[galaxy-commits] commit/galaxy-central: carlfeberhard: history.js: fixed download popupmenu, display apps rendering added; ColumnDataProvider: if a line contains a column value that doesn't match the column type None is returned in it's place (prev. returned string)

28 Sep 2012

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7658dde1dd33/
changeset:   7658dde1dd33
user:        carlfeberhard
date:        2012-09-27 22:25:04
summary:     history.js: fixed download popupmenu, display apps rendering added; ColumnDataProvider: if a line contains a column value that doesn't match the column type None is returned in it's place (prev. returned string)
affected #:  7 files
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f lib/galaxy/visualization/data_providers/basic.py

--- a/lib/galaxy/visualization/data_providers/basic.py
+++ b/lib/galaxy/visualization/data_providers/basic.py
@@ -109,10 +109,10 @@
             """ Cast value based on type. """
             if type == 'int':
                 try: val = int( val )
-                except: pass
+                except: return None
             elif type == 'float':
                 try: val = float( val )
-                except: pass
+                except: return None
             return val
f = open( self.original_dataset.file_name )
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -65,6 +65,9 @@
     });
 };
+/**
+ *  Sets up popupmenu rendering and binds options functions to the appropriate links
+ */
 function make_popupmenu(button_element, initial_options) {
     /*  Use the $.data feature to store options with the link element.
         This allows options to be changed at a later time 
@@ -101,10 +104,10 @@
             x = Math.min( x, $(document).scrollLeft() + $(window).width() - $(wrapper).width() - 5 );
             x = Math.max( x, $(document).scrollLeft() + 5 );
-            wrapper.css( {
+            wrapper.css({
                top: e.pageY,
                left: x
-            } );
+            });
         }, 10);
setTimeout( function() {
@@ -129,27 +132,53 @@
}
-function make_popup_menus() {
-    jQuery( "div[popupmenu]" ).each( function() {
+/**
+ *  Convert two seperate (often adjacent) divs into galaxy popupmenu
+ *  - div 1 contains a number of anchors which become the menu options
+ *  - div 1 should have a 'popupmenu' attribute
+ *  - this popupmenu attribute contains the id of div 2
+ *  - div 2 becomes the 'face' of the popupmenu
+ *
+ *  NOTE: make_popup_menus finds and operates on all divs with a popupmenu attr (no need to point it at something)
+ *          but (since that selector searches the dom on the page), you can send a parent in
+ *  NOTE: make_popup_menus, and make_popupmenu are horrible names
+ */
+function make_popup_menus( parent ) {
+    // find all popupmenu menu divs (divs that contains anchors to be converted to menu options)
+    //  either in the parent or the document if no parent passed
+    parent = parent || document;
+    $( parent ).find( "div[popupmenu]" ).each( function() {
         var options = {};
         var menu = $(this);
+        
+        // find each anchor in the menu, convert them into an options map: { a.text : click_function }
         menu.find( "a" ).each( function() {
             var link = $(this),
-                link_dom = link.get(0);
-            var confirmtext = link_dom.getAttribute( "confirm" ),
+                // why do we need the DOM (mixed with jq)?
+                link_dom = link.get(0),
+                confirmtext = link_dom.getAttribute( "confirm" ),
                 href = link_dom.getAttribute( "href" ),
                 target = link_dom.getAttribute( "target" );
+            // no href - no function (gen. a label)
             if (!href) {
                 options[ link.text() ] = null;
+                
             } else {
                 options[ link.text() ] = function() {
+
+                    // if theres confirm text, send the dialog
                     if ( !confirmtext || confirm( confirmtext ) ) {
                         var f;
+                        // relocate the center panel
                         if ( target == "_parent" ) {
                             window.parent.location = href;
+                            
+                        // relocate the entire window
                         } else if ( target == "_top" ) {
                             window.top.location = href;
+                            
+                        //??...wot?
