February 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jeremy goecks: (1) Update Backbone Config objects and (2) add config options to Circster.
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b2206f4ca10f/ Changeset: b2206f4ca10f User: jeremy goecks Date: 2014-02-06 21:41:05 Summary: (1) Update Backbone Config objects and (2) add config options to Circster. Affected #: 4 files diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".tooltip").removeClass("in");var y=$(this).siblings(".tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:"Configure",body:drawable.config.build_form(),buttons:{Cancel:h,OK:f}})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",f.get_random_color())}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined}},{from_config_dict:function(h){var g=c.map(c.keys(h),function(i){return{key:i,value:h[i]}});return new e(g)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(k,p){if(k.get("hidden")){return}var j="param_"+p,q=k.get("type"),u=k.get("value");var w=$("<div class='form-row' />").appendTo(g);w.append($("<label />").attr("for",j).text(k.get("label")+":"));if(q==="bool"){w.append($('<input type="checkbox" />').attr("id",j).attr("name",j).attr("checked",u))}else{if(q==="text"){w.append($('<input type="text"/>').attr("id",j).val(u).click(function(){$(this).select()}))}else{if(q==="select"){var s=$("<select />").attr("id",j);for(var n=0;n<k.options.length;n++){$("<option/>").text(k.options[n].label).attr("value",k.options[n].value).appendTo(s)}s.val(u);w.append(s)}else{if(q==="color"){var v=$("<div/>").appendTo(w),r=$("<input />").attr("id",j).attr("name",j).val(u).css("float","left").appendTo(v).click(function(x){$(".tooltip").removeClass("in");var i=$(this).siblings(".tooltip").addClass("in");i.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(i).height()/2)+($(this).height()/2)}).show();i.click(function(y){y.stopPropagation()});$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});x.stopPropagation()}),o=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(v).attr("title","Set new random color").tooltip(),t=$("<div class='tooltip right' style='position: absolute;' />").appendTo(v).hide(),l=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(t),h=$("<div class='tooltip-arrow'></div>").appendTo(t),m=$.farbtastic(l,{width:100,height:100,callback:r,color:u});v.append($("<div/>").css("clear","both"));(function(i){o.click(function(){i.setColor(f.get_random_color())})})(m)}else{w.append($("<input />").attr("id",j).attr("name",j).val(u))}}}}if(k.help){w.append($("<div class='help'/>").text(k.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){g.update_from_form();Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=container.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["utils/utils","libs/underscore","libs/d3","viz/visualization","utils/config"],function(h,i,n,k,c){h.cssLoadFile("static/style/circster.css");var o=Backbone.Model.extend({is_visible:function(s,p){var q=s.getBoundingClientRect(),r=$("svg")[0].getBoundingClientRect();if(q.right<0||q.left>r.right||q.bottom<0||q.top>r.bottom){return false}return true}});var j={drawTicks:function(t,s,x,r,p){var w=t.append("g").selectAll("g").data(s).enter().append("g").selectAll("g").data(x).enter().append("g").attr("class","tick").attr("transform",function(y){return"rotate("+(y.angle*180/Math.PI-90)+")translate("+y.radius+",0)"});var v=[],u=[],q=function(y){return y.angle>Math.PI?"end":null};if(p){v=[0,0,0,-4];u=[4,0,"",".35em"];q=null}else{v=[1,0,4,0];u=[0,4,".35em",""]}w.append("line").attr("x1",v[0]).attr("y1",v[1]).attr("x2",v[2]).attr("y1",v[3]).style("stroke","#000");w.append("text").attr("x",u[0]).attr("y",u[1]).attr("dx",u[2]).attr("dy",u[3]).attr("text-anchor",q).attr("transform",r).text(function(y){return y.label})},formatNum:function(q,p){if(p===undefined){p=2}if(q===null){return null}var s=null;if(q<1){s=q.toPrecision(p)}else{var r=Math.round(q.toPrecision(p));if(q<1000){s=r}else{if(q<1000000){s=Math.round((r/1000).toPrecision(3)).toFixed(0)+"K"}else{if(q<1000000000){s=Math.round((r/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return s}};var d=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(p){this.genome=p.genome;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);var q=this.model.get("config");q.get("arc_dataset_height").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(p){return p.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(p){return p.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var r=this.get_circular_tracks(),s=this.model.get("config").get_value("arc_dataset_height"),p=Math.min(this.$el.width(),this.$el.height()),u=p/2-r.length*(s+this.track_gap)-(this.label_arc_height+this.track_gap),t=n.range(u,p/2,s+this.track_gap);var q=this;return i.map(t,function(v){return[v,v+s]})},render:function(){var y=this,p=y.$el.width(),x=y.$el.height(),u=this.get_circular_tracks(),s=this.get_chord_tracks(),r=y.model.get("config").get_value("total_gap"),t=this.get_tracks_bounds(),q=n.select(y.$el[0]).append("svg").attr("width",p).attr("height",x).attr("pointer-events","all").append("svg:g").call(n.behavior.zoom().on("zoom",function(){var z=n.event.scale;q.attr("transform","translate("+n.event.translate+") scale("+z+")");if(y.scale!==z){if(y.zoom_drag_timeout){clearTimeout(y.zoom_drag_timeout)}y.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+p/2+","+x/2+")").append("svg:g").attr("class","tracks");this.circular_views=u.map(function(A,B){var z=new e({el:q.append("g")[0],track:A,radius_bounds:t[B],genome:y.genome,total_gap:r});z.render();return z});this.chords_views=s.map(function(A){var z=new l({el:q.append("g")[0],track:A,radius_bounds:t[0],genome:y.genome,total_gap:r});z.render();return z});var w=this.circular_views[this.circular_views.length-1].radius_bounds[1],v=[w,w+this.label_arc_height];this.label_track_view=new b({el:q.append("g")[0],track:new d(),radius_bounds:v,genome:y.genome,total_gap:r});this.label_track_view.render()},add_track:function(w){var q=this.model.get("config").get_value("total_gap");if(w.get("track_type")==="DiagonalHeatmapTrack"){var s=this.circular_views[0].radius_bounds,v=new l({el:n.select("g.tracks").append("g")[0],track:w,radius_bounds:s,genome:this.genome,total_gap:q});v.render();this.chords_views.push(v)}else{var u=this.get_tracks_bounds();i.each(this.circular_views,function(x,y){x.update_radius_bounds(u[y])});i.each(this.chords_views,function(x){x.update_radius_bounds(u[0])});var t=this.circular_views.length,p=new e({el:n.select("g.tracks").append("g")[0],track:w,radius_bounds:u[t],genome:this.genome,total_gap:q});p.render();this.circular_views.push(p);var r=u[u.length-1];r[1]=r[0];this.label_track_view.update_radius_bounds(r)}},remove_track:function(q,s,r){var p=this.circular_views[r.index];this.circular_views.splice(r.index,1);p.$el.remove();var t=this.get_tracks_bounds();i.each(this.circular_views,function(u,v){u.update_radius_bounds(t[v])})},update_track_bounds:function(){var p=this.get_tracks_bounds();i.each(this.circular_views,function(q,r){q.update_radius_bounds(p[r])})}});var m=Backbone.View.extend({tagName:"g",initialize:function(p){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=p.total_gap;this.track=p.track;this.radius_bounds=p.radius_bounds;this.genome=p.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=n.select(this.$el[0])},get_fill_color:function(){var p=this.track.get("config").get_value("block_color");if(!p){p=this.track.get("config").get_value("color")}return p},render:function(){var t=this.parent_elt;if(!t){console.log("no parent elt")}var s=this.chroms_layout,v=n.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),p=t.selectAll("g").data(s).enter().append("svg:g"),r=p.append("path").attr("d",v).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);r.append("title").text(function(x){return x.data.chrom});var q=this,u=q.track.get("data_manager"),w=(u?u.data_is_ready():true);$.when(w).then(function(){$.when(q._render_data(t)).then(function(){r.style("fill",q.bg_fill);q.render_labels()})})},render_labels:function(){},update_radius_bounds:function(q){this.radius_bounds=q;var p=n.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",p);this._transition_chrom_data();this._transition_labels()},update_scale:function(s){var r=this.scale;this.scale=s;if(s<=r){return}var q=this,p=new o();this.parent_elt.selectAll("path.chrom-data").filter(function(u,t){return p.is_visible(this)}).each(function(z,v){var y=n.select(this),u=y.attr("chrom"),x=q.genome.get_chrom_region(u),w=q.track.get("data_manager"),t;if(!w.can_get_more_detailed_data(x)){return}t=q.track.get("data_manager").get_more_detailed_data(x,"Coverage",0,s);$.when(t).then(function(C){y.remove();q._update_data_bounds();var B=i.find(q.chroms_layout,function(D){return D.data.chrom===u});var A=q.get_fill_color();q._render_chrom_data(q.parent_elt,B,C).style("stroke",A).style("fill",A)})});return q},_transition_chrom_data:function(){var q=this.track,s=this.chroms_layout,p=this.parent_elt.selectAll("g>path.chrom-data"),t=p[0].length;if(t>0){var r=this;$.when(q.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){var u=i.reject(i.map(v,function(w,x){var y=null,z=r._get_path_function(s[x],w);if(z){y=z(w.data)}return y}),function(w){return w===null});p.each(function(x,w){n.select(this).transition().duration(1000).attr("d",u[w])})})}},_transition_labels:function(){},_update_data_bounds:function(){var p=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<p[0]||this.data_bounds[1]>p[1]){this._transition_chrom_data()}},_render_data:function(s){var r=this,q=this.chroms_layout,p=this.track,t=$.Deferred();$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){r.data_bounds=r.get_data_bounds(v);layout_and_data=i.zip(q,v),chroms_data_layout=i.map(layout_and_data,function(w){var x=w[0],y=w[1];return r._render_chrom_data(s,x,y)});var u=r.get_fill_color();r.parent_elt.selectAll("path.chrom-data").style("stroke",u).style("fill",u);t.resolve(s)});return t},_render_chrom_data:function(p,q,r){},_get_path_function:function(q,p){},_chroms_layout:function(){var q=this.genome.get_chroms_info(),s=n.layout.pie().value(function(u){return u.len}).sort(null),t=s(q),p=2*Math.PI*this.total_gap/q.length,r=i.map(t,function(w,v){var u=w.endAngle-p;w.endAngle=(u>w.startAngle?u:w.startAngle);return w});return r}});var b=m.extend({initialize:function(p){m.prototype.initialize.call(this,p);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(r){var q=this,p=r.selectAll("g");p.selectAll("path").attr("id",function(v){return"label-"+v.data.chrom});p.append("svg:text").filter(function(v){return v.endAngle-v.startAngle>q.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(v){return"#label-"+v.data.chrom}).attr("startOffset","25%").text(function(v){return v.data.chrom});var s=function(x){var v=(x.endAngle-x.startAngle)/x.value,w=n.range(0,x.value,25000000).map(function(y,z){return{radius:q.innerRadius,angle:y*v+x.startAngle,label:z===0?0:(z%3?null:q.formatNum(y))}});if(w.length<4){w[w.length-1].label=q.formatNum(Math.round((w[w.length-1].angle-x.startAngle)/v))}return w};var u=function(v){return v.angle>Math.PI?"rotate(180)translate(-16)":null};var t=i.filter(this.chroms_layout,function(v){return v.endAngle-v.startAngle>q.min_arc_len});this.drawTicks(this.parent_elt,t,s,u)}});i.extend(b.prototype,j);var g=m.extend({_quantile:function(q,p){q.sort(n.ascending);return n.quantile(q,p)},_render_chrom_data:function(p,s,q){var t=this._get_path_function(s,q);if(!t){return null}var r=p.datum(q.data),u=r.append("path").attr("class","chrom-data").attr("chrom",s.data.chrom).attr("d",t);return u},_get_path_function:function(s,r){if(typeof r==="string"||!r.data||r.data.length===0){return null}var p=n.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var t=n.scale.linear().domain([0,r.data.length]).range([s.startAngle,s.endAngle]);var q=n.svg.line.radial().interpolate("linear").radius(function(u){return p(u[1])}).angle(function(v,u){return t(u)});return n.svg.area.radial().interpolate(q.interpolate()).innerRadius(p(0)).outerRadius(q.radius()).angle(q.angle())},render_labels:function(){var p=this,q=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var q=this,s=i.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>0.08}),r=i.filter(s,function(u,t){return t%3===0}),p=i.flatten(i.map(r,function(t){return q._data_bounds_ticks_fn()(t)}));this.parent_elt.selectAll("g.tick").data(p).transition().attr("transform",function(t){return"rotate("+(t.angle*180/Math.PI-90)+")translate("+t.radius+",0)"})},_data_bounds_ticks_fn:function(){var p=this;visibleChroms=0;return function(q){return[{radius:p.radius_bounds[0],angle:q.startAngle,label:p.formatNum(p.data_bounds[0])},{radius:p.radius_bounds[1],angle:q.startAngle,label:p.formatNum(p.data_bounds[1])}]}},get_data_bounds:function(p){}});i.extend(g.prototype,j);var e=g.extend({get_data_bounds:function(q){var p=i.flatten(i.map(q,function(r){if(r){return i.map(r.data,function(s){return parseInt(s[1],10)||0})}else{return 0}}));return[i.min(p),this._quantile(p,0.98)||i.max(p)]}});var l=m.extend({render:function(){var p=this;$.when(p.track.get("data_manager").data_is_ready()).then(function(){$.when(p.track.get("data_manager").get_genome_wide_data(p.genome)).then(function(s){var r=[],q=p.genome.get_chroms_info();i.each(s,function(w,v){var t=q[v].chrom;var u=i.map(w.data,function(y){var x=p._get_region_angle(t,y[1]),z=p._get_region_angle(y[3],y[4]);return{source:{startAngle:x,endAngle:x+0.01},target:{startAngle:z,endAngle:z+0.01}}});r=r.concat(u)});p.parent_elt.append("g").attr("class","chord").selectAll("path").data(r).enter().append("path").style("fill",p.get_fill_color()).attr("d",n.svg.chord().radius(p.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(p){this.radius_bounds=p;this.parent_elt.selectAll("path").transition().attr("d",n.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(r,p){var q=i.find(this.chroms_layout,function(s){return s.data.chrom===r});return q.endAngle-((q.endAngle-q.startAngle)*(q.data.len-p)/q.data.len)}});var f=Backbone.View.extend({initialize:function(){var p=new k.Genome(galaxy_config.app.genome),q=new k.GenomeVisualization(galaxy_config.app.viz_config);q.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:0.4,view:"circster",hidden:true}]);var s=new a({el:$("#center .unified-panel-body"),genome:p,model:q});s.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var r=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){k.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",q.get("dbkey"),function(t){q.add_tracks(t)})}},{icon_class:"gear",title:"Settings",on_click:function(){var t=new c.ConfigSettingCollectionView({collection:q.get("config")});t.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:q.get("vis_id"),title:q.get("title"),dbkey:q.get("dbkey"),type:"trackster",vis_json:JSON.stringify(q)}}).success(function(t){Galaxy.modal.hide();q.set("vis_id",t.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});r.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(r.