[galaxy-commits] commit/galaxy-central: jgoecks: Viz framework: (a) improvements in setting dataset type when returning infomation; (b) transition Circster to use GenomeDataManager rather than custom data structures.

25 Sep 2012

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d6d0c963712a/
changeset:   d6d0c963712a
user:        jgoecks
date:        2012-09-25 15:18:00
summary:     Viz framework: (a) improvements in setting dataset type when returning infomation; (b) transition Circster to use GenomeDataManager rather than custom data structures.
affected #:  7 files
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 lib/galaxy/visualization/data_providers/genome.py

--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -113,7 +113,7 @@
 class GenomeDataProvider( BaseDataProvider ):
     """ Base class for genome data providers. """
-    data_type = None
+    dataset_type = None
""" 
     Mapping from column name to payload data; this mapping is used to create
@@ -179,12 +179,21 @@
         """
         Returns data for complete genome.
         """
-        dataset_summary = []
+        genome_data = []
         for chrom_info in chroms_info[ 'chrom_info' ]:
-            summary = self.get_data( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], **kwargs )
-            dataset_summary.append( summary )
+            chrom = chrom_info[ 'chrom' ]
+            chrom_len = chrom_info[ 'len' ]
+            chrom_data = self.get_data( chrom, 0, chrom_len, **kwargs )
+            if chrom_data:
+                chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len )
+                chrom_data[ 'dataset_type' ] = self.dataset_type
+                genome_data.append( chrom_data )
-        return dataset_summary
+        return {
+            'data': genome_data,
+            'dataset_type': self.dataset_type
+        }
+
def get_filters( self ):
         """ 
@@ -316,7 +325,7 @@
class TabixDataProvider( FilterableMixin, GenomeDataProvider ):
-    data_type = 'tabix'
+    dataset_type = 'tabix'
"""
     Tabix index data provider for the Galaxy track browser.
@@ -358,7 +367,7 @@
 #
class IntervalDataProvider( GenomeDataProvider ):
-    data_type = 'interval_index'
+    dataset_type = 'interval_index'
"""
     Processes interval data from native format to payload format.
@@ -444,7 +453,7 @@
     Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]
     """
-    data_type = 'interval_index'
+    dataset_type = 'interval_index'
def get_iterator( self, chrom, start, end ):
         raise Exception( "Unimplemented Method" )
@@ -541,7 +550,7 @@
     for large datasets.
     """
-    data_type = 'interval_index'
+    dataset_type = 'interval_index'
def get_iterator( self, chrom=None, start=None, end=None ):
         # Read first line in order to match chrom naming format.
@@ -581,7 +590,7 @@
col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } }
-    data_type = 'bai'
+    dataset_type = 'bai'
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
         """
@@ -687,7 +696,7 @@
     for large datasets.
     """
-    data_type = 'tabix'
+    dataset_type = 'tabix'
def get_iterator( self, chrom, start, end ):
         # Read first line in order to match chrom naming format.
@@ -721,7 +730,7 @@
     Summary tree data provider for the Galaxy track browser. 
     """
-    data_type = 'summary_tree'
+    dataset_type = 'summary_tree'
CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance
@@ -765,7 +774,13 @@
         if results == "detail" or results == "draw":
             return results
         else:
-            return results, stats[ level ][ "max" ], stats[ level ]["avg" ], stats[ level ][ "delta" ]
+            return {
+                'dataset_type': self.dataset_type,
+                'data': results,
+                'max': stats[ level ][ "max" ],
+                'avg': stats[ level ][ "avg" ],
+                'delta': stats[ level ][ "delta" ]
+            }
def has_data( self, chrom ):
         """
@@ -788,7 +803,7 @@
     is reported in 1-based, closed format, i.e. SAM/BAM format.
