1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f33269063dab/ changeset: f33269063dab user: jgoecks date: 2012-07-09 15:45:34 summary: Visualization framework enhancements: (a) support for unpacking complete genome/trackster visualizations and (b) Circster view now uses genome visualizations rather than individual datasets as model. affected #: 6 files
diff -r e449670f80edec4bec2ac81cd9e3630ff9e6a3b0 -r f33269063dab72e84f1ba7cb1ebc509ee73651e8 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -614,9 +614,23 @@ def valid_chroms( self ): st = summary_tree_from_file( self.converted_dataset.file_name ) return st.chrom_blocks.keys() - + + def get_genome_data( self, chroms_info ): + """ + Returns summary tree data for complete genome. + """ + dataset_summary = [] + for chrom_info in chroms_info[ 'chrom_info' ]: + summary = self.get_summary( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], level=4 ) + dataset_summary.append( summary ) + + return dataset_summary
+ # TODO: rename to get_data to match other providers. def get_summary( self, chrom, start, end, level=None, resolution=None ): + """ + Returns summary tree data for a given genomic region. + """ filename = self.converted_dataset.file_name st = self.CACHE[filename] if st is None:
diff -r e449670f80edec4bec2ac81cd9e3630ff9e6a3b0 -r f33269063dab72e84f1ba7cb1ebc509ee73651e8 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -233,7 +233,7 @@
@web.expose @web.require_login() - def browser(self, trans, id, chrom="", **kwargs): + def browser(self, trans, id, **kwargs): """ Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`. """ @@ -471,6 +471,11 @@
@web.expose def paramamonster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ): + """ + Creates a paramamonster visualization using the incoming parameters. If id is available, + get the visualization with the given id; otherwise, create a new visualization using + a given dataset and regions. + """ # Need to create history if necessary in order to create tool form. trans.get_history( create=True )
@@ -497,27 +502,30 @@ return trans.fill_template_mako( "visualization/paramamonster.mako", config=viz_config )
@web.expose - def circster( self, trans, hda_ldda, dataset_id ): - # Get dataset. - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + def circster( self, trans, id, **kwargs ): + vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + viz_config = self.get_visualization_config( trans, vis )
# Get genome info. - dbkey = dataset.dbkey + dbkey = viz_config[ 'dbkey' ] chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) genome = { 'dbkey': dbkey, 'chroms_info': chroms_info }
- # Get summary tree data for dataset. - data_sources = self._get_datasources( trans, dataset ) - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) - dataset_summary = [] - for chrom_info in chroms_info[ 'chrom_info' ]: - summary = indexer.get_summary( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], level=4 ) - dataset_summary.append( summary ) + # Add genome-wide summary tree data to each track in viz. + tracks = viz_config[ 'tracks' ] + for track in tracks: + # Get dataset and indexed datatype. + dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) + data_sources = self._get_datasources( trans, dataset ) + indexed_type = data_sources['index']['name']
- return trans.fill_template_mako( "visualization/circster.mako", dataset=dataset, dataset_summary=dataset_summary, genome=genome ) - + # Get converted dataset and append track's genome data. + converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) + data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) + track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info ) } + + return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) + # ----------------- # Helper methods. # -----------------
diff -r e449670f80edec4bec2ac81cd9e3630ff9e6a3b0 -r f33269063dab72e84f1ba7cb1ebc509ee73651e8 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",datasets:[]},url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var TracksterVisualization=Visualization.extend({defaults:{bookmarks:[],viewport:{}}});var CircsterVisualization=Visualization.extend({});var HistogramDataset=Backbone.Model.extend({initialize:function(a){this.attributes.data=a;this.attributes.max=_.max(a,function(b){if(!b||typeof b==="string"){return 0}return b[1]})[1]}});var TrackConfig=Backbone.Model.extend({});var CircsterHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.dataset=a.dataset;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height},render:function(){var d=this.radius_start,e=this.dataset_arc_height,j=new CircsterHistogramDatasetLayout({genome:this.genome,total_gap:this.total_gap}),i=j.chroms_layout(),g=_.zip(i,this.dataset.attributes.data),h=this.dataset.attributes.max,b=_.map(g,function(m){var n=m[0],l=m[1];return j.chrom_data_layout(n,l,d,d+e,h)});var c=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height).append("g").attr("transform","translate("+this.width/2+","+this.height/2+")");var k=c.append("g").attr("id","inner-arc"),f=d3.svg.arc().innerRadius(d).outerRadius(d+e),a=k.selectAll("#inner-arc>path").data(i).enter().append("path").attr("d",f).