[galaxy-commits] commit/galaxy-central: jgoecks: Viz framework: (a) fix embedded visualizations and (b) bookmarking.

27 Sep 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/8fcb6ed6e233/
changeset:   8fcb6ed6e233
user:        jgoecks
date:        2012-09-27 23:35:04
summary:     Viz framework: (a) fix embedded visualizations and (b) bookmarking.
affected #:  6 files

diff -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f -r 8fcb6ed6e2336542bb122cbac70c3150464cbbf1 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1278,6 +1278,18 @@
         was converted successfully. 
         """
 
+        # FIXME: copied from controller.py
+        messages = Bunch(
+            PENDING = "pending",
+            NO_DATA = "no data",
+            NO_CHROMOSOME = "no chromosome",
+            NO_CONVERTER = "no converter",
+            NO_TOOL = "no tool",
+            DATA = "data",
+            ERROR = "error",
+            OK = "ok"
+        )
+
         # Get converted dataset; this will start the conversion if necessary.
         try:
             converted_dataset = self.get_converted_dataset( trans, target_type )


diff -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f -r 8fcb6ed6e2336542bb122cbac70c3150464cbbf1 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1,7 +1,7 @@
 define( ["libs/underscore", "viz/visualization", "viz/trackster/util", 
          "viz/trackster/slotting", "viz/trackster/painters", "mvc/data",
-         "viz/trackster/filters" ], 
-         function( _, visualization, util, slotting, painters, data, filters_mod ) {
+         "viz/trackster/filters", "viz/trackster_ui" ], 
+         function( _, visualization, util, slotting, painters, data, filters_mod, trackster_ui_mod ) {
 
 var extend = _.extend;
 var get_random_color = util.get_random_color;
@@ -909,11 +909,15 @@
         // Introduction div shown when there are no tracks.
         this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide();
         var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
-            add_datasets(add_datasets_url, add_track_async_url, function(tracks) {
+            // Does not work because it would create circular dependency b/t trackster_ui and tracks.
+            /*
+            var ui = new trackster_ui_mod.TracksterUI();
+            ui.add_datasets(add_datasets_url, add_track_async_url, function(tracks) {
                 _.each(tracks, function(track) {
                     view.add_drawable( object_from_template(track, view, view) );  
                 });
             });
+            */
         });
         // Another label track at bottom
         this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);


diff -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f -r 8fcb6ed6e2336542bb122cbac70c3150464cbbf1 static/scripts/viz/trackster_ui.js
--- a/static/scripts/viz/trackster_ui.js
+++ b/static/scripts/viz/trackster_ui.js
@@ -1,4 +1,4 @@
-define( ["base","libs/underscore","viz/trackster/slotting", "viz/trackster/painters","viz/trackster/tracks"], function( base, _, slotting, painters, tracks ) {
+define( ["base","libs/underscore","viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/tracks" ], function( base, _, slotting, painters, tracks ) {
 
 /************************************************************************
  * Functions used for creating and managing the Trackster user interface.
@@ -19,9 +19,9 @@
         var self = this,
             menu = create_icon_buttons_menu([
             { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { 
-                add_datasets(add_datasets_url, add_track_async_url, function(tracks) {
+                self.add_datasets(add_datasets_url, add_track_async_url, function(tracks) {
                     _.each(tracks, function(track) {
-                        view.add_drawable( trackster_ui.object_from_template(track, view,  view) );  
+                        view.add_drawable( object_from_template(track, view,  view) );  
                     });
                 });
             } },
@@ -99,7 +99,8 @@
      * Use a popup to select a dataset of create bookmarks from
      */
     add_bookmarks: function() {
-        var baseURL = this.baseURL;
+        var self = this,
+            baseURL = this.baseURL;
         show_modal( "Select dataset for new bookmarks", "progress" );
         $.ajax({
             url: this.baseURL + "/visualization/list_histories",
@@ -129,7 +130,7 @@
                                     }).then( function(data) {
                                         for( i = 0; i < data.data.length; i++ ) {
                                             var row = data.data[i];
-                                            add_bookmark( row[0], row[1] );
+                                            self.add_bookmark( row[0], row[1] );
                                         }
                                     });
                             });
@@ -183,7 +184,8 @@
     create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
         