     """
-    data_type = 'bai'
+    dataset_type = 'bai'
def get_filters( self ):
         """
@@ -970,7 +985,7 @@
class SamDataProvider( BamDataProvider ):
-    data_type = 'bai'
+    dataset_type = 'bai'
def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ):
         """ Create SamDataProvider. """
@@ -987,7 +1002,7 @@
     BBI data provider for the Galaxy track browser. 
     """
-    data_type = 'bigwig'
+    dataset_type = 'bigwig'
def valid_chroms( self ):
         # No way to return this info as of now
@@ -1122,7 +1137,7 @@
     """
     col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } }
-    data_type = 'interval_index'
+    dataset_type = 'interval_index'
def write_data_to_file( self, regions, filename ):
         source = open( self.original_dataset.file_name )
@@ -1201,7 +1216,7 @@
     for large datasets.
     """
-    data_type = 'interval_index'
+    dataset_type = 'interval_index'
def get_iterator( self, chrom, start, end ):
         """
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 lib/galaxy/web/api/datasets.py
--- a/lib/galaxy/web/api/datasets.py
+++ b/lib/galaxy/web/api/datasets.py
@@ -139,12 +139,15 @@
         if mode == "Coverage":
             # Get summary using minimal cutoffs.
             indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' )
-            summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 )
+            summary = indexer.get_data( chrom, low, high, 
+                                        resolution=kwargs[ 'resolution' ], 
+                                        level=kwargs.get( 'level', None ),
+                                        detail_cutoff=0, draw_cutoff=0 )
             if summary == "detail":
                 # Use maximum level of detail--2--to get summary data no matter the resolution.
                 summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 )
             frequencies, max_v, avg_v, delta = summary
-            return { 'dataset_type': indexer.data_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
+            return { 'dataset_type': indexer.dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
             # Only check for summary_tree if it's Auto mode (which is the default)
@@ -153,14 +156,13 @@
             indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' )
             summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] )
             if summary is None:
-                return { 'dataset_type': indexer.data_type, 'data': None }
+                return { 'dataset_type': indexer.dataset_type, 'data': None }
if summary == "draw":
                 kwargs["no_detail"] = True # meh
                 extra_info = "no_detail"
             elif summary != "detail":
-                frequencies, max_v, avg_v, delta = summary
-                return { 'dataset_type': indexer.data_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
+                return summary
# Get data provider.
         data_provider = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='data' )
@@ -171,7 +173,7 @@
# Get and return data from data_provider.
         result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs )
-        result.update( { 'dataset_type': data_provider.data_type, 'extra_info': extra_info } )
+        result.update( { 'dataset_type': data_provider.dataset_type, 'extra_info': extra_info } )
         return result
def _raw_data( self, trans, dataset, **kwargs ):
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -760,7 +760,7 @@
                                                                                 original_dataset=dataset, 
                                                                                 source='index' )
             # HACK: pass in additional params, which are only used for summary tree data, not BBI data.
-            track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) }
+            track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 )
return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome )
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 static/scripts/viz/circster.js
--- a/static/scripts/viz/circster.js
+++ b/static/scripts/viz/circster.js
@@ -1,4 +1,4 @@
-define( ["libs/d3", "viz/visualization"], function( d3, visualization ) {
+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;
@@ -48,7 +48,8 @@
             // Compute radius start based on model, will be centered 
             // and fit entirely inside element by default.
             init_radius_start = ( Math.min(width, height)/2 - 
-                                  this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) );
+                                  this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ),
+            tracks = this.model.get('tracks');
// Set up SVG element.
         var svg = d3.select(self.$el[0])
@@ -59,26 +60,37 @@
               // Set up zooming, dragging.
               .append('svg:g')
                 .call(d3.behavior.zoom().on('zoom', function() {
+                    // Do zoom.
                     svg.attr("transform",
                       "translate(" + d3.event.translate + ")" + 
                       " scale(" + d3.event.scale + ")");
-                    var utils = new SVGUtils();
-                    var visible_elts = d3.selectAll('path').filter(function(d, i) {
+
+                    // Update visible elements with more data.