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:f}}); \ No newline at end of file diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -1,9 +1,10 @@ -define(['libs/underscore', 'viz/trackster/util'], function(_, util_mod) { +define(['libs/underscore', 'viz/trackster/util', 'utils/config'], function(_, util_mod, config_mod) { /** * A configuration setting. Currently key is used as id. */ var ConfigSetting = Backbone.Model.extend({ + initialize: function(options) { // Use key as id for now. var key = this.get('key'); @@ -19,26 +20,24 @@ if (this.get('type') === 'color' && !this.get('value')) { this.set('value', util_mod.get_random_color()); } - - // When value updated, cast is appropriately. - this.on('change:value', this.cast_value, this); }, /** - * Cast value from string to appropriate type. + * Cast and set value. This should be instead of + * setting.set('value', new_value) */ - cast_value: function() { - var type = this.get('type'), - value = this.get('value'); + set_value: function(value) { + var type = this.get('type'); if (type === 'float') { - value = parseFloat( value ); - } else if (type === 'int') { - value = parseInt( value, 10 ); + value = parseFloat(value); + } + else if (type === 'int') { + value = parseInt(value, 10); } // TODO: handle casting from string to bool? - this.set('value'); + this.set('value', value); } }, { // This is a master list of default settings for known settings. @@ -92,7 +91,8 @@ return undefined; } -}, { +}, +{ /** * Utility function that creates a ConfigSettingsCollection from a standard dictionary * with configuration key-value pairs. @@ -120,101 +120,99 @@ * Renders form for editing configuration settings. */ render: function() { - var track_config = this.model; var container = this.$el; - var param; + + this.collection.each(function(param, index) { + // Hidden params have no representation in the form + if (param.get('hidden')) { return; } - // Function to process parameters recursively - function handle_params( params, container ) { - for ( var index = 0; index < params.length; index++ ) { - param = params[index]; - // Hidden params have no representation in the form - if ( param.hidden ) { continue; } - // Build row for param - var id = 'param_' + index; - var value = track_config.values[ param.key ]; - var row = $("<div class='form-row' />").appendTo( container ); - row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); - // Draw parameter as checkbox - if ( type === 'bool' ) { - row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); - // Draw parameter as textbox - } else if ( type === 'text' ) { - row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); - // Draw paramter as select area - } else if ( type === 'select' ) { - var select = $('<select />').attr("id", id); - for ( var i = 0; i < param.options.length; i++ ) { - $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); - } - select.val( value ); - row.append( select ); - // Draw parameter as color picker - } else if ( type === 'color' ) { - var - container_div = $("<div/>").appendTo(row), - input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") - .appendTo(container_div).click(function(e) { - // Hide other pickers. - $(".tooltip").removeClass( "in" ); + // Build row for param. + var id = 'param_' + index, + type = param.get('type'), + value = param.get('value'); + var row = $("<div class='form-row' />").appendTo(container); + row.append($('<label />').attr("for", id ).text(param.get('label') + ":" )); + // Draw parameter as checkbox + if ( type === 'bool' ) { + row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); + } + // Draw parameter as textbox + else if ( type === 'text' ) { + row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); + } + // Draw parameter as select area + else if ( type === 'select' ) { + var select = $('<select />').attr("id", id); + for ( var i = 0; i < param.options.length; i++ ) { + $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); + } + select.val( value ); + row.append( select ); + + } + // Draw parameter as color picker + else if ( type === 'color' ) { + var + container_div = $("<div/>").appendTo(row), + input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") + .appendTo(container_div).click(function(e) { + // Hide other pickers. + $(".tooltip").removeClass( "in" ); + + // Show input's color picker. + var tip = $(this).siblings(".tooltip").addClass( "in" ); + tip.css( { + // left: $(this).position().left + ( $(input).width() / 2 ) - 60, + // top: $(this).position().top + $(this.height) + left: $(this).position().left + $(this).width() + 5, + top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) + } ).show(); - // Show input's color picker. - var tip = $(this).siblings(".tooltip").addClass( "in" ); - tip.css( { - // left: $(this).position().left + ( $(input).width() / 2 ) - 60, - // top: $(this).position().top + $(this.height) - left: $(this).position().left + $(this).width() + 5, - top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) - } ).show(); - - // Click management: - - // Keep showing tip if clicking in tip. - tip.click(function(e) { - e.stopPropagation(); - }); - - // Hide tip if clicking outside of tip. - $(document).bind( "click.color-picker", function() { - tip.hide(); - $(document).unbind( "click.color-picker" ); - }); - - // No propagation to avoid triggering document click (and tip hiding) above. + // Click management: + + // Keep showing tip if clicking in tip. + tip.click(function(e) { e.stopPropagation(); - }), - // Icon for setting a new random color; behavior set below. - new_color_icon = $("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(container_div) - .attr("title", "Set new random color").tooltip(), - // Color picker in tool tip style. - tip = $( "<div class='tooltip right' style='position: absolute;' />" ).appendTo(container_div).hide(), - // Inner div for padding purposes - tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip), - tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip), - farb_obj = $.farbtastic(tip_inner, { width: 100, height: 100, callback: input, color: value }); - - // Clear floating. - container_div.append( $("<div/>").css("clear", "both")); - - // Use function to fix farb_obj value. - (function(fixed_farb_obj) { - new_color_icon.click(function() { - fixed_farb_obj.setColor(util_mod.get_random_color()); - }); - })(farb_obj); - - } - else { - row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); - } - // Help text - if ( param.help ) { - row.append( $("<div class='help'/>").text( param.help ) ); - } + }); + + // Hide tip if clicking outside of tip. + $(document).bind( "click.color-picker", function() { + tip.hide(); + $(document).unbind( "click.color-picker" ); + }); + + // No propagation to avoid triggering document click (and tip hiding) above. + e.stopPropagation(); + }), + // Icon for setting a new random color; behavior set below. + new_color_icon = $("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(container_div) + .attr("title", "Set new random color").tooltip(), + // Color picker in tool tip style. + tip = $( "<div class='tooltip right' style='position: absolute;' />" ).appendTo(container_div).hide(), + // Inner div for padding purposes + tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip), + tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip), + farb_obj = $.farbtastic(tip_inner, { width: 100, height: 100, callback: input, color: value }); + + // Clear floating. + container_div.append( $("<div/>").css("clear", "both")); + + // Use function to fix farb_obj value. + (function(fixed_farb_obj) { + new_color_icon.click(function() { + fixed_farb_obj.setColor(util_mod.get_random_color()); + }); + })(farb_obj); + + } + else { + row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); } - } - // Handle top level parameters in order - handle_params( this.params, container ); + // Help text + if ( param.help ) { + row.append( $("<div class='help'/>").text( param.help ) ); + } + }); return this; }, @@ -222,13 +220,14 @@ /** * Render view in modal. */ - render_in_modal: function() { + render_in_modal: function(title) { // Set up handlers for cancel, ok button and for handling esc key. - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + var self = this, + cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { - this.update_from_form(); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); + self.update_from_form(); + Galaxy.modal.hide(); + $(window).unbind("keypress.check_enter_esc"); }, check_enter_esc = function(e) { if ((e.keyCode || e.which) === 27) { // Escape key @@ -246,8 +245,8 @@ this.render(); } Galaxy.modal.show({ - title: "Configure", - body: drawable.config.build_form(), + title: title || "Configure", + body: this.$el, buttons: { "Cancel": cancel_fn, "OK": ok_fn @@ -265,10 +264,10 @@ // Set value from view. var id = 'param_' + index; var value = self.$el.find( '#' + id ).val(); - if ( type === 'bool' ) { + if ( setting.get('type') === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } - setting.set('value', value); + setting.set_value(value); } }); } diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,4 +1,4 @@ -define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization"], function(utils, _, d3, visualization) { +define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(utils, _, d3, visualization, config) { // Load needed CSS. utils.cssLoadFile("static/style/circster.css"); @@ -133,9 +133,7 @@ className: 'circster', initialize: function(options) { - this.total_gap = options.total_gap; this.genome = options.genome; - this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 10; this.label_arc_height = 50; this.scale = 1; @@ -145,7 +143,10 @@ // When tracks added to/removed from model, update view. this.model.get('drawables').on('add', this.add_track, this); this.model.get('drawables').on('remove', this.remove_track, this); - this.get_circular_tracks(); + + // When config settings change, update view. + var vis_config = this.model.get('config'); + vis_config.get('arc_dataset_height').on('change:value', this.update_track_bounds, this); }, // HACKs: using track_type for circular/chord distinction in the functions below for now. @@ -172,22 +173,22 @@ * Returns a list of circular tracks' radius bounds. */ get_tracks_bounds: function() { - var circular_tracks = this.get_circular_tracks(); - dataset_arc_height = this.dataset_arc_height, + var circular_tracks = this.get_circular_tracks(), + dataset_arc_height = this.model.get('config').get_value('arc_dataset_height'), min_dimension = Math.min(this.$el.width(), this.$el.height()), // Compute radius start based on model, will be centered // and fit entirely inside element by default. radius_start = min_dimension / 2 - - circular_tracks.length * (this.dataset_arc_height + this.track_gap) - + circular_tracks.length * (dataset_arc_height + this.track_gap) - (this.label_arc_height + this.track_gap), // Compute range of track starting radii. - tracks_start_radii = d3.range(radius_start, min_dimension / 2, this.dataset_arc_height + this.track_gap); + tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + this.track_gap); // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { - return [radius, radius + self.dataset_arc_height]; + return [radius, radius + dataset_arc_height]; }); }, @@ -196,11 +197,11 @@ */ render: function() { var self = this, - dataset_arc_height = this.dataset_arc_height, width = self.$el.width(), height = self.$el.height(), circular_tracks = this.get_circular_tracks(), chords_tracks = this.get_chord_tracks(), + total_gap = self.model.get('config').get_value('total_gap'), tracks_bounds = this.get_tracks_bounds(), // Set up SVG element. @@ -249,7 +250,7 @@ track: track, radius_bounds: tracks_bounds[index], genome: self.genome, - total_gap: self.total_gap + total_gap: total_gap }); view.render(); @@ -265,7 +266,7 @@ track: track, radius_bounds: tracks_bounds[0], genome: self.genome, - total_gap: self.total_gap + total_gap: total_gap }); view.render(); @@ -288,7 +289,7 @@ track: new CircsterLabelTrack(), radius_bounds: track_bounds, genome: self.genome, - total_gap: self.total_gap + total_gap: total_gap }); this.label_track_view.render(); @@ -298,6 +299,8 @@ * Render a single track on the outside of the current visualization. */ add_track: function(new_track) { + var total_gap = this.model.get('config').get_value('total_gap'); + if (new_track.get('track_type') === 'DiagonalHeatmapTrack') { // Added chords track. var innermost_radius_bounds = this.circular_views[0].radius_bounds, @@ -306,7 +309,7 @@ track: new_track, radius_bounds: innermost_radius_bounds, genome: this.genome, - total_gap: this.total_gap + total_gap: total_gap }); new_view.render(); this.chords_views.push(new_view); @@ -332,7 +335,7 @@ track: new_track, radius_bounds: new_track_bounds[track_index], genome: this.genome, - total_gap: this.total_gap + total_gap: total_gap }); track_view.render(); this.circular_views.push(track_view); @@ -358,6 +361,14 @@ _.each(this.circular_views, function(track_view, i) { track_view.update_radius_bounds(new_track_bounds[i]); }); + }, + + update_track_bounds: function() { + // Recompute and update track bounds. + var new_track_bounds = this.get_tracks_bounds(); + _.each(this.circular_views, function(track_view, i) { + track_view.update_radius_bounds(new_track_bounds[i]); + }); } }); @@ -630,7 +641,7 @@ var chroms_info = this.genome.get_chroms_info(), pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null), init_arcs = pie_layout(chroms_info), - gap_per_chrom = this.total_gap / chroms_info.length, + gap_per_chrom = 2 * Math.PI * this.total_gap / chroms_info.length, chrom_arcs = _.map(init_arcs, function(arc, index) { // For short chroms, endAngle === startAngle. var new_endAngle = arc.endAngle - gap_per_chrom; @@ -969,22 +980,25 @@ { initialize: function () { - // configure visualization + // -- Configure visualization -- var genome = new visualization.Genome(galaxy_config.app.genome), - vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config), - viz_view = new CircsterView( - { - // view pane - el : $('#center .unified-panel-body'), - - // gaps are difficult to set because it very dependent on chromosome size and organization. - total_gap : 2 * Math.PI * 0.4, - genome : genome, - model : vis, - dataset_arc_height : 25 - }); + vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config); + + // Add Circster-specific config options. + vis.get('config').add([ + { key: 'arc_dataset_height', label: 'Arc Dataset Height', type: 'int', value: 25, view: 'circster' }, + { key: 'total_gap', label: 'Gap [0-1]', type: 'float', value: 0.4, view: 'circster', hidden: true } + ]); + + var viz_view = new CircsterView( + { + // view pane + el : $('#center .unified-panel-body'), + genome : genome, + model : vis + }); - // render vizualization + // Render vizualization viz_view.render(); // setup title @@ -1002,6 +1016,15 @@ } }, { + icon_class: 'gear', title: 'Settings', on_click: function() + { + var view = new config.ConfigSettingCollectionView({ + collection: vis.get('config') + }); + view.render_in_modal('Configure Visualization'); + } + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // show saving dialog box Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ca4c4a24bd6a/ Changeset: ca4c4a24bd6a Branch: next-stable User: carlfeberhard Date: 2014-02-06 21:25:25 Summary: Fix css scoping in hda borders broken in 2b8e4f3 Affected #: 2 files diff -r a66e4111ba2aeca52572d203e1713153a5ee293a -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1573,6 +1573,47 @@ .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} .search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} +.history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} +.history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.history-panel .dataset .dataset-padding{padding:6px 10px 6px 8px} +.history-panel .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.history-panel .dataset .help-text{font-weight:normal;color:#555} +.history-panel .dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.history-panel .dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.history-panel .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.history-panel .dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.history-panel .dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-primary-actions .