                         } else if ( target == "demo" ) {
                             // Http request target is a window named
                             // demolocal on the local box
@@ -157,6 +186,8 @@
                                 f = window.open( href,target );
                                 f.creator = self;
                             }
+                            
+                        // relocate this panel
                         } else {
                             window.location = href;
                         }
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f static/scripts/mvc/history.js
--- a/static/scripts/mvc/history.js
+++ b/static/scripts/mvc/history.js
@@ -191,7 +191,8 @@
         // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
         itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' });
-        make_popup_menus();
+        // we can potentially skip this step and call popupmenu directly on the download button
+        make_popup_menus( itemWrapper );
//TODO: better transition/method than this...
         this.$el.children().remove();
@@ -336,11 +337,13 @@
_render_downloadButton : function(){
         // don't show anything if the data's been purged
-        //if( this.model.get( 'purged' ) ){ return null; }
+        if( this.model.get( 'purged' ) ){ return null; }
// return either: a single download icon-button (if there are no meta files)
         //  or a popupmenu with links to download assoc. meta files (if there are meta files)
         var downloadLinkHTML = HistoryItemView.templates.downloadLinks( this.model.toJSON() );
+        this.log( '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML );
+        
         return $( downloadLinkHTML );
     },
@@ -456,54 +459,23 @@
     },
_render_displayApps : function(){
-        if( !this.model.get( 'display_apps' ) ){ return null; }
-        var displayApps = this.model.get( 'displayApps' ),
-            displayAppsDiv = $( '<div/>' ),
-            displayAppSpan = $( '<span/>' );
-                
-        this.log( this + 'displayApps:', displayApps );
-        ////TODO: grrr...somethings not in the right scope here
-        //for( app_name in displayApps ){
-        //    //TODO: to template
-        //    var display_app = displayApps[ app_name ],
-        //        display_app_HTML = app_name + ' ';
-        //    for( location_name in display_app ){
-        //        display_app_HTML += linkHTMLTemplate({
-        //            text    : location_name,
-        //            href    : display_app[ location_name ].url,
-        //            target  : display_app[ location_name ].target
-        //        }) + ' ';
-        //    }
-        //    display_app_span.append( display_app_HTML );
-        //}
-        //displayAppsDiv.append( display_app_span );
+        // render links to external genome display applications (igb, gbrowse, etc.)
+        if( !this.model.hasData() ){ return null; }
-        //displayAppsDiv.append( '<br />' );
-
-        //var display_appsDiv = $( '<div/>' );
-        //if( this.model.get( 'display_apps' ) ){
-        //
-        //    var display_apps = this.model.get( 'display_apps' ),
-        //        display_app_span = $( '<span/>' );
-        //        
-        //    //TODO: grrr...somethings not in the right scope here
-        //    for( app_name in display_apps ){
-        //        //TODO: to template
-        //        var display_app = display_apps[ app_name ],
-        //            display_app_HTML = app_name + ' ';
-        //        for( location_name in display_app ){
-        //            display_app_HTML += linkHTMLTemplate({
-        //                text    : location_name,
-        //                href    : display_app[ location_name ].url,
-        //                target  : display_app[ location_name ].target
-        //            }) + ' ';
-        //        }
-        //        display_app_span.append( display_app_HTML );
-        //    }
-        //    display_appsDiv.append( display_app_span );
-        //}
-        ////display_appsDiv.append( '<br />' );
-        //parent.append( display_appsDiv );
+        var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' );
+        if( !_.isEmpty( this.model.get( 'display_types' ) ) ){
+            this.log( this + 'display_types:', this.model.get( 'display_types' ) );
+            //TODO:?? does this ever get used?