+                    var utils = new SVGUtils(),
+                        tracks_and_chroms_to_update = {};
+
+                    tracks.each(function(t) {
+                        tracks_and_chroms_to_update[t.id] = [];
+                    });
+
+                    d3.selectAll('path.chrom-data').filter(function(d, i) {
                         return utils.is_visible(this, svg);
+                    }).each(function(d, i) {
+                        var elt_data = $.data(this, "chrom_data");
+                        tracks_and_chroms_to_update[elt_data.track.id].push(elt_data.chrom);
                     });
-                    visible_elts.each(function(d, i) {
-                        // TODO: redraw visible elements.
-                    });
+
+                    // TODO: update tracks and chroms.
+                    //console.log(tracks_and_chroms_to_update);
                 }))
                 .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
               .append('svg:g');
// -- Render each dataset in the visualization. --
-        this.model.get('tracks').each(function(track, index) {
-            var dataset = track.get('genome_wide_data'),
-                radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
-                track_renderer_class = (dataset instanceof visualization.GenomeWideBigWigData ? 
+        tracks.each(function(track, index) {
+            var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
+                track_renderer_class = (track.get('track_type') === 'LineTrack' ? 
                                         CircsterBigWigTrackRenderer : 
                                         CircsterSummaryTreeTrackRenderer );
@@ -160,12 +172,17 @@
     render_data: function(svg) {
         var self = this,
             chrom_arcs = this.chroms_layout(),
-            dataset = this.options.track.get('genome_wide_data'),
+            track = this.options.track,
             r_start = this.options.radius_start,
             r_end = this.options.radius_end,
+
+            genome_wide_data = track.get_genome_wide_data(this.options.genome),
// Merge chroms layout with data.
-            layout_and_data = _.zip(chrom_arcs, dataset.get('data')),
+            layout_and_data = _.zip(chrom_arcs, genome_wide_data),
+
+            // Get min, max in data.
+            bounds = this.get_bounds(genome_wide_data),
// Do dataset layout for each chromosome's data using pie layout.
             chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
@@ -173,7 +190,7 @@
                     data = chrom_info[1];
                 return self.render_chrom_data(svg, chrom_arc, data, 
                                               r_start, r_end, 
-                                              dataset.get('min'), dataset.get('max'));
+                                              bounds.min, bounds.max);
             });
return chroms_data_layout;
@@ -187,7 +204,7 @@
/**
      * Renders quantitative data with the form [x, value] and assumes data is equally spaced across
-     * chromosome.
+     * chromosome. Attachs a dict with track and chrom name information to DOM element.
      */
     render_quantitative_data: function(svg, chrom_arc, data, inner_radius, outer_radius, min, max) {
         // Radius scaler.
@@ -212,14 +229,25 @@
             .angle(line.angle());
// Render data.
-        var parent = svg.datum(data);
-                    
-        parent.append("path")
-            .attr("class", "chrom-data")
-            .attr("d", area);
-    }
+        var parent = svg.datum(data),                    
+            path = parent.append("path")
+                         .attr("class", "chrom-data")
+                         .attr("d", area);
-})
+        // Attach dict with track and chrom info for path.
+        $.data(path[0][0], "chrom_data", {
+            track: this.options.track,
+            chrom: chrom_arc.data.chrom
+        });
+    },
+
+    /**
+     * Returns an object with min, max attributes denoting the minimum and maximum
+     * values for the track.
+     */
+    get_bounds: function() {}
+
+});
/**
  * Layout for summary tree data in a circster visualization.
@@ -235,7 +263,19 @@
             return null;
         }
-        return this.render_quantitative_data(svg, chrom_arc, chrom_data[0], inner_radius, outer_radius, min, max);
+        return this.render_quantitative_data(svg, chrom_arc, chrom_data.data, inner_radius, outer_radius, min, max);
+    },
+
+    get_bounds: function(data) {
+        // Get max across data.