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .prompt:after{content:':'} +.history-panel .dataset .dataset-body .dataset-summary{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.history-panel .dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-actions .right{float:right}.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .tags-display .select2-container{min-width:0px}.history-panel .dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.history-panel .dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty{height:22px} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.history-panel .dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.history-panel .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-peek{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.history-panel .dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.history-panel .dataset .dataset-body .dataset-peek pre.peek table,.history-panel .dataset .dataset-body .dataset-peek pre.peek th,.history-panel .dataset .dataset-body .dataset-peek pre.peek tr,.history-panel .dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.history-panel .dataset .icon-btn-group{display:inline-block}.history-panel .dataset .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} .history-panel .editable-text:hover{cursor:pointer;border:1px dotted #999999} @@ -1604,47 +1645,6 @@ .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-history-message{display:none;margin:0px 10px 0px 10px} .history-panel .tag-button{display:inline-block;height:20px;margin:2px 2px 0px 0px;border:1px solid grey;border-radius:3px 10px 10px 3px;padding:2px 4px 2px 4px;background-color:#EEE;line-height:13px}.history-panel .tag-button .tag-name{margin-right:2px} -.dataset.hda{border:1px solid #bfbfbf}.dataset.hda .vertical-spacing{margin-bottom:8px} -.dataset.hda .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.dataset.hda .dataset-padding{padding:6px 10px 6px 8px} -.dataset.hda [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.dataset.hda .help-text{font-weight:normal;color:#555} -.dataset.hda .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} -.dataset.hda .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.dataset.hda .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.dataset.hda .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset.hda .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-primary-actions .icon-btn{margin-left:2px} -.dataset.hda .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset.hda .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.dataset.hda .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.dataset.hda .dataset-body .prompt{font-weight:normal;color:#555} -.dataset.hda .dataset-body .prompt:after{content:':'} -.dataset.hda .dataset-body .dataset-summary{margin-bottom:8px}.dataset.hda .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} -.dataset.hda .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.dataset.hda .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset.hda .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.dataset.hda .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.dataset.hda .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset.hda .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.dataset.hda .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.dataset.hda .dataset-body .dataset-actions .right{float:right}.dataset.hda .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.dataset.hda .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .tags-display .select2-container{min-width:0px}.dataset.hda .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.dataset.hda .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.dataset.hda .dataset-body .annotation-display .annotation:empty{height:22px} -.dataset.hda .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.dataset.hda .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.dataset.hda .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.dataset.hda .dataset-body .dataset-peek{margin-bottom:8px}.dataset.hda .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset.hda .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.dataset.hda .dataset-body .dataset-peek pre.peek table,.dataset.hda .dataset-body .dataset-peek pre.peek th,.dataset.hda .dataset-body .dataset-peek pre.peek tr,.dataset.hda .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.dataset.hda .icon-btn-group{display:inline-block}.dataset.hda .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} -.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} .dataset.state-ok,.dataset.state-failed_metadata{background:#aff1af}.dataset.state-ok .state-icon,.dataset.state-failed_metadata .state-icon{display:none} diff -r a66e4111ba2aeca52572d203e1713153a5ee293a -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -98,6 +98,275 @@ } +// ---------------------------------------------------------------------------- datasets +//TODO: scope to history panels until embedded item .dataset is changed +.history-panel { + .dataset { + border: 1px solid @border-default-color; + + // body mixins + @vertical-gap: 8px; + .vertical-spacing { + margin-bottom: @vertical-gap; + } + .info-section { + border-radius: 3px; + border: 1px solid fadeout( @layout-border-color, 70% ); + //background-color: fadeout( white, 60% ); + padding: 4px; + } + @spacing-top : 6px; + @spacing-right : 10px; + @spacing-bottom : 6px; + @spacing-left : 8px; + .dataset-padding { + padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; + } + + [class$=messagesmall] { + margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; + font-size: 90%; + } + + .help-text { + font-weight: normal; + // font-style: italic; + // font-size: 90%; + color: #555; + } + + .dataset-selector { + float: left; + // always initially hidden and zero width + display: none; + width: 0px; + //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish + margin: 0px 0px -@spacing-bottom 0px; + padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; + cursor: pointer; + //text-align: center; + vertical-align: middle; + } + + .dataset-title-bar { + cursor: pointer; + outline: none; + .dataset-padding; + + .dataset-state-icon { + } + .dataset-title { + display: inline; + font-weight: bold; + text-decoration: underline; + word-wrap: break-word; + word-break: break-all; + line-height: 16px; + } + } + + .dataset-primary-actions { + .icon-btn-group(); + float: right; + margin: @spacing-top @spacing-right 0; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + + .dataset-body { + display: none; + // background-color: fadeout( white, 70% ); + .dataset-padding; + + [class$=messagesmall] { + margin: 0px 0px 8px 0px; + } + + label { + margin: 0px; + padding: 0px; + font-weight: normal; + } + .prompt { + .help-text; + } + .prompt:after { + content: ':'; + } + + .dataset-summary { + .dataset-blurb { + margin-bottom: 2px; + } + .dataset-datatype, .dataset-dbkey { + display: inline; + .value { + font-weight: bold; + } + } + .dataset-datatype .value:after { + content: ','; + .help-text; + } + .dataset-dbkey:after { + content: ' '; + display: block; + .vertical-spacing; + } + .dataset-info { + .info-section; + .value { + white-space: pre-line; + } + } + + .job-error-text { + .info-section; + overflow: auto; + white-space: pre; + } + + // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) + .vertical-spacing; + } + + .dataset-actions { + .left { + .icon-btn-group(); + float: left; + .icon-btn { + margin-right: @icon-btn-margin; + } + //.icon-btn-group { + // margin-right: @icon-btn-margin; + // .icon-btn { + // margin-right: 0; + // } + //} + &:not(:empty) { + // can't use :empty on dataset-actions - will always have left & right, so + // add gap to left (more likely to have children) + .vertical-spacing; + } + } + .right { + float: right; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + } + + //TODO: move these out + .tags-display { + display: none; + .vertical-spacing; + .select2-container { + min-width: 0px; + .select2-choices { + border-radius: 3px; + } + } + } + .annotation-display { + display: none; + .vertical-spacing; + .annotation { + .info-section; + white-space: pre-line; + } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } + textarea { + margin: 0px 0px 2px 0px; + display: block; + border-radius: 3px; + width: 100%; + } + } + + .dataset-display-applications { + .display-application:last-child { + .vertical-spacing; + } + } + + .dataset-peek { + .vertical-spacing; + pre.peek { + width: 100%; + margin: 0px; + border-radius: 3px; + background: white; + color: black; + font-size: 10px; + overflow: auto; + th { + color: white; + background: @panel-primary-heading-bg; + } + table, th, tr, td { + font-family: @font-family-monospace; + font-size: 10px; + } + } + } + } + + .icon-btn-group { + display: inline-block; + .icon-btn:not(:last-child) { + margin: 0px; + border-radius: 0px; + border-right: none; + } + .icon-btn:first-child { + margin-right: 0px; + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; + } + .icon-btn:last-child { + margin-left: 0px; + border-radius: 0px 3px 3px 0px; + } + } + + } + + .dataset .state-icon { + .fa-icon; + display: inline-block; + vertical-align: middle; + width: 16px; + height: 16px; + line-height: 16px; + text-align: center; + font-size: 16px; + } +} + +.state-icon-error { + background-color: white; + border-radius: 8px; + &:before { + font-size: 20px; + line-height: 16px; + color: red; + content: @fa-var-times-circle; + } +} + // ---------------------------------------------------------------------------- history .history-panel { @@ -268,272 +537,6 @@ } } -// ---------------------------------------------------------------------------- datasets -.dataset.hda { - border: 1px solid @border-default-color; - - // body mixins - @vertical-gap: 8px; - .vertical-spacing { - margin-bottom: @vertical-gap; - } - .info-section { - border-radius: 3px; - border: 1px solid fadeout( @layout-border-color, 70% ); - //background-color: fadeout( white, 60% ); - padding: 4px; - } - @spacing-top : 6px; - @spacing-right : 10px; - @spacing-bottom : 6px; - @spacing-left : 8px; - .dataset-padding { - padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; - } - - [class$=messagesmall] { - margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; - font-size: 90%; - } - - .help-text { - font-weight: normal; - // font-style: italic; - // font-size: 90%; - color: #555; - } - - .dataset-selector { - float: left; - // always initially hidden and zero width - display: none; - width: 0px; - //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish - margin: 0px 0px -@spacing-bottom 0px; - padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; - cursor: pointer; - //text-align: center; - vertical-align: middle; - } - - .dataset-title-bar { - cursor: pointer; - outline: none; - .dataset-padding; - - .dataset-state-icon { - } - .dataset-title { - display: inline; - font-weight: bold; - text-decoration: underline; - word-wrap: break-word; - word-break: break-all; - line-height: 16px; - } - } - - .dataset-primary-actions { - .icon-btn-group(); - float: right; - margin: @spacing-top @spacing-right 0; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - - .dataset-body { - display: none; - // background-color: fadeout( white, 70% ); - .dataset-padding; - - [class$=messagesmall] { - margin: 0px 0px 8px 0px; - } - - label { - margin: 0px; - padding: 0px; - font-weight: normal; - } - .prompt { - .help-text; - } - .prompt:after { - content: ':'; - } - - .dataset-summary { - .dataset-blurb { - margin-bottom: 2px; - } - .dataset-datatype, .dataset-dbkey { - display: inline; - .value { - font-weight: bold; - } - } - .dataset-datatype .value:after { - content: ','; - .help-text; - } - .dataset-dbkey:after { - content: ' '; - display: block; - .vertical-spacing; - } - .dataset-info { - .info-section; - .value { - white-space: pre-line; - } - } - - .job-error-text { - .info-section; - overflow: auto; - white-space: pre; - } - - // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) - .vertical-spacing; - } - - .dataset-actions { - .left { - .icon-btn-group(); - float: left; - .icon-btn { - margin-right: @icon-btn-margin; - } - //.icon-btn-group { - // margin-right: @icon-btn-margin; - // .icon-btn { - // margin-right: 0; - // } - //} - &:not(:empty) { - // can't use :empty on dataset-actions - will always have left & right, so - // add gap to left (more likely to have children) - .vertical-spacing; - } - } - .right { - float: right; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - } - - //TODO: move these out - .tags-display { - display: none; - .vertical-spacing; - .select2-container { - min-width: 0px; - .select2-choices { - border-radius: 3px; - } - } - } - .annotation-display { - display: none; - .vertical-spacing; - .annotation { - .info-section; - white-space: pre-line; - } - .annotation:empty { - height: @icon-btn-size; - } - // fake placeholder for editable text annotation - .annotation:empty:after { - position: relative; - top: -4px; - font-size: 10px; - font-style: italic; - color: grey; - content : 'Click here to edit annotation'; - } - textarea { - margin: 0px 0px 2px 0px; - display: block; - border-radius: 3px; - width: 100%; - } - } - - .dataset-display-applications { - .display-application:last-child { - .vertical-spacing; - } - } - - .dataset-peek { - .vertical-spacing; - pre.peek { - width: 100%; - margin: 0px; - border-radius: 3px; - background: white; - color: black; - font-size: 10px; - overflow: auto; - th { - color: white; - background: @panel-primary-heading-bg; - } - table, th, tr, td { - font-family: @font-family-monospace; - font-size: 10px; - } - } - } - } - - .icon-btn-group { - display: inline-block; - .icon-btn:not(:last-child) { - margin: 0px; - border-radius: 0px; - border-right: none; - } - .icon-btn:first-child { - margin-right: 0px; - border-top-left-radius: 3px; - border-bottom-left-radius: 3px; - } - .icon-btn:last-child { - margin-left: 0px; - border-radius: 0px 3px 3px 0px; - } - } - -} - -.dataset.hda .state-icon { - .fa-icon; - display: inline-block; - vertical-align: middle; - width: 16px; - height: 16px; - line-height: 16px; - text-align: center; - font-size: 16px; -} - -.state-icon-error { - background-color: white; - border-radius: 8px; - &:before { - font-size: 20px; - line-height: 16px; - color: red; - content: @fa-var-times-circle; - } -} - .state-icon-running { //TODO: couldn't find a way to do this with fa/spinning.less as mixin -webkit-animation: spin 2s infinite linear; https://bitbucket.org/galaxy/galaxy-central/commits/c6eac0859bf9/ Changeset: c6eac0859bf9 User: carlfeberhard Date: 2014-02-06 21:25:58 Summary: merge Affected #: 2 files diff -r 3db994bbb5794de782a824b5ea8b2220b99e97ec -r c6eac0859bf917c176ec5995bff92a25841a9420 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1574,6 +1574,47 @@ .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} .search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} +.history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} +.history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.history-panel .dataset .dataset-padding{padding:6px 10px 6px 8px} +.history-panel .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.history-panel .dataset .help-text{font-weight:normal;color:#555} +.history-panel .dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.history-panel .dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.history-panel .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.history-panel .dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.history-panel .dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-primary-actions .