+            displayAppsDiv.append(
+                HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_types })
+            );
+        }
+        if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){
+            this.log( this + 'display_apps:',  this.model.get( 'display_apps' ) );
+            displayAppsDiv.append(
+                HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_apps })
+            );
+        }
         return displayAppsDiv;
     },
@@ -770,10 +742,11 @@
         messages        : 'template-history-warning-messages',
         titleLink       : 'template-history-titleLink',
         hdaSummary      : 'template-history-hdaSummary',
+        downloadLinks   : 'template-history-downloadLinks',
         failedMetadata  : 'template-history-failedMetaData',
         tagArea         : 'template-history-tagArea',
         annotationArea  : 'template-history-annotationArea',
-        downloadLinks   : 'template-history-downloadLinks'
+        displayApps     : 'template-history-displayApps'
     }
 });
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f static/scripts/templates/compiled/template-history-displayApps.js
--- /dev/null
+++ b/static/scripts/templates/compiled/template-history-displayApps.js
@@ -0,0 +1,42 @@
+(function() {
+  var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
+templates['template-history-displayApps'] = template(function (Handlebars,depth0,helpers,partials,data) {
+  helpers = helpers || Handlebars.helpers;
+  var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this;
+
+function program1(depth0,data) {
+  
+  var buffer = "", stack1, foundHelper;
+  buffer += "\n    ";
+  foundHelper = helpers.label;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  buffer += escapeExpression(stack1) + "\n    ";
+  stack1 = depth0.links;
+  stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n    <br />\n";
+  return buffer;}
+function program2(depth0,data) {
+  
+  var buffer = "", stack1, foundHelper;
+  buffer += "\n        <a target="";
+  foundHelper = helpers.target;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  buffer += escapeExpression(stack1) + "" href="";
+  foundHelper = helpers.href;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  buffer += escapeExpression(stack1) + "">";
+  foundHelper = helpers.text;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  buffer += escapeExpression(stack1) + "</a>\n    ";
+  return buffer;}
+
+  stack1 = depth0.displayApps;
+  stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)});
+  if(stack1 || stack1 === 0) { return stack1; }
+  else { return ''; }});
+})();
\ No newline at end of file
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f static/scripts/templates/compiled/template-history-downloadLinks.js
--- a/static/scripts/templates/compiled/template-history-downloadLinks.js
+++ b/static/scripts/templates/compiled/template-history-downloadLinks.js
@@ -46,7 +46,7 @@
 function program4(depth0,data) {
-  return "\n    <a href="" title="Download" class="icon-button disk tooltip"></a>\n";}
+  return "\n<a href="" title="Download" class="icon-button disk tooltip"></a>\n";}
stack1 = depth0.meta_files;
   stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)});
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f static/scripts/templates/history-templates.html
--- a/static/scripts/templates/history-templates.html
+++ b/static/scripts/templates/history-templates.html
@@ -51,6 +51,23 @@
 {{/warningmessagesmall}}
 </script>
+<script type="text/template" class="template-history" id="template-history-downloadLinks">
+{{#if meta_files}}
+<div popupmenu="dataset-{{id}}-popup">
+    <a class="action-button" href="{{download_url}}">Download Dataset</a>
+    <a>Additional Files</a>
+    {{#each meta_files}}
+    <a class="action-button" href="{{meta_download_url}}">Download {{meta_file_type}}</a>
+    {{/each}}
+</div>
+<div style="float:left;" class="menubutton split popup" id="dataset-{{id}}-popup">
+    <a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a>
+</div>
+{{else}}
+<a href="" title="Download" class="icon-button disk tooltip"></a>
+{{/if}}
+</script>
+
 <script type="text/template" class="template-history" id="template-history-tagArea">
 {{! TODO: move to mvc/tag.js templates }}
 <div class="tag-area" style="display: none;">
@@ -70,21 +87,12 @@
 </div></script>
-<script type="text/template" class="template-history" id="template-history-downloadLinks">
-{{#if meta_files}}
-<div popupmenu="dataset-{{id}}-popup">
-    <a class="action-button" href="{{download_url}}">Download Dataset</a>
-    <a>Additional Files</a>
-    {{#each meta_files}}
-    <a class="action-button" href="{{meta_download_url}}">Download {{meta_file_type}}</a>
+<script type="text/template" class="template-history" id="template-history-displayApps">
+{{#each displayApps}}
+    {{label}}
+    {{#each links}}
+        <a target="{{target}}" href="{{href}}">{{text}}</a>
     {{/each}}
-</div>
-<div style="float:left;" class="menubutton split popup" id="dataset-{{id}}-popup">
-    <a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a>
-</div>
-{{else}}
-    <a href="" title="Download" class="icon-button disk tooltip"></a>
-{{/if}}
+    <br />
+{{/each}}
 </script>
-
-
diff -r a995f7aca75c03bd180689aead6a8870928d8fdf -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f templates/root/alternate_history.mako
--- a/templates/root/alternate_history.mako
+++ b/templates/root/alternate_history.mako