         // Create view.
-        view = new tracks.View(view_config);
+        var self = this,
+            view = new tracks.View(view_config);
         view.editor = true;
         $.when( view.load_chroms_deferred ).then(function() {
             // Viewport config.
@@ -227,7 +229,7 @@
                 var bookmark;
                 for (var i = 0; i < bookmarks_config.length; i++) {
                     bookmark = bookmarks_config[i];
-                    add_bookmark(bookmark['position'], bookmark['annotation'], editable);
+                    self.add_bookmark(bookmark['position'], bookmark['annotation'], editable);
                 }
             }
 
@@ -239,6 +241,58 @@
     },
 
     /**
+     * Use a popup grid to add more datasets.
+    */
+    add_datasets: function(dataset_url, add_track_async_url, success_fn) {
+        $.ajax({
+            url: dataset_url,
+            data: { "f-dbkey": view.dbkey },
+            error: function() { alert( "Grid failed" ); },
+            success: function(table_html) {
+                show_modal(
+                    "Select datasets for new tracks",
+                    table_html, {
+                        "Cancel": function() {
+                            hide_modal();
+                        },
+                        "Add": function() {
+                            var requests = [];
+                            $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() {
+                                var data = {
+                                        data_type: 'track_config',
+                                        'hda_ldda': 'hda'
+                                    },
+                                    id = $(this).val();
+                                    if ($(this).attr("name") !== "id") {
+                                        data.hda_ldda = 'ldda';
+                                    }
+                                    requests[requests.length] = $.ajax({
+                                        url: add_track_async_url + "/" + id,
+                                        data: data,
+                                        dataType: "json"
+                                    });
+                            });
+                            // To preserve order, wait until there are definitions for all tracks and then add 
+                            // them sequentially.
+                            $.when.apply($, requests).then(function() {
+                                // jQuery always returns an Array for arguments, so need to look at first element
+                                // to determine whether multiple requests were made and consequently how to 
+                                // map arguments to track definitions.
+                                var track_defs = (arguments[0] instanceof Array ?  
+                                                   $.map(arguments, function(arg) { return arg[0]; }) :
+                                                   [ arguments[0] ]
+                                                   );
+                                success_fn(track_defs);
+                            });
+                            hide_modal();
+                        }
+                    }
+                );
+            }
+        });
+    },
+
+    /**
      * Set up keyboard navigation for a visualization.
      */
      init_keyboard_nav: function(view) {


diff -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f -r 8fcb6ed6e2336542bb122cbac70c3150464cbbf1 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -672,62 +672,6 @@
     }
 });
 
-/**
- * -- Helper functions.
- */
- 
-/**
- * Use a popup grid to add more datasets.
- */
-var add_datasets = function(dataset_url, add_track_async_url, success_fn) {
-    $.ajax({
-        url: dataset_url,
-        data: { "f-dbkey": view.dbkey },
-        error: function() { alert( "Grid failed" ); },
-        success: function(table_html) {
-            show_modal(
-                "Select datasets for new tracks",
-                table_html, {
-                    "Cancel": function() {
-                        hide_modal();
-                    },
-                    "Add": function() {
-                        var requests = [];
-                        $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() {
-                            var data = {
-                                    data_type: 'track_config',
-                                    'hda_ldda': 'hda'
-                                },
-                                id = $(this).val();
-                                if ($(this).attr("name") !== "id") {
-                                    data.hda_ldda = 'ldda';
-                                }
-                                requests[requests.length] = $.ajax({
-                                    url: add_track_async_url + "/" + id,
-                                    data: data,
-                                    dataType: "json"
-                                });
-                        });
-                        // To preserve order, wait until there are definitions for all tracks and then add 
-                        // them sequentially.
-                        $.when.apply($, requests).then(function() {
-                            // jQuery always returns an Array for arguments, so need to look at first element
-                            // to determine whether multiple requests were made and consequently how to 
-                            // map arguments to track definitions.
-                            var track_defs = (arguments[0] instanceof Array ?  
-                                               $.map(arguments, function(arg) { return arg[0]; }) :
-                                               [ arguments[0] ]
-                                               );
-                            success_fn(track_defs);
-                        });
-                        hide_modal();
-                    }
-                }
-            );
-        }
-    });
-};
-
 return {
     BrowserBookmark: BrowserBookmark,
     BrowserBookmarkCollection: BrowserBookmarkCollection,
@@ -741,8 +685,7 @@
     ReferenceTrackDataManager: ReferenceTrackDataManager,
     TrackBrowserRouter: TrackBrowserRouter,
     TrackConfig: TrackConfig,
-    Visualization: Visualization,
-    add_datasets: add_datasets
+    Visualization: Visualization
 };
 