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(l){return l.data.chrom});_.each(b,function(l){if(!l){return}var o=c.append("g"),n=d3.svg.arc().innerRadius(d),m=o.selectAll("path").data(l).enter().append("path").attr("d",n).style("stroke","red").style("fill","red")})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})}; \ No newline at end of file +var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,genome_wide_summary_data:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var GenomeWideSummaryData=Backbone.RelationalModel.extend({defaults:{data:null,max:0},initialize:function(b){var a=_.max(this.get("data"),function(c){if(!c||typeof c==="string"){return 0}return c[1]});this.attributes.max=(a&&typeof a!=="string"?a[1]:0)}});var BackboneTrack=Dataset.extend({initialize:function(a){this.set("id",a.dataset_id)},relations:[{type:Backbone.HasOne,key:"genome_wide_data",relatedModel:"GenomeWideSummaryData"}]});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:"BackboneTrack"}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var GenomeVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{bookmarks:null,viewport:null})});var TrackConfig=Backbone.Model.extend({});var CircsterHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height},render:function(){var c=this.model.get("tracks").at(0).get("genome_wide_data");var e=this.radius_start,f=this.dataset_arc_height,k=new CircsterHistogramDatasetLayout({genome:this.genome,total_gap:this.total_gap}),j=k.chroms_layout(),h=_.zip(j,c.get("data")),i=c.get("max"),b=_.map(h,function(n){var o=n[0],m=n[1];return k.chrom_data_layout(o,m,e,e+f,i)});var d=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height).append("g").attr("transform","translate("+this.width/2+","+this.height/2+")");var l=d.append("g").attr("id","inner-arc"),g=d3.svg.arc().innerRadius(e).outerRadius(e+f),a=l.selectAll("#inner-arc>path").data(j).enter().append("path").attr("d",g).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(m){return m.data.chrom});_.each(b,function(m){if(!m){return}var p=d.append("g"),o=d3.svg.arc().innerRadius(e),n=p.selectAll("path").data(m).enter().append("path").attr("d",o).style("stroke","red").style("fill","red")})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})}; \ No newline at end of file
diff -r e449670f80edec4bec2ac81cd9e3630ff9e6a3b0 -r f33269063dab72e84f1ba7cb1ebc509ee73651e8 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -169,6 +169,7 @@ filters_manager: null, data_url: null, dataset_state_url: null, + genome_wide_summary_data: null, data_mode_compatible: function(entry, mode) { return true; }, can_subset: function(entry) { return false; } }), @@ -549,17 +550,64 @@ });
/** + * Genome-wide summary data. + */ +var GenomeWideSummaryData = Backbone.RelationalModel.extend({ + defaults: { + data: null, + 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 = Dataset.extend({ + + initialize: function(options) { + // Dataset id is unique ID for now. + this.set('id', options.dataset_id); + }, + + relations: [ + { + type: Backbone.HasOne, + key: 'genome_wide_data', + relatedModel: 'GenomeWideSummaryData' + } + ] +}); + +/** * A visualization. */ var Visualization = Backbone.RelationalModel.extend({ defaults: { - id: "", - title: "", - type: "", - dbkey: "", - datasets: [] + id: '', + title: '', + type: '', + dbkey: '', + tracks: null }, - + + relations: [ + { + type: Backbone.HasMany, + key: 'tracks', + relatedModel: 'BackboneTrack' + } + ], + // Use function because visualization_url changes depending on viz. // FIXME: all visualizations should save to the same URL (and hence // this function won't be needed). @@ -585,42 +633,13 @@ });