@@ -7,40 +7,6 @@
 ## ?? add: if string != _(string)
 </%def>
-##<%def name="render_download_links( data, dataset_id )">
-##    ##
-##    %if data.purged: return
-##    <%
-##        from galaxy.datatypes.metadata import FileParameter
-##        download_url = h.url_for( controller='/dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )
-##        meta_files = []
-##        for k in data.metadata.spec.keys():
-##            if isinstance( data.metadata.spec[ k ].param, FileParameter ):
-##                file_type = k
-##                download_url = h.url_for( controller='/dataset', action='get_metadata_file', 
-##                                          hda_id=dataset_id, metadata_name=file_type )
-##                meta_files.append( ( file_type, download_url ) )
-##    %>
-##    
-##    %if meta_files:
-##        <div popupmenu="dataset-${dataset_id}-popup">
-##            <a class="action-button" href="${download_url}">Download Dataset</a>
-##            
-##            <a>Additional Files</a>
-##            %for meta_file_type, meta_download_url in zip( meta_download_types, meta_download_urls ):
-##                <a class="action-button" href="${meta_download_url}">Download ${meta_file_type}</a>
-##            %endfor
-##
-##            <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup">
-##                <a href="${download_url}" title='${_("Download")}' class="icon-button disk tooltip"></a>
-##            </div>
-##        </div>
-##        
-##    %else
-##        <a href="${download_url}" title='${_("Download")}' class="icon-button disk tooltip"></a>
-##    %endif
-##</%def>
-
 <%def name="get_page_localized_strings()">
     ## a list of localized strings used in the backbone views, etc. (to be loaded and cached)
     ##! change on per page basis
@@ -98,26 +64,8 @@
     deleted = hda.deleted
     purged  = hda.purged
-    # download links (for both main hda and associated meta files)
-    if not hda.purged:
-        add_to_data( download_url=h.url_for( controller='/dataset', action='display',
-                                             dataset_id=encoded_data_id, to_ext=hda.ext ) )
-    
-        meta_files = []
-        for k in hda.metadata.spec.keys():
-            if isinstance( hda.metadata.spec[ k ].param, FileParameter ):
-                file_type = k
-                download_url = h.url_for( controller='/dataset', action='get_metadata_file', 
-                                          hda_id=encoded_data_id, metadata_name=file_type )
-                meta_files.append( dict( meta_file_type=file_type, meta_download_url=download_url ) )
-                
-        if meta_files:
-            print hda.name, meta_files
-            add_to_data( meta_files=meta_files )
-                
-        
+    # ................................................................ link actions 
     #purged  = purged or hda.dataset.purged //??
-    
     # all of these urls are 'datasets/data_id/<action>
     if not ( dataset_purged or purged ) and for_editing:
         add_to_data( undelete_url=h.url_for( controller='dataset', action='undelete', dataset_id=encoded_data_id ) )
@@ -128,6 +76,8 @@
     if not hda.visible:
         add_to_data( unhide_url=h.url_for( controller='dataset', action='unhide', dataset_id=encoded_data_id ) )
+    
+    # ................................................................ title actions (display, edit, delete)
     display_url = ''
     if for_editing:
         display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' )
@@ -157,11 +107,29 @@
                                            show_deleted_on_refresh=show_deleted
         ))
+    # ................................................................ primary actions (error, info, download)
+    # download links (hda and associated meta files)
+    if not hda.purged:
+        add_to_data( download_url=h.url_for( controller='/dataset', action='display',
+                                             dataset_id=encoded_data_id, to_ext=hda.ext ) )
+    
+        meta_files = []
+        for k in hda.metadata.spec.keys():
+            if isinstance( hda.metadata.spec[ k ].param, FileParameter ):
+                file_type = k
+                download_url = h.url_for( controller='/dataset', action='get_metadata_file', 
+                                          hda_id=encoded_data_id, metadata_name=file_type )
+                meta_files.append( dict( meta_file_type=file_type, meta_download_url=download_url ) )
+                
+        if meta_files:
+            add_to_data( meta_files=meta_files )
+                
     # error report
     if for_editing:
         #NOTE: no state == 'error' check
         add_to_data( report_error_url=h.url_for( h.url_for( controller='dataset', action='errors', id=encoded_data_id ) ) )
-            
+    
+    # visualizations
     if hda.ext in app.datatypes_registry.get_available_tracks():
         # do these need _localized_ dbkeys?
         trackster_urls = {}
@@ -175,6 +143,48 @@
         trackster_urls[ 'new-url' ]    = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id, default_dbkey=hda.dbkey )
         add_to_data( trackster_url=trackster_urls )
+    # display apps (igv, uscs)
+    display_types = []
+    display_apps = []
+    if( hda.state in [ 'ok', 'failed_metadata' ]
+    and hda.has_data() ):
+        #NOTE: these two data share structures
+        #TODO: this doesn't seem to get called with the hda I'm using. What would call this? How can I spoof it?
