icon_dark.png;
-}
-
 div.historyItemBody div {
     padding-top: 2px;
 }
diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/scripts/galaxy.base.js	Mon Feb 01 16:30:18 2010 -0500
@@ -207,3 +207,47 @@
         });
     }
 } // end replace_dbkey_select()
+
+//
+// Edit and save text asynchronously.
+// 
+function async_save_text(click_to_edit_elt, text_elt_id, save_url, text_parm_name, use_textarea, num_rows)
+{
+    $("#" + click_to_edit_elt).click( function() {
+        var old_text = $("#" + text_elt_id).text()
+        if (use_textarea)
+            var t = $("<textarea rows='" + num_rows + "'>" + old_text + "</textarea>" );
+        else
+            var t = $("<input type='text' value='" + old_text + "'></input>" );
+        t.blur( function() {
+            $(this).remove();
+            $("#" + text_elt_id).show();
+        });
+        t.keyup( function( e ) {
+            if ( e.keyCode == 27 ) {
+                // Escape key
+                $(this).trigger( "blur" );
+            } else if ( e.keyCode == 13 ) {
+                // Enter key
+                new_text = this.value;
+                $(this).trigger( "blur" );
+                var ajax_data = new Object();
+                ajax_data[text_parm_name] = new_text;
+                $.ajax({
+                    url: save_url,
+                    data: ajax_data,
+                    error: function() { alert( "Text editing for elt " + text_elt_id + " failed" ) },
+                    success: function() {
+                        $("#" + text_elt_id).text( new_text );
+                    }
+                });
+            }
+        });
+        $("#" + text_elt_id).hide();
+        t.insertAfter( $("#" + text_elt_id) );
+        t.focus();
+        t.select();
+        return false;
+    });
+    
+}
diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/galaxy.workflow_editor.canvas.js
--- a/static/scripts/galaxy.workflow_editor.canvas.js	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/scripts/galaxy.workflow_editor.canvas.js	Mon Feb 01 16:30:18 2010 -0500
@@ -272,6 +272,7 @@
         this.tool_state = data.tool_state;
         this.tool_errors = data.tool_errors;
         this.tooltip = data.tooltip ? data.tooltip : ""
+        this.annotation = data.annotation;
         
