[galaxy-commits] commit/galaxy-central: 2 new changesets

16 Oct 2012

2 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/605f4d69d5db/
changeset:   605f4d69d5db
user:        jgoecks
date:        2012-10-16 19:43:57
summary:     Circster cleanup: remove track indexes and make renderers into views.
affected #:  1 file

diff -r 0391351559dd124f305245a9d27f071f28debc54 -r 605f4d69d5db3f9bbfc949ac22ba5ee744649a5f static/scripts/viz/circster.js

--- a/static/scripts/viz/circster.js
+++ b/static/scripts/viz/circster.js
@@ -1,8 +1,5 @@
 define(["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) {
 
-// General backbone style inheritence
-var Base = function() { this.initialize && this.initialize.apply(this, arguments); }; Base.extend = Backbone.Model.extend;
-
 var SVGUtils = Backbone.Model.extend({
 
     /**
@@ -51,11 +48,10 @@
         this.track_gap = 5;
         this.label_arc_height = 20;
         this.scale = 1;
-        this.track_renderers = null;
+        this.track_views = null;
 
         // When track added to the model, add to view as well.
         this.model.get('tracks').on('add', this.add_track, this);
-
     },
 
     /**
@@ -103,7 +99,7 @@
                       "translate(" + d3.event.translate + ")" + 
                       " scale(" + scale + ")");
 
-                    // Propagate scale changes to renderers.
+                    // Propagate scale changes to views.
                     if (self.scale !== scale) {
                         // Use timeout to wait for zooming/dragging to stop before rendering more detail.
                         if (self.zoom_drag_timeout) {
@@ -111,8 +107,8 @@
                         }
                         self.zoom_drag_timeout = setTimeout(function() {
                             // Render more detail in tracks' visible elements.
-                            _.each(self.track_renderers, function(renderer) {
-                                renderer.update_scale(scale);
+                            _.each(self.track_views, function(view) {
+                                view.update_scale(scale);
                             });
                         }, 400);
                     }
@@ -123,23 +119,23 @@
 
         // -- Render each dataset in the visualization. --
 
-        // Create a renderer for each track in the visualiation and render.
-        this.track_renderers = tracks.map(function(track, index) {
-            track_renderer_class = (track.get('track_type') === 'LineTrack' ? 
-                                    CircsterBigWigTrackRenderer : 
-                                    CircsterSummaryTreeTrackRenderer );
+        // Create a view for each track in the visualiation and render.
+        this.track_views = tracks.map(function(track, index) {
+            track_view_class = (track.get('track_type') === 'LineTrack' ? 
+                                    CircsterBigWigTrackView : 
+                                    CircsterSummaryTreeTrackView );
             
-            return new track_renderer_class({
+            return new track_view_class({
+                el: svg.append('g')[0],
                 track: track,
-                track_index: index,
                 radius_bounds: tracks_bounds[index],
                 genome: self.genome,
                 total_gap: self.total_gap
             });
         });
 
-        _.each(this.track_renderers, function(renderer) {
-            renderer.render(svg);
+        _.each(this.track_views, function(view) {
+            view.render();
         });
 
         // -- Render chromosome labels. --
@@ -147,56 +143,57 @@
         // Set radius start = end for track bounds.
         var track_bounds = tracks_bounds[tracks.length];
         track_bounds[1] = track_bounds[0];
-        this.label_track_renderer = new CircsterLabelTrackRenderer({
+        this.label_track_view = new CircsterLabelTrackView({
+            el: svg.append('g')[0],
             track: new CircsterLabelTrack(),
-            track_index: tracks.length,
             radius_bounds: track_bounds,
             genome: self.genome,
             total_gap: self.total_gap
         });
         
-        this.label_track_renderer.render(svg);
+        this.label_track_view.render();
     },
 
     /**
      * Render a single track on the outside of the current visualization.
      */
     add_track: function(new_track) {
-        // Reset scale and zoom.
+        // TODO: Reset scale and zoom.
 
         // Recompute and update track bounds.
         var new_track_bounds = this.get_tracks_bounds();
-        _.each(this.track_renderers, function(track_renderer, i) {
+        _.each(this.track_views, function(track_view, i) {
             //console.log(self.get_tracks_bounds(), i);
-            track_renderer.update_radius_bounds(new_track_bounds[i]);
+            track_view.update_radius_bounds(new_track_bounds[i]);
         });
 
         // Render new track.
-        var track_index = this.track_renderers.length
-            track_renderer_class = (new_track.get('track_type') === 'LineTrack' ? 
-                                    CircsterBigWigTrackRenderer : 
-                                    CircsterSummaryTreeTrackRenderer ),
-            track_renderer = new track_renderer_class({
+        var track_index = this.track_views.length
+            track_view_class = (new_track.get('track_type') === 'LineTrack' ? 
+                                    CircsterBigWigTrackView : 
+                                    CircsterSummaryTreeTrackView ),
+            track_view = new track_view_class({
+                el: d3.select('g.tracks').append('g')[0],
                 track: new_track,
-                track_index: track_index,
                 radius_bounds: new_track_bounds[track_index],
                 genome: this.genome,
                 total_gap: this.total_gap
             });
-        track_renderer.render(d3.select('g.tracks'));
-        this.track_renderers.push(track_renderer);
+        track_view.render();
+        this.track_views.push(track_view);
 