+        var max_data = _.map(data, function(d) {
+            if (!d || typeof d === 'string') { return 0; }
+            return d.max;
+        });
+        return {
+            min: 0,
+            max: (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0)
+        };
     }
 });
@@ -252,6 +292,27 @@
         if (data.length === 0) { return; }
return this.render_quantitative_data(svg, chrom_arc, data, inner_radius, outer_radius, min, max);
+    },
+
+    get_bounds: function(data) {
+        // Set max across dataset by extracting all values, flattening them into a 
+        // single array, and getting the min and max.
+        var values = _.flatten( _.map(data, function(d) {
+            if (d) {
+                // Each data point has the form [position, value], so return all values.
+                return _.map(d.data, function(p) {
+                    return p[1];
+                });
+            }
+            else {
+                return 0;
+            }
+        }) );
+
+        return {
+            min: _.min(values),
+            max: _.max(values)
+        };
     }
 });
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -3550,8 +3550,7 @@
         track.vertical_range = undefined;
         return $.getJSON( track.dataset.url(), 
             {  data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, 
-               high: track.view.max_high, hda_ldda: track.hda_ldda, dataset_id: 
-               track.dataset_id }, function(result) {
+               high: track.view.max_high, hda_ldda: track.hda_ldda }, function(result) {
             track.container_div.addClass( "line-track" );
             var data = result.data;
             if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -1,4 +1,4 @@
-define( ["mvc/data", "viz/trackster/util" ], function(data, util) {
+define( ["mvc/data", "viz/trackster/util" ], function(data_mod, util_mod) {
/**
  * Model, view, and controller objects for Galaxy visualization framework.
@@ -138,7 +138,6 @@
         dataset: null,
         filters_manager: null,
         data_type: "data",
-        genome_wide_summary_data: null,
         data_mode_compatible: function(entry, mode) { return true; },
         can_subset: function(entry) { return false; }
     }),
@@ -150,7 +149,7 @@
     data_is_ready: function() {
         var dataset = this.get('dataset'),
             ready_deferred = $.Deferred(),
-            ss_deferred = new util.ServerStateDeferred({
+            ss_deferred = new util_mod.ServerStateDeferred({
                 ajax_settings: {
                     url: this.get('dataset').url(),
                     data: {
@@ -176,7 +175,6 @@
         var dataset = this.get('dataset'),
             params = {
                 query: query,
-                dataset_id: dataset.id,
                 hda_ldda: dataset.get('hda_ldda'),
                 data_type: 'features'
             };
@@ -188,22 +186,17 @@
      */
     load_data: function(region, mode, resolution, extra_params) {
         // Setup data request params.
-        var params = {
+        var dataset = this.get('dataset'),
+            params = {
                         "data_type": this.get('data_type'),
                         "chrom": region.get('chrom'), 
                         "low": region.get('start'), 
                         "high": region.get('end'), 
                         "mode": mode,
-                        "resolution": resolution
-                     },
-            dataset = this.get('dataset');
-                        
-        // ReferenceDataManager does not have dataset.
-        if (dataset) {
-            params.dataset_id = dataset.id;
-            params.hda_ldda = dataset.get('hda_ldda');
-        }
-        
+                        "resolution": resolution,
+                        "hda_ldda": dataset.get('hda_ldda')
+                     };
+
         $.extend(params, extra_params);
// Add track filters to params.
@@ -533,69 +526,53 @@
     model: BrowserBookmark
 });
-var GenomeWideBigWigData = Backbone.Model.extend({
-    defaults: {
-        data: null,
-        min: 0,
-        max: 0
-    },
-
-    initialize: function(options) {
-        // Set max across dataset by extracting all values, flattening them into a 
-        // single array, and getting the min and max.
-        var values = _.flatten( _.map(this.get('data'), function(d) {
-            if (d.data.length !== 0) {
-                // Each data point has the form [position, value], so return all values.
-                return _.map(d.data, function(p) {
-                    return p[1];
-                });
-            }
-            else {
-                return 0;
-            }
-        }) );
-        this.set('max', _.max(values));
-        this.set('min', _.min(values));
-    }
-});
-
-/**
- * Genome-wide summary tree dataset.