         if ( this.tool_errors ) {
             f.addClass( "tool-node-error" );
@@ -306,6 +307,7 @@
             node = this;
         this.tool_state = data.tool_state;
         this.form_html = data.form_html;
+        this.annotation = data.annotation;
         this.tool_errors = data.tool_errors;
         if ( this.tool_errors ) {
                 el.addClass( "tool-node-error" );
@@ -405,7 +407,8 @@
                 tool_state : node.tool_state,
                 tool_errors : node.tool_errors,
                 input_connections : input_connections,
-                position : $(node.element).position()
+                position : $(node.element).position(),
+                annotation: node.annotation
             };
             nodes[ node.id ] = node_data;
         });
diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/scripts/packed/galaxy.base.js	Mon Feb 01 16:30:18 2010 -0500
@@ -1,1 +1,1 @@
-$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t
 op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element
  in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.
 attr("value","?")}}}})}};
\ No newline at end of file
+$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t
 op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element
  in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.
 attr("value","?")}}}})}};function async_save_text(d,c,a,e,f,b){$("#"+d).click(function(){var h=$("#"+c).text();if(f){var g=$("<textarea rows='"+b+"'>"+h+"</textarea>")}else{var g=$("<input type='text' value='"+h+"'></input>")}g.blur(function(){$(this).remove();$("#"+c).show()});g.keyup(function(j){if(j.keyCode==27){$(this).trigger("blur")}else{if(j.keyCode==13){new_text=this.value;$(this).trigger("blur");var i=new Object();i[e]=new_text;$.ajax({url:a,data:i,error:function(){alert("Text editing for elt "+c+" failed")},success:function(){$("#"+c).text(new_text)}})}}});$("#"+c).hide();g.insertAfter($("#"+c));g.focus();g.select();return false})};
\ No newline at end of file
diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/packed/galaxy.workflow_editor.canvas.js
--- a/static/scripts/packed/galaxy.workflow_editor.canvas.js	Mon Feb 01 13:34:44 2010 -0500
+++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js	Mon Feb 01 16:30:18 2010 -0500
@@ -1,1 +1,1 @@
-function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a)
 {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;
 this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov
 er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret
 urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b
 .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.ext
 ension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal")
 .each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g
 ,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear
 _active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f
  in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Mat
 h.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h
 ;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.red
 raw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.time
 out=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent(
 ).offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-
 k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
+function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a)
 {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;
 this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov
 er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret
 urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b
 .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.ext
 ension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.annotation=f.annotation;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))})
 ;g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,
 function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$(
 "#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}
 }if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();
 var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/l
 oading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(thi
 s).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.mi
 n(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b
 .cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b)
 {k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/dataset/edit_attributes.mako
--- a/templates/dataset/edit_attributes.mako	Mon Feb 01 13:34:44 2010 -0500
+++ b/templates/dataset/edit_attributes.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -58,21 +58,32 @@
                 <div style="clear: both"></div>
             </div>
             %if trans.get_user() is not None:
-			<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" />
-            <div class="form-row">
-                <label>
-                    Tags:
-                </label>
-                <div style="float: left; width: 295px; margin-right: 10px; border-style: inset; border-width: 1px">
-                    <style>
-                        .tag-area {
-                            border: none;
-                        }
-                    </style>
-                    ${render_individual_tagging_element(user=trans.get_user(), tagged_item=data, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")}
+    			<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" />
+                <div class="form-row">
+                    <label>
+                        Tags:
+                    </label>
+                    <div style="float: left; width: 295px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px">
+                        <style>
+                            .tag-area {
+                                border: none;
+                            }
+                        </style>
+                        ${render_individual_tagging_element(user=trans.get_user(), tagged_item=data, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")}
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div>
                 </div>
-                <div style="clear: both"></div>
-            </div>
+                <div class="form-row">                    
+                    <label>
+                        Annotation / Notes:
+                    </label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <textarea name="annotation" cols="40" rows="2">${data_annotation}</textarea>
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="toolParamHelp">Add an annotation or notes to a dataset; annotations are available when a history is viewed.</div>
+                </div>
             %endif
             %for name, spec in data.metadata.spec.items():
                 %if spec.visible:
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/grid_base.mako
--- a/templates/grid_base.mako	Mon Feb 01 13:34:44 2010 -0500
+++ b/templates/grid_base.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -844,7 +844,7 @@
                 ## Item selection column
                 %if show_item_checkboxes:
                     <td style="width: 1.5em;">
-                        <input type="checkbox" id="${encoded_id}" name="id" value="${encoded_id}" class="grid-row-select-checkbox" />
+                        <input type="checkbox" name="id" value="${encoded_id}" id="${encoded_id}" class="grid-row-select-checkbox" />
                     </td>
                 %endif
                 ## Data columns
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/root/history.mako
--- a/templates/root/history.mako	Mon Feb 01 13:34:44 2010 -0500
+++ b/templates/root/history.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -15,7 +15,7 @@
 <meta http-equiv="Pragma" content="no-cache">
 
 ${h.css( "base", "history", "autocomplete_tagging" )}
-${h.js( "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )}
+${h.js( "galaxy.base", "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )}
 
 <script type="text/javascript">
 $(function() {
@@ -42,36 +42,20 @@
         $.jStore.remove("history_expand_state");
     }));
     
-    $("#history-rename").click( function() {
-        var old_name = $("#history-name").text()
-        var t = $("<input type='text' value='" + old_name + "'></input>" );
-        t.blur( function() {
-            $(this).remove();
-            $("#history-name").show();
-        });
-        t.keyup( function( e ) {
-            if ( e.keyCode == 27 ) {
-                // Escape key
-                $(this).trigger( "blur" );
-            } else if ( e.keyCode == 13 ) {
-                // Enter key
-                new_value = this.value;
-                $(this).trigger( "blur" );
-                $.ajax({
-                    url: "${h.url_for( controller='history', action='rename_async', id=history.id )}",
-                    data: { "_": true, new_name: new_value },
-                    error: function() { alert( "Rename failed" ) },
-                    success: function() {
-                        $("#history-name").text( new_value );
-                    }
-                });
-            }
-        });
-        $("#history-name").hide();
-        $("#history-name-area").append( t );
-        t.focus();
-        return false;
-    });
+    // Rename async.
+    async_save_text("history-rename", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name");
+    
+    // Annotation async.
+    // Tag async. Simply have the workflow tag element generate a click on the tag element to activate tagging.
+	$('#workflow-tag').click( function() 
+	{
+	    $('.tag-area').click();
+	    return false;
+	});
+					
+	// Annotate async.
+	async_save_text("history-annotate", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", true, 4);
+    
     // Updater
     updater({
         <% updateable = [data for data in reversed( datasets ) if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]] %>
@@ -266,6 +250,9 @@
 .historyItemBody {
     display: none;
 }
+div.form-row {
+    padding: 5px 5px 5px 0px;
+}
 </style>
 