         // Update label track.
         var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];
         track_bounds[1] = track_bounds[0];
-        this.label_track_renderer.update_radius_bounds(track_bounds);
+        this.label_track_view.update_radius_bounds(track_bounds);
     }
 });
 
 /**
  * Renders a track in a Circster visualization.
  */
-var CircsterTrackRenderer = Base.extend({
+var CircsterTrackView = Backbone.View.extend({
+    tagName: 'g',
 
     /* ----------------------- Public Methods ------------------------- */
 
@@ -210,17 +207,20 @@
         this.options.chroms_layout = this._chroms_layout();
         this.options.data_bounds = [];
         this.options.scale = 1;
-        this.options.parent_elt = null;
+        this.options.parent_elt = d3.select(this.$el[0]);
     },
 
     /**
      * Render track's data by adding SVG elements to parent.
      */
-    render: function(parent) {
+    render: function() {
         // -- Create track group element. --
-        this.options.parent_elt = parent.append("g").attr("id", "parent-" + this.options.track_index);
         var track_parent_elt = this.options.parent_elt;
 
+        if (!track_parent_elt) {
+            console.log('no parent elt');
+        }
+
         // -- Render background arcs. --
         var genome_arcs = this.options.chroms_layout,
             arc_gen = d3.svg.arc()
@@ -306,7 +306,7 @@
     },
 
     /**
-     * Update renderer scale. This fetches more data if scale is increased.
+     * Update view scale. This fetches more data if scale is increased.
      */
     update_scale: function(new_scale) {
         // -- Update scale and return if new scale is less than old scale. --
@@ -432,13 +432,12 @@
 /**
  * Render chromosome labels.
  */
-var CircsterLabelTrackRenderer = CircsterTrackRenderer.extend({
+var CircsterLabelTrackView = CircsterTrackView.extend({
 
     initialize: function(options) {
-        this.options = options;
+        CircsterTrackView.prototype.initialize.call(this, options);
         this.options.bg_stroke = 'fff';
         this.options.bg_fill = 'fff';
-        this.options.chroms_layout = this._chroms_layout();
     },
 
     /**
@@ -467,9 +466,9 @@
 });
 
 /**
- * Rendered for quantitative data.
+ * View for quantitative track in Circster.
  */
-var CircsterQuantitativeTrackRenderer = CircsterTrackRenderer.extend({
+var CircsterQuantitativeTrackView = CircsterTrackView.extend({
 
     /**
      * Renders quantitative data with the form [x, value] and assumes data is equally spaced across
@@ -533,7 +532,7 @@
 /**
  * Layout for summary tree data in a circster visualization.
  */
-var CircsterSummaryTreeTrackRenderer = CircsterQuantitativeTrackRenderer.extend({
+var CircsterSummaryTreeTrackView = CircsterQuantitativeTrackView.extend({
 
     get_data_bounds: function(data) {
         // Get max across data.
@@ -546,9 +545,9 @@
 });
 
 /**
- * Layout for BigWig data in a circster visualization.
+ * Bigwig track view in Circster
  */
-var CircsterBigWigTrackRenderer = CircsterQuantitativeTrackRenderer.extend({
+var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
 
     get_data_bounds: function(data) {
         // Set max across dataset by extracting all values, flattening them into a 



https://bitbucket.org/galaxy/galaxy-central/changeset/e1ea65232d19/
changeset:   e1ea65232d19
user:        jgoecks
date:        2012-10-16 19:45:08
summary:     Merge
affected #:  1 file

diff -r 605f4d69d5db3f9bbfc949ac22ba5ee744649a5f -r e1ea65232d19a053be0725a91b47a1d81e309ee6 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -259,7 +259,7 @@
             can_generate_dependency_metadata = False
             tool_dependency_name = elem.get( 'name', None )
             if tool_dependency_name and tool_dependency_version:
-                for tool_dict in metadata_dict[ 'tools' ]:
+                for tool_dict in metadata_dict.get( 'tools', [] ):
                     requirements = tool_dict.get( 'requirements', [] )
                     for requirement_dict in requirements:
                         req_name = requirement_dict.get( 'name', None )
@@ -281,7 +281,7 @@
                 # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
                 env_var_name = env_var_elem.get( 'name', None )
                 if env_var_name:
-                    for tool_dict in metadata_dict[ 'tools' ]:
+                    for tool_dict in metadata_dict.get( 'tools', [] ):
                         requirements = tool_dict.get( 'requirements', [] )
                         for requirement_dict in requirements:
                             # {"name": "R_SCRIPT_PATH", "type": "set_environment", "version": null}

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

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[galaxy-commits] commit/galaxy-central: 2 new changesets

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