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .prompt:after{content:':'} +.history-panel .dataset .dataset-body .dataset-summary{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.history-panel .dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-actions .right{float:right}.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .tags-display .select2-container{min-width:0px}.history-panel .dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.history-panel .dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty{height:22px} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.history-panel .dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.history-panel .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-peek{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.history-panel .dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.history-panel .dataset .dataset-body .dataset-peek pre.peek table,.history-panel .dataset .dataset-body .dataset-peek pre.peek th,.history-panel .dataset .dataset-body .dataset-peek pre.peek tr,.history-panel .dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.history-panel .dataset .icon-btn-group{display:inline-block}.history-panel .dataset .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} .history-panel .editable-text:hover{cursor:pointer;border:1px dotted #999999} @@ -1605,47 +1646,6 @@ .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-history-message{display:none;margin:0px 10px 0px 10px} .history-panel .tag-button{display:inline-block;height:20px;margin:2px 2px 0px 0px;border:1px solid grey;border-radius:3px 10px 10px 3px;padding:2px 4px 2px 4px;background-color:#EEE;line-height:13px}.history-panel .tag-button .tag-name{margin-right:2px} -.dataset.hda{border:1px solid #bfbfbf}.dataset.hda .vertical-spacing{margin-bottom:8px} -.dataset.hda .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.dataset.hda .dataset-padding{padding:6px 10px 6px 8px} -.dataset.hda [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.dataset.hda .help-text{font-weight:normal;color:#555} -.dataset.hda .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} -.dataset.hda .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.dataset.hda .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.dataset.hda .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset.hda .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-primary-actions .icon-btn{margin-left:2px} -.dataset.hda .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset.hda .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.dataset.hda .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.dataset.hda .dataset-body .prompt{font-weight:normal;color:#555} -.dataset.hda .dataset-body .prompt:after{content:':'} -.dataset.hda .dataset-body .dataset-summary{margin-bottom:8px}.dataset.hda .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} -.dataset.hda .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.dataset.hda .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset.hda .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.dataset.hda .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.dataset.hda .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset.hda .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.dataset.hda .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.dataset.hda .dataset-body .dataset-actions .right{float:right}.dataset.hda .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.dataset.hda .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .tags-display .select2-container{min-width:0px}.dataset.hda .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.dataset.hda .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.dataset.hda .dataset-body .annotation-display .annotation:empty{height:22px} -.dataset.hda .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.dataset.hda .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.dataset.hda .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.dataset.hda .dataset-body .dataset-peek{margin-bottom:8px}.dataset.hda .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset.hda .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.dataset.hda .dataset-body .dataset-peek pre.peek table,.dataset.hda .dataset-body .dataset-peek pre.peek th,.dataset.hda .dataset-body .dataset-peek pre.peek tr,.dataset.hda .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.dataset.hda .icon-btn-group{display:inline-block}.dataset.hda .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} -.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} .dataset.state-ok,.dataset.state-failed_metadata{background:#aff1af}.dataset.state-ok .state-icon,.dataset.state-failed_metadata .state-icon{display:none} diff -r 3db994bbb5794de782a824b5ea8b2220b99e97ec -r c6eac0859bf917c176ec5995bff92a25841a9420 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -98,6 +98,275 @@ } +// ---------------------------------------------------------------------------- datasets +//TODO: scope to history panels until embedded item .dataset is changed +.history-panel { + .dataset { + border: 1px solid @border-default-color; + + // body mixins + @vertical-gap: 8px; + .vertical-spacing { + margin-bottom: @vertical-gap; + } + .info-section { + border-radius: 3px; + border: 1px solid fadeout( @layout-border-color, 70% ); + //background-color: fadeout( white, 60% ); + padding: 4px; + } + @spacing-top : 6px; + @spacing-right : 10px; + @spacing-bottom : 6px; + @spacing-left : 8px; + .dataset-padding { + padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; + } + + [class$=messagesmall] { + margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; + font-size: 90%; + } + + .help-text { + font-weight: normal; + // font-style: italic; + // font-size: 90%; + color: #555; + } + + .dataset-selector { + float: left; + // always initially hidden and zero width + display: none; + width: 0px; + //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish + margin: 0px 0px -@spacing-bottom 0px; + padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; + cursor: pointer; + //text-align: center; + vertical-align: middle; + } + + .dataset-title-bar { + cursor: pointer; + outline: none; + .dataset-padding; + + .dataset-state-icon { + } + .dataset-title { + display: inline; + font-weight: bold; + text-decoration: underline; + word-wrap: break-word; + word-break: break-all; + line-height: 16px; + } + } + + .dataset-primary-actions { + .icon-btn-group(); + float: right; + margin: @spacing-top @spacing-right 0; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + + .dataset-body { + display: none; + // background-color: fadeout( white, 70% ); + .dataset-padding; + + [class$=messagesmall] { + margin: 0px 0px 8px 0px; + } + + label { + margin: 0px; + padding: 0px; + font-weight: normal; + } + .prompt { + .help-text; + } + .prompt:after { + content: ':'; + } + + .dataset-summary { + .dataset-blurb { + margin-bottom: 2px; + } + .dataset-datatype, .dataset-dbkey { + display: inline; + .value { + font-weight: bold; + } + } + .dataset-datatype .value:after { + content: ','; + .help-text; + } + .dataset-dbkey:after { + content: ' '; + display: block; + .vertical-spacing; + } + .dataset-info { + .info-section; + .value { + white-space: pre-line; + } + } + + .job-error-text { + .info-section; + overflow: auto; + white-space: pre; + } + + // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) + .vertical-spacing; + } + + .dataset-actions { + .left { + .icon-btn-group(); + float: left; + .icon-btn { + margin-right: @icon-btn-margin; + } + //.icon-btn-group { + // margin-right: @icon-btn-margin; + // .icon-btn { + // margin-right: 0; + // } + //} + &:not(:empty) { + // can't use :empty on dataset-actions - will always have left & right, so + // add gap to left (more likely to have children) + .vertical-spacing; + } + } + .right { + float: right; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + } + + //TODO: move these out + .tags-display { + display: none; + .vertical-spacing; + .select2-container { + min-width: 0px; + .select2-choices { + border-radius: 3px; + } + } + } + .annotation-display { + display: none; + .vertical-spacing; + .annotation { + .info-section; + white-space: pre-line; + } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } + textarea { + margin: 0px 0px 2px 0px; + display: block; + border-radius: 3px; + width: 100%; + } + } + + .dataset-display-applications { + .display-application:last-child { + .vertical-spacing; + } + } + + .dataset-peek { + .vertical-spacing; + pre.peek { + width: 100%; + margin: 0px; + border-radius: 3px; + background: white; + color: black; + font-size: 10px; + overflow: auto; + th { + color: white; + background: @panel-primary-heading-bg; + } + table, th, tr, td { + font-family: @font-family-monospace; + font-size: 10px; + } + } + } + } + + .icon-btn-group { + display: inline-block; + .icon-btn:not(:last-child) { + margin: 0px; + border-radius: 0px; + border-right: none; + } + .icon-btn:first-child { + margin-right: 0px; + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; + } + .icon-btn:last-child { + margin-left: 0px; + border-radius: 0px 3px 3px 0px; + } + } + + } + + .dataset .state-icon { + .fa-icon; + display: inline-block; + vertical-align: middle; + width: 16px; + height: 16px; + line-height: 16px; + text-align: center; + font-size: 16px; + } +} + +.state-icon-error { + background-color: white; + border-radius: 8px; + &:before { + font-size: 20px; + line-height: 16px; + color: red; + content: @fa-var-times-circle; + } +} + // ---------------------------------------------------------------------------- history .history-panel { @@ -268,272 +537,6 @@ } } -// ---------------------------------------------------------------------------- datasets -.dataset.hda { - border: 1px solid @border-default-color; - - // body mixins - @vertical-gap: 8px; - .vertical-spacing { - margin-bottom: @vertical-gap; - } - .info-section { - border-radius: 3px; - border: 1px solid fadeout( @layout-border-color, 70% ); - //background-color: fadeout( white, 60% ); - padding: 4px; - } - @spacing-top : 6px; - @spacing-right : 10px; - @spacing-bottom : 6px; - @spacing-left : 8px; - .dataset-padding { - padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; - } - - [class$=messagesmall] { - margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; - font-size: 90%; - } - - .help-text { - font-weight: normal; - // font-style: italic; - // font-size: 90%; - color: #555; - } - - .dataset-selector { - float: left; - // always initially hidden and zero width - display: none; - width: 0px; - //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish - margin: 0px 0px -@spacing-bottom 0px; - padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; - cursor: pointer; - //text-align: center; - vertical-align: middle; - } - - .dataset-title-bar { - cursor: pointer; - outline: none; - .dataset-padding; - - .dataset-state-icon { - } - .dataset-title { - display: inline; - font-weight: bold; - text-decoration: underline; - word-wrap: break-word; - word-break: break-all; - line-height: 16px; - } - } - - .dataset-primary-actions { - .icon-btn-group(); - float: right; - margin: @spacing-top @spacing-right 0; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - - .dataset-body { - display: none; - // background-color: fadeout( white, 70% ); - .dataset-padding; - - [class$=messagesmall] { - margin: 0px 0px 8px 0px; - } - - label { - margin: 0px; - padding: 0px; - font-weight: normal; - } - .prompt { - .help-text; - } - .prompt:after { - content: ':'; - } - - .dataset-summary { - .dataset-blurb { - margin-bottom: 2px; - } - .dataset-datatype, .dataset-dbkey { - display: inline; - .value { - font-weight: bold; - } - } - .dataset-datatype .value:after { - content: ','; - .help-text; - } - .dataset-dbkey:after { - content: ' '; - display: block; - .vertical-spacing; - } - .dataset-info { - .info-section; - .value { - white-space: pre-line; - } - } - - .job-error-text { - .info-section; - overflow: auto; - white-space: pre; - } - - // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) - .vertical-spacing; - } - - .dataset-actions { - .left { - .icon-btn-group(); - float: left; - .icon-btn { - margin-right: @icon-btn-margin; - } - //.icon-btn-group { - // margin-right: @icon-btn-margin; - // .icon-btn { - // margin-right: 0; - // } - //} - &:not(:empty) { - // can't use :empty on dataset-actions - will always have left & right, so - // add gap to left (more likely to have children) - .vertical-spacing; - } - } - .right { - float: right; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - } - - //TODO: move these out - .tags-display { - display: none; - .vertical-spacing; - .select2-container { - min-width: 0px; - .select2-choices { - border-radius: 3px; - } - } - } - .annotation-display { - display: none; - .vertical-spacing; - .annotation { - .info-section; - white-space: pre-line; - } - .annotation:empty { - height: @icon-btn-size; - } - // fake placeholder for editable text annotation - .annotation:empty:after { - position: relative; - top: -4px; - font-size: 10px; - font-style: italic; - color: grey; - content : 'Click here to edit annotation'; - } - textarea { - margin: 0px 0px 2px 0px; - display: block; - border-radius: 3px; - width: 100%; - } - } - - .dataset-display-applications { - .display-application:last-child { - .vertical-spacing; - } - } - - .dataset-peek { - .vertical-spacing; - pre.peek { - width: 100%; - margin: 0px; - border-radius: 3px; - background: white; - color: black; - font-size: 10px; - overflow: auto; - th { - color: white; - background: @panel-primary-heading-bg; - } - table, th, tr, td { - font-family: @font-family-monospace; - font-size: 10px; - } - } - } - } - - .icon-btn-group { - display: inline-block; - .icon-btn:not(:last-child) { - margin: 0px; - border-radius: 0px; - border-right: none; - } - .icon-btn:first-child { - margin-right: 0px; - border-top-left-radius: 3px; - border-bottom-left-radius: 3px; - } - .icon-btn:last-child { - margin-left: 0px; - border-radius: 0px 3px 3px 0px; - } - } - -} - -.dataset.hda .state-icon { - .fa-icon; - display: inline-block; - vertical-align: middle; - width: 16px; - height: 16px; - line-height: 16px; - text-align: center; - font-size: 16px; -} - -.state-icon-error { - background-color: white; - border-radius: 8px; - &:before { - font-size: 20px; - line-height: 16px; - color: red; - content: @fa-var-times-circle; - } -} - .state-icon-running { //TODO: couldn't find a way to do this with fa/spinning.less as mixin -webkit-animation: spin 2s infinite linear; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a66e4111ba2a/ Changeset: a66e4111ba2a Branch: next-stable User: carlfeberhard Date: 2014-02-06 19:21:24 Summary: Fix: HDA API show on imported, non-shared histories (thanks, John Chilton) Affected #: 1 file diff -r 7dd1f6db0e3ff3affa9a01a63b8c11efbaa2380b -r a66e4111ba2aeca52572d203e1713153a5ee293a lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -616,11 +616,12 @@ check_ownership=False, check_accessible=False ) if check_accessible: - if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): + if( not trans.user_is_admin() + and not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) ): error( "You are not allowed to access this dataset" ) - if check_state and hda.state == trans.model.Dataset.states.UPLOAD: - error( "Please wait until this dataset finishes uploading before attempting to view it." ) + if check_state and hda.state == trans.model.Dataset.states.UPLOAD: + error( "Please wait until this dataset finishes uploading before attempting to view it." ) return hda def get_history_dataset_association_from_ids( self, trans, id, history_id ): @@ -646,8 +647,6 @@ check_ownership=True, check_accessible=True ) return hda - - def get_hda_list( self, trans, hda_ids, check_ownership=True, check_accessible=False, check_state=True ): """ Returns one or more datasets in a list. https://bitbucket.org/galaxy/galaxy-central/commits/3db994bbb579/ Changeset: 3db994bbb579 User: carlfeberhard Date: 2014-02-06 19:21:55 Summary: merge Affected #: 1 file diff -r 8922d9e14d83d2bbcb06ea8498b17c2e3ea460b2 -r 3db994bbb5794de782a824b5ea8b2220b99e97ec lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -659,11 +659,12 @@ check_ownership=False, check_accessible=False ) if check_accessible: - if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): + if( not trans.user_is_admin() + and not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) ): error( "You are not allowed to access this dataset" ) - if check_state and hda.state == trans.model.Dataset.states.UPLOAD: - error( "Please wait until this dataset finishes uploading before attempting to view it." ) + if check_state and hda.state == trans.model.Dataset.states.UPLOAD: + error( "Please wait until this dataset finishes uploading before attempting to view it." ) return hda def get_history_dataset_association_from_ids( self, trans, id, history_id ): @@ -689,8 +690,6 @@ check_ownership=True, check_accessible=True ) return hda - - def get_hda_list( self, trans, hda_ids, check_ownership=True, check_accessible=False, check_state=True ): """ Returns one or more datasets in a list. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7dd1f6db0e3f/ Changeset: 7dd1f6db0e3f Branch: next-stable User: jmchilton Date: 2014-02-06 17:48:02 Summary: Bugfix: Allow users to 'unshare' histories shared with them. Affected #: 1 file diff -r d557d5dd942f5bbf820e19ec3fe7278401489555 -r 7dd1f6db0e3ff3affa9a01a63b8c11efbaa2380b lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -413,7 +413,9 @@ if not ids: message = "Select a history to unshare" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) - histories = [ self.get_history( trans, history_id ) for history_id in ids ] + # No need to check security, association below won't yield a + # hit if this user isn't having the history shared with her. + histories = [ self.get_history( trans, history_id, check_ownership=False ) for history_id in ids ] for history in histories: # Current user is the user with which the histories were shared association = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=trans.user, history=history ).one() https://bitbucket.org/galaxy/galaxy-central/commits/8922d9e14d83/ Changeset: 8922d9e14d83 User: jmchilton Date: 2014-02-06 17:48:18 Summary: Merge next-stable. Affected #: 1 file diff -r 75a81fcf38c477420f96035c9ed4b27edb55dd94 -r 8922d9e14d83d2bbcb06ea8498b17c2e3ea460b2 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -417,7 +417,9 @@ if not ids: message = "Select a history to unshare" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) - histories = [ self.get_history( trans, history_id ) for history_id in ids ] + # No need to check security, association below won't yield a + # hit if this user isn't having the history shared with her. + histories = [ self.get_history( trans, history_id, check_ownership=False ) for history_id in ids ] for history in histories: # Current user is the user with which the histories were shared association = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=trans.user, history=history ).one() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 05 Feb '14

05 Feb '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b86d73f9aea/ Changeset: 9b86d73f9aea Branch: next-stable User: jeremy goecks Date: 2014-02-05 22:22:17 Summary: Fix bugs that prevented saving visualizations from Circster. To do this, introduced a mixin for custom toJSON methods. Pack scripts. Affected #: 4 files diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 9b86d73f9aea574862eed1f6a0c02c9171ed2c3e static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var s=galaxy_config.app.viz_config;$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:s.vis_id,title:s.title,dbkey:s.dbkey,type:"trackster",vis_json:JSON.stringify(s)}}).success(function(t){Galaxy.modal.hide();s.vis_id=t.vis_id;s.has_changes=false;window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 9b86d73f9aea574862eed1f6a0c02c9171ed2c3e static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,j,m,p){var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var k=function(v){return("promise" in v)};var f=function(v){this.default_font=v!==undefined?v:"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")};t.extend(f.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(k(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(k(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!k(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new g({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new g({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var g=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({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.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return g.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=g.overlap_results.BEFORE}else{if(z<x){v=g.overlap_results.OVERLAP_START}else{v=g.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=g.overlap_results.AFTER}else{if(z<=x){v=g.overlap_results.CONTAINED_BY}else{v=g.overlap_results.OVERLAP_END}}}else{v=(z>=x?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===g.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:g});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new g(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend({initialize:function(v){this.set("dataset",new j.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}});var i=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("tracks",new i(v.tracks))},add_tracks:function(v){this.get("tracks").add(v)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(u,k,n,q){var f={toJSON:function(){var w=this,x={};u.each(w.constructor.to_json_keys,function(y){var z=w.get(y);if(y in w.constructor.to_json_mappers){z=w.constructor.to_json_mappers[y](z,w)}x[y]=z});return x}};var a=function(w,z,y,x){$.ajax({url:w,data:y,error:function(){alert("Grid failed")},success:function(A){Galaxy.modal.show({title:"Select datasets for new tracks",body:A,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var B=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var C={data_type:"track_config",hda_ldda:"hda"},D=$(this).val();if($(this).attr("name")!=="id"){C.hda_ldda="ldda"}B[B.length]=$.ajax({url:z+"/"+D,data:C,dataType:"json"})});$.when.apply($,B).then(function(){var C=(arguments[0] instanceof Array?$.map(arguments,function(D){return D[0]}):[arguments[0]]);x(C)});Galaxy.modal.hide()}}})}})};var l=function(w){return("promise" in w)};var g=function(w){this.default_font=w!==undefined?w:"9px Monaco, Lucida Console, 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s=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(w){this.clear()},get_elt:function(y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,x=y.toString(),w=u.indexOf(A,function(B){return B.toString()===x});if(w!==-1){if(z[x].stale){A.splice(w,1);delete z[x]}else{this.move_key_to_end(y,w)}}return z[x]},set_elt:function(y,A){var B=this.attributes.obj_cache,C=this.attributes.key_ary,x=y.toString(),z=this.attributes.num_elements;if(!B[x]){if(C.length>=z){var w=C.shift();delete B[w.toString()]}C.push(y)}B[x]=A;return A},move_key_to_end:function(x,w){this.attributes.key_ary.splice(w,1);this.attributes.key_ary.push(x)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=s.extend({defaults:u.extend({},s.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(w,x){return true},can_subset:function(w){return false}}),initialize:function(w){s.prototype.initialize.call(this);var x=this.get("init_data");if(x){this.add_data(x)}},add_data:function(w){if(this.get("num_elements")<w.length){this.set("num_elements",w.length)}var x=this;u.each(w,function(y){x.set_data(y.region,y)})},data_is_ready:function(){var z=this.get("dataset"),y=$.Deferred(),w=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),x=new n.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:z.get("hda_ldda"),data_type:w},dataType:"json"},interval:5000,success_fn:function(A){return A!=="pending"}});$.when(x.go()).then(function(A){y.resolve(A==="ok"||A==="data")});return y},search_features:function(w){var x=this.get("dataset"),y={query:w,hda_ldda:x.get("hda_ldda"),data_type:"features"};return $.getJSON(x.url(),y)},load_data:function(E,D,x,C){var A=this.get("dataset"),z={data_type:this.get("data_type"),chrom:E.get("chrom"),low:E.get("start"),high:E.get("end"),mode:D,resolution:x,hda_ldda:A.get("hda_ldda")};$.extend(z,C);var G=this.get("filters_manager");if(G){var H=[];var w=G.filters;for(var B=0;B<w.length;B++){H.push(w[B].name)}z.filter_cols=JSON.stringify(H)}var y=this,F=$.getJSON(A.url(),z,function(I){I.region=E;y.set_data(E,I)});this.set_data(E,F);return F},get_data:function(D,C,y,A){var E=this.get_elt(D);if(E&&(l(E)||this.get("data_mode_compatible")(E,C))){return E}var F=this.get("key_ary"),w=this.get("obj_cache"),x,B;for(var z=0;z<F.length;z++){x=F[z];if(x.contains(D)){B=true;E=w[x.toString()];if(l(E)||(this.get("data_mode_compatible")(E,C)&&this.get("can_subset")(E))){this.move_key_to_end(x,z);if(!l(E)){var H=this.subset_entry(E,D);this.set(D,H);E=H}return E}}}if(!B&&D.length()<this.attributes.min_region_size){D=D.copy();var G=this.most_recently_added();if(!G||(D.get("start")>G.get("start"))){D.set("end",D.get("start")+this.attributes.min_region_size)}else{D.set("start",D.get("end")-this.attributes.min_region_size)}D.set("genome",this.attributes.genome);D.trim()}return this.load_data(D,C,y,A)},set_data:function(x,w){this.set_elt(x,w)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(E,D,z,C,A){var G=this._mark_stale(E);if(!(G&&this.get("data_mode_compatible")(G,D))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var y=E.get("start");if(A===this.DEEP_DATA_REQ){$.extend(C,{start_val:G.data.length+1})}else{if(A===this.BROAD_DATA_REQ){y=(G.max_high?G.max_high:G.data[G.data.length-1][2])+1}}var F=E.copy().set("start",y);var x=this,B=this.load_data(F,D,z,C),w=$.Deferred();this.set_data(E,w);$.when(B).then(function(H){if(H.data){H.data=G.data.concat(H.data);if(H.max_low){H.max_low=G.max_low}if(H.message){H.message=H.message.replace(/[0-9]+/,H.data.length)}}x.set_data(E,H);w.resolve(H)});return w},can_get_more_detailed_data:function(x){var w=this.get_elt(x);return(w.dataset_type==="bigwig"&&w.data.length<8000)},get_more_detailed_data:function(z,B,x,A,y){var w=this._mark_stale(z);if(!w){console.log("ERROR getting more detailed data: no current data");return}if(!y){y={}}if(w.dataset_type==="bigwig"){y.num_samples=1000*A}return this.load_data(z,B,x,y)},_mark_stale:function(x){var w=this.get_elt(x);if(!w){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),x.toString())}w.stale=true;return w},get_genome_wide_data:function(w){var y=this,A=true,z=u.map(w.get("chroms_info").chrom_info,function(C){var B=y.get_elt(new h({chrom:C.chrom,start:0,end:C.len}));if(!B){A=false}return B});if(A){return z}var x=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(B){y.add_data(B.data);x.resolve(B.data)});return x},subset_entry:function(y,z){var w={bigwig:function(A,B){return u.filter(A,function(C){return C[0]>=B.get("start")&&C[0]<=B.get("end")})},refseq:function(B,C){var D=C.get("start")-y.region.get("start"),A=y.data.length-(y.region.get("end")-C.get("end"));return y.data.slice(D,A)}};var x=y.data;if(!y.region.same(z)&&y.dataset_type in w){x=w[y.dataset_type](y.data,z)}return{region:z,data:x,dataset_type:y.dataset_type}}});var r=d.extend({initialize:function(w){var x=new Backbone.Model();x.urlRoot=w.data_url;this.set("dataset",x)},load_data:function(y,z,w,x){return(y.length()<=100000?d.prototype.load_data.call(this,y,z,w,x):{data:null,region:y})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(w){this.id=w.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(w){var x=u.find(this.get_chroms_info(),function(y){return y.chrom===w});return new h({chrom:x.chrom,end:x.len})},get_chrom_len:function(w){return u.find(this.get_chroms_info(),function(x){return x.chrom===w}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(w){return this.attributes.chrom===w.get("chrom")&&this.attributes.start===w.get("start")&&this.attributes.end===w.get("end")},initialize:function(x){if(x.from_str){var z=x.from_str.split(":"),y=z[0],w=z[1].split("-");this.set({chrom:y,start:parseInt(w[0],10),end:parseInt(w[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({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.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(D){var x=this.get("chrom"),C=D.get("chrom"),B=this.get("start"),z=D.get("start"),A=this.get("end"),y=D.get("end"),w;if(x&&C&&x!==C){return h.overlap_results.DIF_CHROMS}if(B<z){if(A<z){w=h.overlap_results.BEFORE}else{if(A<y){w=h.overlap_results.OVERLAP_START}else{w=h.overlap_results.CONTAINS}}}else{if(B>z){if(B>y){w=h.overlap_results.AFTER}else{if(A<=y){w=h.overlap_results.CONTAINED_BY}else{w=h.overlap_results.OVERLAP_END}}}else{w=(A>=y?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return w},trim:function(w){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var x=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>x){this.attributes.end=x-1}}return this},contains:function(w){return this.compute_overlap(w)===h.overlap_results.CONTAINS},overlaps:function(w){return u.intersection([this.compute_overlap(w)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var o=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(w){this.set("region",new h(w.region))}});var t=Backbone.Collection.extend({model:e});var v=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(w){this.set("dataset",new k.Dataset(w.dataset));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var x=this.get("preloaded_data");if(x){x=x.data}else{x=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:x}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(x,w){if(u.size(x)===0){x={name:w.get("config").get("name").get("value"),color:w.get("config").get("color").get("value")}}return x},dataset:function(w){return{id:w.id,hda_ldda:w.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:v});var p=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var m=p.extend(f).extend({defaults:u.extend({},p.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(w){this.set("drawables",new j(w.tracks));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs||{}));this.unset("tracks");this.get("drawables").each(function(x){x.unset("preloaded_data")})},add_tracks:function(w){this.get("drawables").add(w)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(x,w){return{obj_type:"View",prefs:{name:w.get("title"),content_visible:true},drawables:w.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(x){this.view=x.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var w=this;w.view.on("navigate",function(y){w.navigate(y)})},change_location:function(w){this.view.go_to(w)}});return{BackboneTrack:v,BrowserBookmark:e,BrowserBookmarkCollection:t,Cache:s,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:o,GenomeVisualization:m,GenomeReferenceDataManager:r,TrackBrowserRouter:i,TrackConfig:b,Visualization:p,select_datasets:a}}); \ No newline at end of file diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 9b86d73f9aea574862eed1f6a0c02c9171ed2c3e static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -143,8 +143,8 @@ this.chords_views = null; // When tracks added to/removed from model, update view. - this.model.get('tracks').on('add', this.add_track, this); - this.model.get('tracks').on('remove', this.remove_track, this); + this.model.get('drawables').on('add', this.add_track, this); + this.model.get('drawables').on('remove', this.remove_track, this); this.get_circular_tracks(); }, @@ -154,7 +154,7 @@ * Returns tracks to be rendered using circular view. */ get_circular_tracks: function() { - return this.model.get('tracks').filter(function(track) { + return this.model.get('drawables').filter(function(track) { return track.get('track_type') !