 <noscript>
@@ -303,12 +290,31 @@
 <%namespace file="history_common.mako" import="render_dataset" />
 
 %if trans.get_user() is not None:
-    <style>
-        .tag-element {
-            margin-bottom: 0.5em;
-        }
-    </style>
-    ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='history.mako' )}
+    <div style="margin: 0px 0px 5px 10px">
+        <a href="#" onclick="$('#tags-and-annotation').toggle('fast')">Edit Tags and Annotation/Notes</a>
+        <div id="tags-and-annotation" style="display: none">    
+            ## Tagging elt.
+            <div class="form-row">
+                <label>Tags:</label>
+                <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div>
+                <style>
+                    .tag-area {
+                        border: none;
+                    }
+                </style>
+                ${render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)}
+                <div style="clear: both"></div>
+            </div>
+        
+            ## Annotation elt.
+            <div id="history-annotation-area" class="form-row">
+       	        <label>Annotation / Notes:</label>
+    		    <div style="float: right"><a id="history-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='annotate_async' )}"></a></div>
+    		    <div id="history-annotation">${annotation}</div>
+                <div style="clear: both"></div>
+    		</div>
+        </div>
+    </div>
 %endif
 
 %if not datasets:
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/sharing_base.mako
--- a/templates/sharing_base.mako	Mon Feb 01 13:34:44 2010 -0500
+++ b/templates/sharing_base.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -67,7 +67,7 @@
 		<div class="indent" style="margin-top: 2em">
 		<h3>Making ${item_class_name} Accessible via Link and Publishing It</h3>
     
-		    <div class="indent">
+		    <div>
 		        %if item.importable:
 					<% 
 						item_status = "accessible via link" 
@@ -75,7 +75,7 @@
 							item_status = item_status + " and published"	
 					%>
 					This ${item_class_name_lc} <strong>${item_status}</strong>. 
-					<div class="indent">
+					<div>
 						<p>Anyone can view and import this ${item_class_name_lc} by visiting the following URL:
 			            <% url = h.url_for( action='display_by_username_and_slug', username=trans.get_user().username, slug=item.slug, qualified=True ) %>
 						<blockquote>
@@ -88,7 +88,7 @@
 					</div>
 		
 					<p>You can:
-					<div class="indent">
+					<div>
 		           	<form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" 
 							method="POST">
 							%if not item.published:
@@ -130,7 +130,7 @@
 
 		<h3>Sharing ${item_class_name} with Specific Users</h3>
 
-		    <div class="indent">
+		    <div>
 		        %if item.users_shared_with:
 
 		            <p>
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/tagging_common.mako
--- a/templates/tagging_common.mako	Mon Feb 01 13:34:44 2010 -0500
+++ b/templates/tagging_common.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -20,7 +20,7 @@
 %endif
 
 ## Render HTML for a list of tags.
-<%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False, tag_type='individual')">
+<%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False, tag_type='individual', render_add_tag_button=True)">
     ## Useful attributes.
     <% 
         num_tags = len( tags )
@@ -79,7 +79,9 @@
                     <input class="tag-input" type='text' size='${input_size}'/>
                 %endif
                 ## Add "add tag" button.
-                <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/>
+                %if render_add_tag_button:
+                    <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/>
+                %endif
             %endif
         </div>
     </div>
@@ -102,7 +104,7 @@
 
 
 ## Render individual tagging element.
-<%def name="render_individual_tagging_element(user=None, tagged_item=None, elt_context=None, use_toggle_link=True, in_form=False, input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable=True)">
+<%def name="render_individual_tagging_element(user=None, tagged_item=None, elt_context=None, use_toggle_link=True, in_form=False, input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable=True, render_add_tag_button=True)">
     ## Useful attributes.
     <%
         # Useful ids.
@@ -114,7 +116,7 @@
     %>
     