+        for display_type in hda.datatype.get_display_types():
+            display_label = hda.datatype.get_display_label( display_type )
+            target_frame, display_links = hda.datatype.get_display_links( hda, display_type, app, request.base )
+            if display_links:
+                display_links = []
+                for display_name, display_href in display_links:
+                    display_type_link = dict(
+                        target  = target_frame,
+                        href    = display_href,
+                        text    = display_name
+                    )
+                    display_links.append( display_type_link )
+                
+                # append the link list to the main map using the display_label
+                display_types.append( dict( label=display_label, links=display_links ) )
+
+        for display_app in hda.get_display_applications( trans ).itervalues():
+            app_links = []
+            for display_app_link in display_app.links.itervalues():
+                app_link = dict(
+                    target = display_app_link.url.get( 'target_frame', '_blank' ),
+                    href = display_app_link.get_display_url( hda, trans ),
+                    text = _( display_app_link.name )
+                )
+                app_links.append( app_link )
+            
+            display_apps.append( dict( label=display_app.name, links=app_links ) )
+                
+    # attach the display types and apps (if any) to the hda obj
+    #if display_types: print 'display_types:', display_types
+    #if display_apps: print 'display_apps:', display_apps
+    add_to_data( display_types=display_types )
+    add_to_data( display_apps=display_apps )
+
+    # ................................................................ secondary actions (tagging, annotation)
     if trans.user:
         add_to_data( ajax_get_tag_url=( h.url_for(
             controller='tag', action='get_tagging_elt_async',
@@ -189,34 +199,6 @@
         add_to_data( ajax_set_annotation_url=( h.url_for(
             controller='/dataset', action='annotate_async', id=encoded_data_id ) ) )
-    display_type_display_links = {}
-    #TODO: this doesn't seem to get called with the hda I'm using. What would call this? How can I spoof it?
-    for display_app in hda.datatype.get_display_types():
-        # print "display_app:", display_app
-        target_frame, display_links = hda.datatype.get_display_links( hda, display_app, app, request.base )
-        # print "target_frame:", target_frame, "display_links:", display_links
-        #if len( display_links ) > 0:
-        #    display_type_display_links[ display_app ] = {}
-        #    for display_name, display_link in display_links:
-        #NOTE!: localized name
-            #<a target="${target_frame}" href="${display_link}">${_(display_name)}</a>
-            #pass
-        # <br />
-    
-    display_apps = {}
-    for display_app in hda.get_display_applications( trans ).itervalues():
-        display_app_dict = display_apps[ display_app.name ] = {}
-        for link_app in display_app.links.itervalues():
-            # print link_app.name, link_app.get_display_url( hda, trans )
-            #NOTE!: localized name
-            display_app_dict[ _( link_app.name ) ] = {
-                'url' : link_app.get_display_url( hda, trans ),
-                'target' : link_app.url.get( 'target_frame', '_blank' )
-            }
-    if display_apps:
-        # print display_apps
-        add_to_data( display_apps=display_apps )
-
     return data_dict
 %></%def>
@@ -337,11 +319,12 @@
"template-history-warning-messages",
         "template-history-titleLink",
+        "template-history-failedMetadata",
         "template-history-hdaSummary",
-        "template-history-failedMetadata",
+        "template-history-downloadLinks",
         "template-history-tagArea",
         "template-history-annotationArea",
-        "template-history-downloadLinks"
+        "template-history-displayApps"
     )}
## if using in-dom templates they need to go here (before the Backbone classes are defined)
@@ -382,9 +365,6 @@
                 glx_history_view = new HistoryView({ model: glx_history });
                 glx_history_view.render();
-                hi = glx_history.items.at( 0 );
-                hi_view = new HistoryItemView({ model: hi });
-                $( 'body' ).append( hi_view.render() );
                 return;
             }
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: carlfeberhard: history.js: fixed download popupmenu, display apps rendering added; ColumnDataProvider: if a line contains a column value that doesn't match the column type None is returned in it's place (prev. returned string)