== 'DiagonalHeatmapTrack'; }); }, @@ -163,7 +163,7 @@ * Returns tracks to be rendered using chords view. */ get_chord_tracks: function() { - return this.model.get('tracks').filter(function(track) { + return this.model.get('drawables').filter(function(track) { return track.get('track_type') === 'DiagonalHeatmapTrack'; }); }, @@ -992,41 +992,36 @@ // setup menu var menu = create_icon_buttons_menu([ - { icon_class: 'plus-button', title: 'Add tracks', on_click: function() + { + icon_class: 'plus-button', title: 'Add tracks', on_click: function() { visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", vis.get('dbkey'), function(tracks) { vis.add_tracks(tracks); }); } - },{ + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // show saving dialog box Galaxy.modal.show({title: "Saving...", body: "progress" }); - // link configuration - var view = galaxy_config.app.viz_config; - // send to server $.ajax({ url: galaxy_config.root + "visualization/save", type: "POST", dataType: "json", data: { - 'id' : view.vis_id, - 'title' : view.title, - 'dbkey' : view.dbkey, + 'id' : vis.get('vis_id'), + 'title' : vis.get('title'), + 'dbkey' : vis.get('dbkey'), 'type' : 'trackster', - 'vis_json' : JSON.stringify(view) + 'vis_json' : JSON.stringify(vis) } }).success(function(vis_info) { Galaxy.modal.hide(); - 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); + vis.set('vis_id', vis_info.vis_id); }).error(function() { // show dialog Galaxy.modal.show({ @@ -1036,7 +1031,8 @@ }); }); } - },{ + }, + { icon_class: 'cross-circle', title: 'Close', on_click: function() { window.location = galaxy_config.root + "visualization/list"; diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 9b86d73f9aea574862eed1f6a0c02c9171ed2c3e static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,6 +1,28 @@ define( ["libs/underscore", "mvc/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) { /** + * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes + * to include in the representation; to_json_mappers defines mappers for returned objects. + */ +var CustomToJSON = { + /** + * Returns JSON representation of object using to_json_keys and to_json_mappers. + */ + toJSON: function() { + var self = this, + json = {}; + _.each(self.constructor.to_json_keys, function(k) { + var val = self.get(k); + if (k in self.constructor.to_json_mappers) { + val = self.constructor.to_json_mappers[k](val, self); + } + json[k] = val; + }); + return json; + } +}; + +/** * Model, view, and controller objects for Galaxy visualization framework. * * Models have no references to views, instead using events to indicate state @@ -872,7 +894,10 @@ * A track of data in a genome visualization. */ // TODO: rename to Track and merge with Trackster's Track object. -var BackboneTrack = Backbone.Model.extend({ +var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend({ + defaults: { + mode: 'Auto' + }, initialize: function(options) { this.set('dataset', new data_mod.Dataset(options.dataset)); @@ -883,7 +908,7 @@ // Set up some minimal config. this.get('config').add( [ - { key: 'name', value: this.get('name') }, + { key: 'name', value: this.get('dataset').get('name') }, { key: 'color' } ] ); @@ -900,6 +925,34 @@ init_data: preloaded_data })); } +}, +{ + // This definition matches that produced by to_dict() methods in tracks.js + to_json_keys: [ + 'track_type', + 'dataset', + 'prefs', + 'mode', + 'filters', + 'tool_state' + ], + to_json_mappers: { + prefs: function(p, self) { + if (_.size(p) === 0) { + p = { + name: self.get('config').get('name').get('value'), + color: self.get('config').get('color').get('value') + }; + } + return p; + }, + dataset: function(d) { + return { + id: d.id, + hda_ldda: d.get('hda_ldda') + }; + } + } }); var BackboneTrackCollection = Backbone.Collection.extend({ @@ -938,25 +991,55 @@ /** * A visualization of genome data. */ -var GenomeVisualization = Visualization.extend({ +var GenomeVisualization = Visualization.extend(CustomToJSON).extend({ defaults: _.extend({}, Visualization.prototype.defaults, { dbkey: '', - tracks: null, + drawables: null, bookmarks: null, viewport: null }), initialize: function(options) { - this.set('tracks', new BackboneTrackCollection(options.tracks)); + // Replace drawables with tracks. + this.set('drawables', new BackboneTrackCollection(options.tracks)); + this.set('config', config_mod.ConfigSettingCollection.from_config_dict(options.prefs || {})); + + // Clear track and data definitions to avoid storing large objects. + this.unset('tracks'); + this.get('drawables').each(function(d) { + d.unset('preloaded_data'); + }); }, /** * Add a track or array of tracks to the visualization. */ add_tracks: function(tracks) { - this.get('tracks').add(tracks); + this.get('drawables').add(tracks); } -}); +}, +{ + // This definition matches that produced by to_dict() methods in tracks.js + to_json_keys: [ + 'view', + 'viewport', + 'bookmarks' + ], + + to_json_mappers: { + 'view': function(dummy, self) { + return { + obj_type: 'View', + prefs: { + name: self.get('title'), + content_visible: true + }, + drawables: self.get('drawables') + }; + } + } +} +); /** * Configuration data for a Trackster track. https://bitbucket.org/galaxy/galaxy-central/commits/c98072c51cf0/ Changeset: c98072c51cf0 User: jeremy goecks Date: 2014-02-05 22:22:45 Summary: Merge next-stable into default. Affected #: 4 files diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r c98072c51cf05de686c631739a5deb18c15734bf static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var s=galaxy_config.app.viz_config;$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:s.vis_id,title:s.title,dbkey:s.dbkey,type:"trackster",vis_json:JSON.stringify(s)}}).success(function(t){Galaxy.modal.hide();s.vis_id=t.vis_id;s.has_changes=false;window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r c98072c51cf05de686c631739a5deb18c15734bf static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,j,m,p){var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var k=function(v){return("promise" in v)};var f=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(f.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(k(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(k(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!k(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new g({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new g({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var g=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({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.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return g.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=g.overlap_results.BEFORE}else{if(z<x){v=g.overlap_results.OVERLAP_START}else{v=g.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=g.overlap_results.AFTER}else{if(z<=x){v=g.overlap_results.CONTAINED_BY}else{v=g.overlap_results.OVERLAP_END}}}else{v=(z>=x?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===g.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:g});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new g(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend({initialize:function(v){this.set("dataset",new j.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}});var i=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("tracks",new i(v.tracks))},add_tracks:function(v){this.get("tracks").add(v)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(u,k,n,q){var f={toJSON:function(){var w=this,x={};u.each(w.constructor.to_json_keys,function(y){var z=w.get(y);if(y in w.constructor.to_json_mappers){z=w.constructor.to_json_mappers[y](z,w)}x[y]=z});return x}};var a=function(w,z,y,x){$.ajax({url:w,data:y,error:function(){alert("Grid failed")},success:function(A){Galaxy.modal.show({title:"Select datasets for new tracks",body:A,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var B=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var C={data_type:"track_config",hda_ldda:"hda"},D=$(this).val();if($(this).attr("name")!=="id"){C.hda_ldda="ldda"}B[B.length]=$.ajax({url:z+"/"+D,data:C,dataType:"json"})});$.when.apply($,B).then(function(){var C=(arguments[0] instanceof Array?$.map(arguments,function(D){return D[0]}):[arguments[0]]);x(C)});Galaxy.modal.hide()}}})}})};var l=function(w){return("promise" in w)};var g=function(w){this.default_font=w!==undefined?w:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};u.extend(g.prototype,{load_pattern:function(w,A){var x=this.patterns,y=this.dummy_context,z=new Image();z.src=galaxy_config.root+"static/images"+A;z.onload=function(){x[w]=y.createPattern(z,"repeat")}},get_pattern:function(w){return this.patterns[w]},new_canvas:function(){var w=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(w)}w.manager=this;return w}});var s=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(w){this.clear()},get_elt:function(y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,x=y.toString(),w=u.indexOf(A,function(B){return B.toString()===x});if(w!==-1){if(z[x].stale){A.splice(w,1);delete z[x]}else{this.move_key_to_end(y,w)}}return z[x]},set_elt:function(y,A){var B=this.attributes.obj_cache,C=this.attributes.key_ary,x=y.toString(),z=this.attributes.num_elements;if(!B[x]){if(C.length>=z){var w=C.shift();delete B[w.toString()]}C.push(y)}B[x]=A;return A},move_key_to_end:function(x,w){this.attributes.key_ary.splice(w,1);this.attributes.key_ary.push(x)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=s.extend({defaults:u.extend({},s.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(w,x){return true},can_subset:function(w){return false}}),initialize:function(w){s.prototype.initialize.call(this);var x=this.get("init_data");if(x){this.add_data(x)}},add_data:function(w){if(this.get("num_elements")<w.length){this.set("num_elements",w.length)}var x=this;u.each(w,function(y){x.set_data(y.region,y)})},data_is_ready:function(){var z=this.get("dataset"),y=$.Deferred(),w=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),x=new n.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:z.get("hda_ldda"),data_type:w},dataType:"json"},interval:5000,success_fn:function(A){return A!=="pending"}});$.when(x.go()).then(function(A){y.resolve(A==="ok"||A==="data")});return y},search_features:function(w){var x=this.get("dataset"),y={query:w,hda_ldda:x.get("hda_ldda"),data_type:"features"};return $.getJSON(x.url(),y)},load_data:function(E,D,x,C){var A=this.get("dataset"),z={data_type:this.get("data_type"),chrom:E.get("chrom"),low:E.get("start"),high:E.get("end"),mode:D,resolution:x,hda_ldda:A.get("hda_ldda")};$.extend(z,C);var G=this.get("filters_manager");if(G){var H=[];var w=G.filters;for(var B=0;B<w.length;B++){H.push(w[B].name)}z.filter_cols=JSON.stringify(H)}var y=this,F=$.getJSON(A.url(),z,function(I){I.region=E;y.set_data(E,I)});this.set_data(E,F);return F},get_data:function(D,C,y,A){var E=this.get_elt(D);if(E&&(l(E)||this.get("data_mode_compatible")(E,C))){return E}var F=this.get("key_ary"),w=this.get("obj_cache"),x,B;for(var z=0;z<F.length;z++){x=F[z];if(x.contains(D)){B=true;E=w[x.toString()];if(l(E)||(this.get("data_mode_compatible")(E,C)&&this.get("can_subset")(E))){this.move_key_to_end(x,z);if(!l(E)){var H=this.subset_entry(E,D);this.set(D,H);E=H}return E}}}if(!B&&D.length()<this.attributes.min_region_size){D=D.copy();var G=this.most_recently_added();if(!G||(D.get("start")>G.get("start"))){D.set("end",D.get("start")+this.attributes.min_region_size)}else{D.set("start",D.get("end")-this.attributes.min_region_size)}D.set("genome",this.attributes.genome);D.trim()}return this.load_data(D,C,y,A)},set_data:function(x,w){this.set_elt(x,w)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(E,D,z,C,A){var G=this._mark_stale(E);if(!(G&&this.get("data_mode_compatible")(G,D))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var y=E.get("start");if(A===this.DEEP_DATA_REQ){$.extend(C,{start_val:G.data.length+1})}else{if(A===this.BROAD_DATA_REQ){y=(G.max_high?G.max_high:G.data[G.data.length-1][2])+1}}var F=E.copy().set("start",y);var x=this,B=this.load_data(F,D,z,C),w=$.Deferred();this.set_data(E,w);$.when(B).then(function(H){if(H.data){H.data=G.data.concat(H.data);if(H.max_low){H.max_low=G.max_low}if(H.message){H.message=H.message.replace(/[0-9]+/,H.data.length)}}x.set_data(E,H);w.resolve(H)});return w},can_get_more_detailed_data:function(x){var w=this.get_elt(x);return(w.dataset_type==="bigwig"&&w.data.length<8000)},get_more_detailed_data:function(z,B,x,A,y){var w=this._mark_stale(z);if(!w){console.log("ERROR getting more detailed data: no current data");return}if(!y){y={}}if(w.dataset_type==="bigwig"){y.num_samples=1000*A}return this.load_data(z,B,x,y)},_mark_stale:function(x){var w=this.get_elt(x);if(!w){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),x.toString())}w.stale=true;return w},get_genome_wide_data:function(w){var y=this,A=true,z=u.map(w.get("chroms_info").chrom_info,function(C){var B=y.get_elt(new h({chrom:C.chrom,start:0,end:C.len}));if(!B){A=false}return B});if(A){return z}var x=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(B){y.add_data(B.data);x.resolve(B.data)});return x},subset_entry:function(y,z){var w={bigwig:function(A,B){return u.filter(A,function(C){return C[0]>=B.get("start")&&C[0]<=B.get("end")})},refseq:function(B,C){var D=C.get("start")-y.region.get("start"),A=y.data.length-(y.region.get("end")-C.get("end"));return y.data.slice(D,A)}};var x=y.data;if(!y.region.same(z)&&y.dataset_type in w){x=w[y.dataset_type](y.data,z)}return{region:z,data:x,dataset_type:y.dataset_type}}});var r=d.extend({initialize:function(w){var x=new Backbone.Model();x.urlRoot=w.data_url;this.set("dataset",x)},load_data:function(y,z,w,x){return(y.length()<=100000?d.prototype.load_data.call(this,y,z,w,x):{data:null,region:y})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(w){this.id=w.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(w){var x=u.find(this.get_chroms_info(),function(y){return y.chrom===w});return new h({chrom:x.chrom,end:x.len})},get_chrom_len:function(w){return u.find(this.get_chroms_info(),function(x){return x.chrom===w}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(w){return this.attributes.chrom===w.get("chrom")&&this.attributes.start===w.get("start")&&this.attributes.end===w.get("end")},initialize:function(x){if(x.from_str){var z=x.from_str.split(":"),y=z[0],w=z[1].split("-");this.set({chrom:y,start:parseInt(w[0],10),end:parseInt(w[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({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.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(D){var x=this.get("chrom"),C=D.get("chrom"),B=this.get("start"),z=D.get("start"),A=this.get("end"),y=D.get("end"),w;if(x&&C&&x!==C){return h.overlap_results.DIF_CHROMS}if(B<z){if(A<z){w=h.overlap_results.BEFORE}else{if(A<y){w=h.overlap_results.OVERLAP_START}else{w=h.overlap_results.CONTAINS}}}else{if(B>z){if(B>y){w=h.overlap_results.AFTER}else{if(A<=y){w=h.overlap_results.CONTAINED_BY}else{w=h.overlap_results.OVERLAP_END}}}else{w=(A>=y?