     ## Build HTML.
-    ${self.render_tagging_element_html(elt_id, item_tags, editable, use_toggle_link, input_size, in_form)}
+    ${self.render_tagging_element_html(elt_id=elt_id, tags=item_tags, editable=editable, use_toggle_link=use_toggle_link, input_size=input_size, in_form=in_form, render_add_tag_button=render_add_tag_button)}
     
     ## Build script that augments tags using progressive javascript.
     <script type="text/javascript">
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/workflow/edit_attributes.mako
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/workflow/edit_attributes.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -0,0 +1,66 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">${_('Edit Workflow Attributes')}</%def>
+
+<%def name="stylesheets()">
+    ${h.css( "base", "autocomplete_tagging" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+</%def>
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<%def name="body()">
+	<div class="toolForm">
+	    <div class="toolFormTitle">${_('Edit Workflow Attributes')}</div>
+	    <div class="toolFormBody">
+	        <form name="edit_attributes" action="${h.url_for( action='edit_attributes' )}" method="post">
+	            <input type="hidden" name="id" value="${trans.security.encode_id( stored.id )}"/>
+	            <div class="form-row">
+	                <label>
+	                    Name:
+	                </label>
+	                <div style="float: left; width: 225px; margin-right: 10px;">
+	                    <input type="text" name="name" value="${stored.name}" size="30"/>
+	                </div>
+                    <div style="clear: both"></div>
+	            </div>
+				<%namespace file="/tagging_common.mako" import="render_individual_tagging_element" />
+                <div class="form-row">
+                    <label>
+                        Tags:
+                    </label>
+                    <div style="float: left; width: 265px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px">
+                        <style>
+                            .tag-area {
+                                border: none;
+                            }
+                        </style>
+                        ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="25")}
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div>
+                </div>
+                <div class="form-row">                    
+                    <label>
+                        Annotation / Notes:
+                    </label>
+                    <div style="float: left; width: 225px; margin-right: 10px;">
+                        <textarea name="annotation" cols="30" rows="2">${annotation}</textarea>
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="toolParamHelp">Add an annotation notes to a workflow; annotations are available when a workflow is viewed.</div>
+                </div>
+	            <div class="form-row">
+	                <input type="submit" name="save" value="${_('Save')}"/>
+	            </div>
+	        </form>
+		</div>
+	</div>
+</%def>
\ No newline at end of file
diff -r d24f0190c2a8 -r 068d572a2bf8 templates/workflow/editor.mako
--- a/templates/workflow/editor.mako	Mon Feb 01 13:34:44 2010 -0500
+++ b/templates/workflow/editor.mako	Mon Feb 01 16:30:18 2010 -0500
@@ -34,7 +34,9 @@
             "jquery.jstore-all", 
             "json2",
             "galaxy.base",
-            "galaxy.workflow_editor.canvas" )}
+            "galaxy.workflow_editor.canvas",
+			"jquery.autocomplete",
+ 			"autocomplete_tagging")}
 
     <!--[if lt IE 7]>
     <script type='text/javascript'>
@@ -77,7 +79,7 @@
                 // Load workflow definition
                 $.ajax( {
                     url: "${h.url_for( action='load_workflow' )}",
-                    data: { id: "${trans.security.encode_id( workflow_id )}", "_": "true" },
+                    data: { id: "${trans.security.encode_id( stored.id )}", "_": "true" },
                     dataType: 'json',
                     cache: false,
                     success: function( data ) {
@@ -142,6 +144,12 @@
             canvas_manager.draw_overview();
         });
         
+        $('#edit-attributes-button').click( function() {
+            workflow.clear_active_node();
+            $('#edit-attributes').show();
+            $('#right-content').hide();
+        });
+        
         $.jStore.ready(function(engine) {
             engine.ready(function() {
                 // On load, set the size to the pref stored in local storage if it exists
@@ -209,6 +217,19 @@
                }
            });
         });
+
+		// Rename async.
+		async_save_text("workflow-rename", "workflow-name", "${h.url_for( action="rename_async", id=trans.security.encode_id(stored.id) )}", "new_name");
+		
+		// Tag async. Simply have the workflow tag element generate a click on the tag element to activate tagging.
+		$('#workflow-tag').click( function() 
+		{
+		    $('.tag-area').click();
+		    return false;
+		});
+						
+		// Annotate async.
+		async_save_text("workflow-annotate", "workflow-annotation", "${h.url_for( action="annotate_async", id=trans.security.encode_id(stored.id) )}", "new_annotation", true, 4);
     });
 