 });
\ No newline at end of file


diff -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f -r 8fcb6ed6e2336542bb122cbac70c3150464cbbf1 templates/tracks/browser.mako
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -48,8 +48,10 @@
 
     ${render_trackster_js_vars()}
 
-    var view,
-        browser_router,
+    // FIXME: deliberate global required for now due to requireJS integration.
+    view = null;
+
+    var browser_router,
         ui = new (trackster_ui.TracksterUI)( "${h.url_for('/')}" );
 
     /**


diff -r 7658dde1dd3356bfeb6b92bdcdf8f1c4b3537a0f -r 8fcb6ed6e2336542bb122cbac70c3150464cbbf1 templates/visualization/display.mako
--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -54,44 +54,59 @@
     <div id="${trans.security.encode_id( visualization.id )}" class="unified-panel-body" style="overflow:none;top:0px;"></div><script type="text/javascript">
-        // TODO: much of this code is copied from browser.mako -- create shared base and use in both places.
-        ${render_trackster_js_vars()}
+        require.config({ 
+            baseUrl: "${h.url_for('/static/scripts') }",
+            shim: {
+                "libs/underscore": { exports: "_" },
+                "libs/backbone/backbone": { exports: "Backbone" },
+                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
+            }
+        });
+        require( ["base", "viz/visualization", "viz/trackster_ui", "viz/trackster/tracks"], 
+             function( base, visualization, trackster_ui, tracks ) {
 
-        var view,
-            container_element = $("#${trans.security.encode_id( visualization.id )}");
-        
-        $(function() {
-            var is_embedded = (container_element.parents(".item-content").length > 0);
+            ${render_trackster_js_vars()}
+
+            // FIXME: deliberate global required for now due to requireJS integration.
+            view = null;
+
+            var ui = new (trackster_ui.TracksterUI)( "${h.url_for('/')}" )
+                container_element = $("#${trans.security.encode_id( visualization.id )}");
             
-            // HTML setup.
-            if (is_embedded) {
-                container_element.css( { "position": "relative" } );
-            } else { // Viewing just one shared viz
-                $("#right-border").click(function() { view.resize_window(); });
-            }
-            
-            // Create visualization.
-            var callback;
-            %if 'viewport' in config:
-                var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); }
-            %endif
-            view = create_visualization( {
-                                            container: container_element,
-                                            name: "${config.get('title') | h}",
-                                            vis_id: "${config.get('vis_id')}", 
-                                            dbkey: "${config.get('dbkey')}"
-                                         }, 
-                                         JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'),
-                                         JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'),
-                                         JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }')
-                                         );
-            
-            // Set up keyboard navigation.
-            init_keyboard_nav(view);
-            
-            // HACK: set viewport height because it cannot be set automatically. Currently, max height for embedded
-            // elts is 25em, so use 20em.
-            view.viewport_container.height("20em");
+            $(function() {
+                var is_embedded = (container_element.parents(".item-content").length > 0);
+                
+                // HTML setup.
+                if (is_embedded) {
+                    container_element.css( { "position": "relative" } );
+                } else { // Viewing just one shared viz
+                    $("#right-border").click(function() { view.resize_window(); });
+                }
+                
+                // Create visualization.
+                var callback;
+                %if 'viewport' in config:
+                    var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); }
+                %endif
+                view = ui.create_visualization( {
+                                                container: container_element,
+                                                name: "${config.get('title') | h}",
+                                                vis_id: "${config.get('vis_id')}", 
+                                                dbkey: "${config.get('dbkey')}"
+                                             }, 
+                                             JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'),
+                                             JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'),
+                                             JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }')
+                                             );
+                
+                // Set up keyboard navigation.
+                ui.init_keyboard_nav(view);
+                
+                // HACK: set viewport height because it cannot be set automatically. Currently, max height for embedded
+                // elts is 25em, so use 20em.
+                view.viewport_container.height("20em");
+            });
+
         });
 
     </script>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: jgoecks: Viz framework: (a) fix embedded visualizations and (b) bookmarking.

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