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return w},trim:function(w){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var x=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>x){this.attributes.end=x-1}}return this},contains:function(w){return this.compute_overlap(w)===h.overlap_results.CONTAINS},overlaps:function(w){return u.intersection([this.compute_overlap(w)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var o=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(w){this.set("region",new h(w.region))}});var t=Backbone.Collection.extend({model:e});var v=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(w){this.set("dataset",new k.Dataset(w.dataset));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var x=this.get("preloaded_data");if(x){x=x.data}else{x=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:x}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(x,w){if(u.size(x)===0){x={name:w.get("config").get("name").get("value"),color:w.get("config").get("color").get("value")}}return x},dataset:function(w){return{id:w.id,hda_ldda:w.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:v});var p=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var m=p.extend(f).extend({defaults:u.extend({},p.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(w){this.set("drawables",new j(w.tracks));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs||{}));this.unset("tracks");this.get("drawables").each(function(x){x.unset("preloaded_data")})},add_tracks:function(w){this.get("drawables").add(w)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(x,w){return{obj_type:"View",prefs:{name:w.get("title"),content_visible:true},drawables:w.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(x){this.view=x.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var w=this;w.view.on("navigate",function(y){w.navigate(y)})},change_location:function(w){this.view.go_to(w)}});return{BackboneTrack:v,BrowserBookmark:e,BrowserBookmarkCollection:t,Cache:s,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:o,GenomeVisualization:m,GenomeReferenceDataManager:r,TrackBrowserRouter:i,TrackConfig:b,Visualization:p,select_datasets:a}}); \ No newline at end of file diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r c98072c51cf05de686c631739a5deb18c15734bf static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -143,8 +143,8 @@ this.chords_views = null; // When tracks added to/removed from model, update view. - this.model.get('tracks').on('add', this.add_track, this); - this.model.get('tracks').on('remove', this.remove_track, this); + this.model.get('drawables').on('add', this.add_track, this); + this.model.get('drawables').on('remove', this.remove_track, this); this.get_circular_tracks(); }, @@ -154,7 +154,7 @@ * Returns tracks to be rendered using circular view. */ get_circular_tracks: function() { - return this.model.get('tracks').filter(function(track) { + return this.model.get('drawables').filter(function(track) { return track.get('track_type') !== 'DiagonalHeatmapTrack'; }); }, @@ -163,7 +163,7 @@ * Returns tracks to be rendered using chords view. */ get_chord_tracks: function() { - return this.model.get('tracks').filter(function(track) { + return this.model.get('drawables').filter(function(track) { return track.get('track_type') === 'DiagonalHeatmapTrack'; }); }, @@ -992,41 +992,36 @@ // setup menu var menu = create_icon_buttons_menu([ - { icon_class: 'plus-button', title: 'Add tracks', on_click: function() + { + icon_class: 'plus-button', title: 'Add tracks', on_click: function() { visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", vis.get('dbkey'), function(tracks) { vis.add_tracks(tracks); }); } - },{ + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // show saving dialog box Galaxy.modal.show({title: "Saving...", body: "progress" }); - // link configuration - var view = galaxy_config.app.viz_config; - // send to server $.ajax({ url: galaxy_config.root + "visualization/save", type: "POST", dataType: "json", data: { - 'id' : view.vis_id, - 'title' : view.title, - 'dbkey' : view.dbkey, + 'id' : vis.get('vis_id'), + 'title' : vis.get('title'), + 'dbkey' : vis.get('dbkey'), 'type' : 'trackster', - 'vis_json' : JSON.stringify(view) + 'vis_json' : JSON.stringify(vis) } }).success(function(vis_info) { Galaxy.modal.hide(); - 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); + vis.set('vis_id', vis_info.vis_id); }).error(function() { // show dialog Galaxy.modal.show({ @@ -1036,7 +1031,8 @@ }); }); } - },{ + }, + { icon_class: 'cross-circle', title: 'Close', on_click: function() { window.location = galaxy_config.root + "visualization/list"; diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r c98072c51cf05de686c631739a5deb18c15734bf static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,6 +1,28 @@ define( ["libs/underscore", "mvc/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) { /** + * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes + * to include in the representation; to_json_mappers defines mappers for returned objects. + */ +var CustomToJSON = { + /** + * Returns JSON representation of object using to_json_keys and to_json_mappers. + */ + toJSON: function() { + var self = this, + json = {}; + _.each(self.constructor.to_json_keys, function(k) { + var val = self.get(k); + if (k in self.constructor.to_json_mappers) { + val = self.constructor.to_json_mappers[k](val, self); + } + json[k] = val; + }); + return json; + } +}; + +/** * Model, view, and controller objects for Galaxy visualization framework. * * Models have no references to views, instead using events to indicate state @@ -872,7 +894,10 @@ * A track of data in a genome visualization. */ // TODO: rename to Track and merge with Trackster's Track object. -var BackboneTrack = Backbone.Model.extend({ +var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend({ + defaults: { + mode: 'Auto' + }, initialize: function(options) { this.set('dataset', new data_mod.Dataset(options.dataset)); @@ -883,7 +908,7 @@ // Set up some minimal config. this.get('config').add( [ - { key: 'name', value: this.get('name') }, + { key: 'name', value: this.get('dataset').get('name') }, { key: 'color' } ] ); @@ -900,6 +925,34 @@ init_data: preloaded_data })); } +}, +{ + // This definition matches that produced by to_dict() methods in tracks.js + to_json_keys: [ + 'track_type', + 'dataset', + 'prefs', + 'mode', + 'filters', + 'tool_state' + ], + to_json_mappers: { + prefs: function(p, self) { + if (_.size(p) === 0) { + p = { + name: self.get('config').get('name').get('value'), + color: self.get('config').get('color').get('value') + }; + } + return p; + }, + dataset: function(d) { + return { + id: d.id, + hda_ldda: d.get('hda_ldda') + }; + } + } }); var BackboneTrackCollection = Backbone.Collection.extend({ @@ -938,25 +991,55 @@ /** * A visualization of genome data. */ -var GenomeVisualization = Visualization.extend({ +var GenomeVisualization = Visualization.extend(CustomToJSON).extend({ defaults: _.extend({}, Visualization.prototype.defaults, { dbkey: '', - tracks: null, + drawables: null, bookmarks: null, viewport: null }), initialize: function(options) { - this.set('tracks', new BackboneTrackCollection(options.tracks)); + // Replace drawables with tracks. + this.set('drawables', new BackboneTrackCollection(options.tracks)); + this.set('config', config_mod.ConfigSettingCollection.from_config_dict(options.prefs || {})); + + // Clear track and data definitions to avoid storing large objects. + this.unset('tracks'); + this.get('drawables').each(function(d) { + d.unset('preloaded_data'); + }); }, /** * Add a track or array of tracks to the visualization. */ add_tracks: function(tracks) { - this.get('tracks').add(tracks); + this.get('drawables').add(tracks); } -}); +}, +{ + // This definition matches that produced by to_dict() methods in tracks.js + to_json_keys: [ + 'view', + 'viewport', + 'bookmarks' + ], + + to_json_mappers: { + 'view': function(dummy, self) { + return { + obj_type: 'View', + prefs: { + name: self.get('title'), + content_visible: true + }, + drawables: self.get('drawables') + }; + } + } +} +); /** * Configuration data for a Trackster track. https://bitbucket.org/galaxy/galaxy-central/commits/90b76033686b/ Changeset: 90b76033686b User: jeremy goecks Date: 2014-02-05 22:23:24 Summary: Merge local into default. 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.state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} .state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} diff -r c98072c51cf05de686c631739a5deb18c15734bf -r 90b76033686b5c363bca32edf7f6c292a1d0d080 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -269,7 +269,7 @@ } // ---------------------------------------------------------------------------- datasets -.dataset { +.dataset.hda { border: 1px solid @border-default-color; // body mixins @@ -512,7 +512,7 @@ } -.dataset .state-icon { +.dataset.hda .state-icon { .fa-icon; display: inline-block; vertical-align: middle; diff -r c98072c51cf05de686c631739a5deb18c15734bf -r 90b76033686b5c363bca32edf7f6c292a1d0d080 templates/webapps/galaxy/dataset/embed.mako --- a/templates/webapps/galaxy/dataset/embed.mako +++ b/templates/webapps/galaxy/dataset/embed.mako @@ -4,10 +4,10 @@ %><%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a> + <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk"></a> ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import tooltip"></a> - <a class="icon-button go-to-full-screen tooltip" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> + <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import"></a> + <a class="icon-button go-to-full-screen" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a></%def> https://bitbucket.org/galaxy/galaxy-central/commits/d557d5dd942f/ Changeset: d557d5dd942f Branch: next-stable User: jeremy goecks Date: 2014-02-05 22:24:21 Summary: Automated merge. Affected #: 4 files diff -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 -r d557d5dd942f5bbf820e19ec3fe7278401489555 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var s=galaxy_config.app.viz_config;$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:s.vis_id,title:s.title,dbkey:s.dbkey,type:"trackster",vis_json:JSON.stringify(s)}}).success(function(t){Galaxy.modal.hide();s.vis_id=t.vis_id;s.has_changes=false;window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file diff -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 -r d557d5dd942f5bbf820e19ec3fe7278401489555 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,j,m,p){var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var k=function(v){return("promise" in v)};var f=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(f.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(k(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(k(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!k(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new g({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new g({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var g=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({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.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return g.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=g.overlap_results.BEFORE}else{if(z<x){v=g.overlap_results.OVERLAP_START}else{v=g.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=g.overlap_results.AFTER}else{if(z<=x){v=g.overlap_results.CONTAINED_BY}else{v=g.overlap_results.OVERLAP_END}}}else{v=(z>=x?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===g.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:g});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new g(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend({initialize:function(v){this.set("dataset",new j.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}});var i=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("tracks",new i(v.tracks))},add_tracks:function(v){this.get("tracks").add(v)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(u,k,n,q){var f={toJSON:function(){var w=this,x={};u.each(w.constructor.to_json_keys,function(y){var z=w.get(y);if(y in w.constructor.to_json_mappers){z=w.constructor.to_json_mappers[y](z,w)}x[y]=z});return x}};var a=function(w,z,y,x){$.ajax({url:w,data:y,error:function(){alert("Grid failed")},success:function(A){Galaxy.modal.show({title:"Select datasets for new tracks",body:A,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var B=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var C={data_type:"track_config",hda_ldda:"hda"},D=$(this).val();if($(this).attr("name")!=="id"){C.hda_ldda="ldda"}B[B.length]=$.ajax({url:z+"/"+D,data:C,dataType:"json"})});$.when.apply($,B).then(function(){var C=(arguments[0] instanceof Array?$.map(arguments,function(D){return D[0]}):[arguments[0]]);x(C)});Galaxy.modal.hide()}}})}})};var l=function(w){return("promise" in w)};var g=function(w){this.default_font=w!==undefined?w:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};u.extend(g.prototype,{load_pattern:function(w,A){var x=this.patterns,y=this.dummy_context,z=new Image();z.src=galaxy_config.root+"static/images"+A;z.onload=function(){x[w]=y.createPattern(z,"repeat")}},get_pattern:function(w){return this.patterns[w]},new_canvas:function(){var w=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(w)}w.manager=this;return w}});var s=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(w){this.clear()},get_elt:function(y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,x=y.toString(),w=u.indexOf(A,function(B){return B.toString()===x});if(w!==-1){if(z[x].stale){A.splice(w,1);delete z[x]}else{this.move_key_to_end(y,w)}}return z[x]},set_elt:function(y,A){var B=this.attributes.obj_cache,C=this.attributes.key_ary,x=y.toString(),z=this.attributes.num_elements;if(!B[x]){if(C.length>=z){var w=C.shift();delete B[w.toString()]}C.push(y)}B[x]=A;return A},move_key_to_end:function(x,w){this.attributes.key_ary.splice(w,1);this.attributes.key_ary.push(x)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=s.extend({defaults:u.extend({},s.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(w,x){return true},can_subset:function(w){return false}}),initialize:function(w){s.prototype.initialize.call(this);var x=this.get("init_data");if(x){this.add_data(x)}},add_data:function(w){if(this.get("num_elements")<w.length){this.set("num_elements",w.length)}var x=this;u.each(w,function(y){x.set_data(y.region,y)})},data_is_ready:function(){var z=this.get("dataset"),y=$.Deferred(),w=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),x=new n.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:z.get("hda_ldda"),data_type:w},dataType:"json"},interval:5000,success_fn:function(A){return A!=="pending"}});$.when(x.go()).then(function(A){y.resolve(A==="ok"||A==="data")});return y},search_features:function(w){var x=this.get("dataset"),y={query:w,hda_ldda:x.get("hda_ldda"),data_type:"features"};return $.getJSON(x.url(),y)},load_data:function(E,D,x,C){var A=this.get("dataset"),z={data_type:this.get("data_type"),chrom:E.get("chrom"),low:E.get("start"),high:E.get("end"),mode:D,resolution:x,hda_ldda:A.get("hda_ldda")};$.extend(z,C);var G=this.get("filters_manager");if(G){var H=[];var w=G.filters;for(var B=0;B<w.length;B++){H.push(w[B].name)}z.filter_cols=JSON.stringify(H)}var y=this,F=$.getJSON(A.url(),z,function(I){I.region=E;y.set_data(E,I)});this.set_data(E,F);return F},get_data:function(D,C,y,A){var E=this.get_elt(D);if(E&&(l(E)||this.get("data_mode_compatible")(E,C))){return E}var F=this.get("key_ary"),w=this.get("obj_cache"),x,B;for(var z=0;z<F.length;z++){x=F[z];if(x.contains(D)){B=true;E=w[x.toString()];if(l(E)||(this.get("data_mode_compatible")(E,C)&&this.get("can_subset")(E))){this.move_key_to_end(x,z);if(!l(E)){var H=this.subset_entry(E,D);this.set(D,H);E=H}return E}}}if(!B&&D.length()<this.attributes.min_region_size){D=D.copy();var G=this.most_recently_added();if(!G||(D.get("start")>G.get("start"))){D.set("end",D.get("start")+this.attributes.min_region_size)}else{D.set("start",D.get("end")-this.attributes.min_region_size)}D.set("genome",this.attributes.genome);D.trim()}return this.load_data(D,C,y,A)},set_data:function(x,w){this.set_elt(x,w)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(E,D,z,C,A){var G=this._mark_stale(E);if(!