- */
-var GenomeWideSummaryTreeData = Backbone.RelationalModel.extend({
-    defaults: {
-        data: null,
-        min: 0,
-        max: 0
-    },
-    
-    initialize: function(options) {
-        // Set max across dataset.
-        var max_data = _.max(this.get('data'), function(d) {
-            if (!d || typeof d === 'string') { return 0; }
-            return d[1];
-        });
-        this.attributes.max = (max_data && typeof max_data !== 'string' ? max_data[1] : 0);
-    }
-});
-
 /**
  * A track of data in a genome visualization.
  */
 // TODO: rename to Track and merge with Trackster's Track object.
-var BackboneTrack = data.Dataset.extend({
+var BackboneTrack = data_mod.Dataset.extend({
initialize: function(options) {
         // Dataset id is unique ID for now.
         this.set('id', options.dataset_id);
-        // Create genome-wide dataset if available.
-        var genome_wide_data = this.get('genome_wide_data');
-        if (genome_wide_data) {
-            var gwd_class = (this.get('track_type') === 'LineTrack' ? 
-                             GenomeWideBigWigData : GenomeWideSummaryTreeData);
-            this.set('genome_wide_data', new gwd_class(genome_wide_data));
+        // Set up data manager.
+        var data_manager = new GenomeDataManager({
+            dataset: this
+        });
+        this.set('data_manager', data_manager);
+
+        // If there's preloaded data, add it to data manager.
+        var preloaded_data = this.get('preloaded_data');
+        if (preloaded_data) {
+            // Increase size to accomodate all preloaded data.
+            data_manager.set('num_elements', preloaded_data.data.length);
+
+            // Put data into manager.
+            _.each(preloaded_data.data, function(entry) {
+                data_manager.set_data(entry.region, entry);
+            });
         }
+    },
+
+    /**
+     * Returns an array of data with each entry representing one chromosome/contig
+     * of data.
+     */
+    get_genome_wide_data: function(genome) {
+        var self = this,
+            data_manager = this.get('data_manager');
+
+        //  Map chromosome data into track data.
+        return _.map(genome.get('chroms_info').chrom_info, function(chrom_info) {
+            return data_manager.get_elt(
+                new GenomeRegion({
+                    chrom: chrom_info.chrom,
+                    start: 0,
+                    end: chrom_info.len
+                })
+            );
+        });
     }
 });
@@ -716,7 +693,7 @@
                                 },
                                 id = $(this).val();
                                 if ($(this).attr("name") !== "id") {
-                                    data['hda_ldda'] = 'ldda';
+                                    data.hda_ldda = 'ldda';
                                 }
                                 requests[requests.length] = $.ajax({
                                     url: add_track_async_url + "/" + id,
@@ -754,8 +731,6 @@
     GenomeRegion: GenomeRegion,
     GenomeRegionCollection: GenomeRegionCollection,
     GenomeVisualization: GenomeVisualization,
-    GenomeWideBigWigData: GenomeWideBigWigData,
-    GenomeWideSummaryTreeData: GenomeWideSummaryTreeData,
     ReferenceTrackDataManager: ReferenceTrackDataManager,
     TrackBrowserRouter: TrackBrowserRouter,
     TrackConfig: TrackConfig,
diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 templates/visualization/circster.mako
--- a/templates/visualization/circster.mako
+++ b/templates/visualization/circster.mako
@@ -23,6 +23,7 @@
         require.config({ 
             baseUrl: "${h.url_for('/static/scripts')}",
             shim: {
+                "libs/underscore": { exports: "_" },
                 "libs/d3": { exports: "d3" }
             }
         });
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[galaxy-commits] commit/galaxy-central: jgoecks: Viz framework: (a) improvements in setting dataset type when returning infomation; (b) transition Circster to use GenomeDataManager rather than custom data structures.