/** - * A Trackster visualization. + * A Genome space visualization. */ -var TracksterVisualization = Visualization.extend({ - defaults: { - bookmarks: [], - viewport: {} - } -}); - -/** - * A Circster visualization. - */ -var CircsterVisualization = Visualization.extend({ -}); - -/** - * A histogram dataset. - */ -var HistogramDataset = Backbone.Model.extend({ - /* - defaults: { - data: [], - dataset: null, - max: 0 - }, - */ - - initialize: function(data) { - // Set max across dataset. - this.attributes.data = data; - this.attributes.max = _.max(data, function(d) { - if (!d || typeof d === "string") { return 0; } - return d[1]; - })[1]; - } - +var GenomeVisualization = Visualization.extend({ + defaults: _.extend({}, Visualization.prototype.defaults, { + bookmarks: null, + viewport: null + }) });
/** @@ -701,13 +720,15 @@ this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; - this.dataset = options.dataset; this.radius_start = options.radius_start; this.dataset_arc_height = options.dataset_arc_height; },
render: function() { // -- Layout viz. -- + + // FOR TESTING: + var dataset = this.model.get('tracks').at(0).get('genome_wide_data');
var radius_start = this.radius_start, dataset_arc_height = this.dataset_arc_height, @@ -720,8 +741,8 @@ chrom_arcs = arcs_layout.chroms_layout(),
// Merge chroms layout with data. - layout_and_data = _.zip(chrom_arcs, this.dataset.attributes.data), - dataset_max = this.dataset.attributes.max, + layout_and_data = _.zip(chrom_arcs, dataset.get('data')), + dataset_max = dataset.get('max'),
// Do dataset layout for each chromosome's data using pie layout. chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
diff -r e449670f80edec4bec2ac81cd9e3630ff9e6a3b0 -r f33269063dab72e84f1ba7cb1ebc509ee73651e8 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -127,30 +127,36 @@ });
// FIXME: give unique IDs to Drawables and save overview as ID. - var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null); - var visualization = new TracksterVisualization({ - 'id': view.vis_id, - 'title': view.name, - 'dbkey': view.dbkey, - 'type': 'trackster', - 'datasets': view.to_dict(), - 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, - 'bookmarks': bookmarks + var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null), + viz_config = { + 'id': view.vis_id, + 'title': view.name, + 'dbkey': view.dbkey, + 'type': 'trackster', + 'datasets': view.to_dict(), + 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, + 'bookmarks': bookmarks + }; + + $.ajax({ + url: galaxy_paths.get("visualization_url"), + type: "POST", + dataType: "json", + data: { + vis_json: JSON.stringify(viz_config) + } + }).success(function(vis_info) { + hide_modal(); + view.vis_id = vis_info.vis_id; + view.has_changes = false; + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url + window.location.hash); + }) + .error(function() { + show_modal( "Could Not Save", "Could not save visualization. Please try again later.", + { "Close" : hide_modal } ); }); - - visualization.save() - .success(function(vis_info) { - hide_modal(); - view.vis_id = vis_info.vis_id; - view.has_changes = false; - - // Needed to set URL when first saving a visualization. - window.history.pushState({}, "", vis_info.url + window.location.hash); - }) - .error(function() { - show_modal( "Could Not Save", "Could not save visualization. Please try again later.", - { "Close" : hide_modal } ); - }); } }, { icon_class: 'cross-circle', title: 'Close', on_click: function() { window.location = "${h.url_for( controller='visualization', action='list' )}";
diff -r e449670f80edec4bec2ac81cd9e3630ff9e6a3b0 -r f33269063dab72e84f1ba7cb1ebc509ee73651e8 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -16,7 +16,7 @@ <%def name="javascripts()"> ${parent.javascripts()}
- ${h.js( "libs/d3", "viz/visualization" )} + ${h.js( "libs/d3", "mvc/data", "viz/visualization" )}
<script type="text/javascript"> $(function() { @@ -65,23 +65,23 @@
// -- Viz set up. --
- var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')), - dataset = new HistogramDataset(JSON.parse('${ h.to_json_string( dataset_summary ) }')), - circster = new CircsterView({ + var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) + visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), + viz_view = new CircsterView({ width: 600, height: 600, // Gap is difficult to set because it very dependent on chromosome size and organization. total_gap: 2 * Math.PI * 0.5, genome: genome, - dataset: dataset, + model: visualization, radius_start: 100, dataset_arc_height: 50 });
// -- Render viz. --
- circster.render(); - $('#vis').append(circster.$el); + viz_view.render(); + $('#vis').append(viz_view.$el); }); </script></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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