     // Global state for the whole workflow
@@ -285,7 +306,8 @@
     };
 
     function show_form_for_tool( text, node ) {
-        $("#right-content").html( text );    
+        $("#edit-attributes").hide();
+		$("#right-content").show().html( text );    
         $("#right-content").find( "form" ).ajaxForm( {
             type: 'POST',
             dataType: 'json',
@@ -316,6 +338,17 @@
                 $(this).remove();
                 make_popupmenu( b, options );
             });
+			// Add annotation field to form.
+			// TODO: need to set the annotation for this tool.
+			var annotation_div = 
+				$( "<div class='form-row'> \
+						<label>Annotation / Notes:</label> \
+						<div style='margin-right: 10px;'> \
+							<textarea name='annotation' rows='3' style='width: 100%'>" + node.annotation + "</textarea> \
+							<div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div> \
+						</div> \
+					</div>");
+			$(this).append( annotation_div );
             // Implements auto-saving based on whether the inputs change. We consider
             // "changed" to be when a field is accessed and not necessarily modified
             // because of an issue where "onchange" is not triggered when activating
@@ -366,7 +399,7 @@
                 url: "${h.url_for( action='save_workflow' )}",
                 type: "POST",
                 data: {
-                    id: "${trans.security.encode_id( workflow_id )}",
+                    id: "${trans.security.encode_id( stored.id )}",
                     workflow_data: function() { return JSON.stringify( workflow.to_simple() ) },
                     "_": "true"
                 },
@@ -421,10 +454,10 @@
 <%def name="stylesheets()">
 
     ## Include "base.css" for styling tool menu and forms (details)
-    <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+	${h.css( "base", "autocomplete_tagging")}
 
     ## But make sure styles for the layout take precedence
-    ${parent.stylesheets()}    
+    ${parent.stylesheets()}
 
     <style type="text/css">
     body { margin: 0; padding: 0; overflow: hidden; }
@@ -508,9 +541,8 @@
     div.toolFormRow {
         position: relative;
     }
-    
-    
-    #right-content {
+
+    .right-content {
         margin: 5px;
     }
     
@@ -575,7 +607,6 @@
     }
     
     .form-row {
-        
     }
     div.toolFormInCanvas div.toolFormBody {
         padding: 0;
@@ -740,9 +771,52 @@
     <div class="unified-panel-header" unselectable="on">
         <div class="unified-panel-header-inner">
             Details
+            <div style="float: right">
+                <a id="edit-attributes-button" class="panel-header-button">Edit Workflow Attributes</a>
+            </div>
         </div>
     </div>
     <div class="unified-panel-body" style="overflow: auto;">
-        <div id="right-content"></div>
+		## Div for elements to modify workflow attributes.
+		<div id="edit-attributes" class="toolForm right-content">
+    	    <div class="toolFormTitle">Edit Workflow Attributes</div>
+    	    <div class="toolFormBody">
+    	        ## Workflow name.
+    	        <div id="workflow-name-area" class="form-row">
+           	        <label>Name:</label>
+        		    <div style="float: right"><a id="workflow-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='rename_sync' )}"></a></div>
+        		    <div id="workflow-name">${stored.name}</div>
+                    <div style="clear: both"></div>
+        		</div>
+        		## Workflow tags.
+        		<%namespace file="/tagging_common.mako" import="render_individual_tagging_element" />
+        		<div class="form-row">
+                    <label>
+                        Tags:
+                    </label>
+                    <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div>
+                    <div style="float: left; width: 225px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px">
+                        <style>
+                            .tag-area {
+                                border: none;
+                            }
+                        </style>
+                        ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)}
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div>
+                </div>
+        		## Workflow annotation.
+    	        <div id="workflow-annotation-area" class="form-row">
+           	        <label>Annotation / Notes:</label>
+        		    <div style="float: right"><a id="workflow-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div>
+        		    <div id="workflow-annotation">${annotation}</div>
+                    <div style="clear: both"></div>
+        		    <div class="toolParamHelp">Add an annotation or notes to a workflow; annotations are available when a workflow is viewed.</div>
+        		</div>
+    	    </div>
+    	</div>
+		## Div where tool details are loaded and modified.
+		<div id="right-content" class="right-content"></div>
     </div>
 </%def>

    

Greg Von Kuster

tags

participants (1)