(G&&this.get("data_mode_compatible")(G,D))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var y=E.get("start");if(A===this.DEEP_DATA_REQ){$.extend(C,{start_val:G.data.length+1})}else{if(A===this.BROAD_DATA_REQ){y=(G.max_high?G.max_high:G.data[G.data.length-1][2])+1}}var F=E.copy().set("start",y);var x=this,B=this.load_data(F,D,z,C),w=$.Deferred();this.set_data(E,w);$.when(B).then(function(H){if(H.data){H.data=G.data.concat(H.data);if(H.max_low){H.max_low=G.max_low}if(H.message){H.message=H.message.replace(/[0-9]+/,H.data.length)}}x.set_data(E,H);w.resolve(H)});return w},can_get_more_detailed_data:function(x){var w=this.get_elt(x);return(w.dataset_type==="bigwig"&&w.data.length<8000)},get_more_detailed_data:function(z,B,x,A,y){var w=this._mark_stale(z);if(!w){console.log("ERROR getting more detailed data: no current data");return}if(!y){y={}}if(w.dataset_type==="bigwig"){y.num_samples=1000*A}return this.load_data(z,B,x,y)},_mark_stale:function(x){var w=this.get_elt(x);if(!w){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),x.toString())}w.stale=true;return w},get_genome_wide_data:function(w){var y=this,A=true,z=u.map(w.get("chroms_info").chrom_info,function(C){var B=y.get_elt(new h({chrom:C.chrom,start:0,end:C.len}));if(!B){A=false}return B});if(A){return z}var x=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(B){y.add_data(B.data);x.resolve(B.data)});return x},subset_entry:function(y,z){var w={bigwig:function(A,B){return u.filter(A,function(C){return C[0]>=B.get("start")&&C[0]<=B.get("end")})},refseq:function(B,C){var D=C.get("start")-y.region.get("start"),A=y.data.length-(y.region.get("end")-C.get("end"));return y.data.slice(D,A)}};var x=y.data;if(!y.region.same(z)&&y.dataset_type in w){x=w[y.dataset_type](y.data,z)}return{region:z,data:x,dataset_type:y.dataset_type}}});var r=d.extend({initialize:function(w){var x=new Backbone.Model();x.urlRoot=w.data_url;this.set("dataset",x)},load_data:function(y,z,w,x){return(y.length()<=100000?d.prototype.load_data.call(this,y,z,w,x):{data:null,region:y})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(w){this.id=w.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(w){var x=u.find(this.get_chroms_info(),function(y){return y.chrom===w});return new h({chrom:x.chrom,end:x.len})},get_chrom_len:function(w){return u.find(this.get_chroms_info(),function(x){return x.chrom===w}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(w){return this.attributes.chrom===w.get("chrom")&&this.attributes.start===w.get("start")&&this.attributes.end===w.get("end")},initialize:function(x){if(x.from_str){var z=x.from_str.split(":"),y=z[0],w=z[1].split("-");this.set({chrom:y,start:parseInt(w[0],10),end:parseInt(w[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({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.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(D){var x=this.get("chrom"),C=D.get("chrom"),B=this.get("start"),z=D.get("start"),A=this.get("end"),y=D.get("end"),w;if(x&&C&&x!==C){return h.overlap_results.DIF_CHROMS}if(B<z){if(A<z){w=h.overlap_results.BEFORE}else{if(A<y){w=h.overlap_results.OVERLAP_START}else{w=h.overlap_results.CONTAINS}}}else{if(B>z){if(B>y){w=h.overlap_results.AFTER}else{if(A<=y){w=h.overlap_results.CONTAINED_BY}else{w=h.overlap_results.OVERLAP_END}}}else{w=(A>=y?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return w},trim:function(w){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var x=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>x){this.attributes.end=x-1}}return this},contains:function(w){return this.compute_overlap(w)===h.overlap_results.CONTAINS},overlaps:function(w){return u.intersection([this.compute_overlap(w)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var o=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(w){this.set("region",new h(w.region))}});var t=Backbone.Collection.extend({model:e});var v=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(w){this.set("dataset",new k.Dataset(w.dataset));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var x=this.get("preloaded_data");if(x){x=x.data}else{x=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:x}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(x,w){if(u.size(x)===0){x={name:w.get("config").get("name").get("value"),color:w.get("config").get("color").get("value")}}return x},dataset:function(w){return{id:w.id,hda_ldda:w.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:v});var p=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var m=p.extend(f).extend({defaults:u.extend({},p.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(w){this.set("drawables",new j(w.tracks));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs||{}));this.unset("tracks");this.get("drawables").each(function(x){x.unset("preloaded_data")})},add_tracks:function(w){this.get("drawables").add(w)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(x,w){return{obj_type:"View",prefs:{name:w.get("title"),content_visible:true},drawables:w.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(x){this.view=x.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var w=this;w.view.on("navigate",function(y){w.navigate(y)})},change_location:function(w){this.view.go_to(w)}});return{BackboneTrack:v,BrowserBookmark:e,BrowserBookmarkCollection:t,Cache:s,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:o,GenomeVisualization:m,GenomeReferenceDataManager:r,TrackBrowserRouter:i,TrackConfig:b,Visualization:p,select_datasets:a}}); \ No newline at end of file diff -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 -r d557d5dd942f5bbf820e19ec3fe7278401489555 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -143,8 +143,8 @@ this.chords_views = null; // When tracks added to/removed from model, update view. - this.model.get('tracks').on('add', this.add_track, this); - this.model.get('tracks').on('remove', this.remove_track, this); + this.model.get('drawables').on('add', this.add_track, this); + this.model.get('drawables').on('remove', this.remove_track, this); this.get_circular_tracks(); }, @@ -154,7 +154,7 @@ * Returns tracks to be rendered using circular view. */ get_circular_tracks: function() { - return this.model.get('tracks').filter(function(track) { + return this.model.get('drawables').filter(function(track) { return track.get('track_type') !== 'DiagonalHeatmapTrack'; }); }, @@ -163,7 +163,7 @@ * Returns tracks to be rendered using chords view. */ get_chord_tracks: function() { - return this.model.get('tracks').filter(function(track) { + return this.model.get('drawables').filter(function(track) { return track.get('track_type') === 'DiagonalHeatmapTrack'; }); }, @@ -992,41 +992,36 @@ // setup menu var menu = create_icon_buttons_menu([ - { icon_class: 'plus-button', title: 'Add tracks', on_click: function() + { + icon_class: 'plus-button', title: 'Add tracks', on_click: function() { visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", vis.get('dbkey'), function(tracks) { vis.add_tracks(tracks); }); } - },{ + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // show saving dialog box Galaxy.modal.show({title: "Saving...", body: "progress" }); - // link configuration - var view = galaxy_config.app.viz_config; - // send to server $.ajax({ url: galaxy_config.root + "visualization/save", type: "POST", dataType: "json", data: { - 'id' : view.vis_id, - 'title' : view.title, - 'dbkey' : view.dbkey, + 'id' : vis.get('vis_id'), + 'title' : vis.get('title'), + 'dbkey' : vis.get('dbkey'), 'type' : 'trackster', - 'vis_json' : JSON.stringify(view) + 'vis_json' : JSON.stringify(vis) } }).success(function(vis_info) { Galaxy.modal.hide(); - 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); + vis.set('vis_id', vis_info.vis_id); }).error(function() { // show dialog Galaxy.modal.show({ @@ -1036,7 +1031,8 @@ }); }); } - },{ + }, + { icon_class: 'cross-circle', title: 'Close', on_click: function() { window.location = galaxy_config.root + "visualization/list"; diff -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 -r d557d5dd942f5bbf820e19ec3fe7278401489555 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,6 +1,28 @@ define( ["libs/underscore", "mvc/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) { /** + * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes + * to include in the representation; to_json_mappers defines mappers for returned objects. + */ +var CustomToJSON = { + /** + * Returns JSON representation of object using to_json_keys and to_json_mappers. + */ + toJSON: function() { + var self = this, + json = {}; + _.each(self.constructor.to_json_keys, function(k) { + var val = self.get(k); + if (k in self.constructor.to_json_mappers) { + val = self.constructor.to_json_mappers[k](val, self); + } + json[k] = val; + }); + return json; + } +}; + +/** * Model, view, and controller objects for Galaxy visualization framework. * * Models have no references to views, instead using events to indicate state @@ -872,7 +894,10 @@ * A track of data in a genome visualization. */ // TODO: rename to Track and merge with Trackster's Track object. -var BackboneTrack = Backbone.Model.extend({ +var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend({ + defaults: { + mode: 'Auto' + }, initialize: function(options) { this.set('dataset', new data_mod.Dataset(options.dataset)); @@ -883,7 +908,7 @@ // Set up some minimal config. this.get('config').add( [ - { key: 'name', value: this.get('name') }, + { key: 'name', value: this.get('dataset').get('name') }, { key: 'color' } ] ); @@ -900,6 +925,34 @@ init_data: preloaded_data })); } +}, +{ + // This definition matches that produced by to_dict() methods in tracks.js + to_json_keys: [ + 'track_type', + 'dataset', + 'prefs', + 'mode', + 'filters', + 'tool_state' + ], + to_json_mappers: { + prefs: function(p, self) { + if (_.size(p) === 0) { + p = { + name: self.get('config').get('name').get('value'), + color: self.get('config').get('color').get('value') + }; + } + return p; + }, + dataset: function(d) { + return { + id: d.id, + hda_ldda: d.get('hda_ldda') + }; + } + } }); var BackboneTrackCollection = Backbone.Collection.extend({ @@ -938,25 +991,55 @@ /** * A visualization of genome data. */ -var GenomeVisualization = Visualization.extend({ +var GenomeVisualization = Visualization.extend(CustomToJSON).extend({ defaults: _.extend({}, Visualization.prototype.defaults, { dbkey: '', - tracks: null, + drawables: null, bookmarks: null, viewport: null }), initialize: function(options) { - this.set('tracks', new BackboneTrackCollection(options.tracks)); + // Replace drawables with tracks. + this.set('drawables', new BackboneTrackCollection(options.tracks)); + this.set('config', config_mod.ConfigSettingCollection.from_config_dict(options.prefs || {})); + + // Clear track and data definitions to avoid storing large objects. + this.unset('tracks'); + this.get('drawables').each(function(d) { + d.unset('preloaded_data'); + }); }, /** * Add a track or array of tracks to the visualization. */ add_tracks: function(tracks) { - this.get('tracks').add(tracks); + this.get('drawables').add(tracks); } -}); +}, +{ + // This definition matches that produced by to_dict() methods in tracks.js + to_json_keys: [ + 'view', + 'viewport', + 'bookmarks' + ], + + to_json_mappers: { + 'view': function(dummy, self) { + return { + obj_type: 'View', + prefs: { + name: self.get('title'), + content_visible: true + }, + drawables: self.get('drawables') + }; + } + } +} +); /** * Configuration data for a Trackster track. https://bitbucket.org/galaxy/galaxy-central/commits/75a81fcf38c4/ Changeset: 75a81fcf38c4 User: jeremy goecks Date: 2014-02-05 22:24:47 Summary: Merge next-stable with default. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Feb '14

05 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b8e4f343a9a/ Changeset: 2b8e4f343a9a Branch: next-stable User: carlfeberhard Date: 2014-02-05 22:17:16 Summary: Fix to bootstrap tooltip class hiding icons in embedded datasets within pages Affected #: 3 files diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1604,46 +1604,46 @@ .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-history-message{display:none;margin:0px 10px 0px 10px} .history-panel .tag-button{display:inline-block;height:20px;margin:2px 2px 0px 0px;border:1px solid grey;border-radius:3px 10px 10px 3px;padding:2px 4px 2px 4px;background-color:#EEE;line-height:13px}.history-panel .tag-button .tag-name{margin-right:2px} -.dataset{border:1px solid #bfbfbf}.dataset .vertical-spacing{margin-bottom:8px} -.dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.dataset .dataset-padding{padding:6px 10px 6px 8px} -.dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.dataset .help-text{font-weight:normal;color:#555} -.dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} -.dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset .dataset-primary-actions .icon-btn{margin-left:2px} -.dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.dataset .dataset-body .prompt{font-weight:normal;color:#555} -.dataset .dataset-body .prompt:after{content:':'} -.dataset .dataset-body .dataset-summary{margin-bottom:8px}.dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.dataset .dataset-body .dataset-summary .dataset-datatype,.dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset .dataset-body .dataset-summary .dataset-datatype .value,.dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} -.dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.dataset .dataset-body .dataset-actions .right{float:right}.dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset .dataset-body .tags-display .select2-container{min-width:0px}.dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.dataset .dataset-body .annotation-display .annotation:empty{height:22px} -.dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.dataset .dataset-body .dataset-peek{margin-bottom:8px}.dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.dataset .dataset-body .dataset-peek pre.peek table,.dataset .dataset-body .dataset-peek pre.peek th,.dataset .dataset-body .dataset-peek pre.peek tr,.dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.dataset .icon-btn-group{display:inline-block}.dataset .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.dataset.hda{border:1px solid #bfbfbf}.dataset.hda .vertical-spacing{margin-bottom:8px} +.dataset.hda .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.dataset.hda .dataset-padding{padding:6px 10px 6px 8px} +.dataset.hda [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.dataset.hda .help-text{font-weight:normal;color:#555} +.dataset.hda .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.dataset.hda .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.dataset.hda .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.dataset.hda .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset.hda .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.dataset.hda .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.dataset.hda .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.dataset.hda .dataset-primary-actions .icon-btn{margin-left:2px} +.dataset.hda .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset.hda .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.dataset.hda .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.dataset.hda .dataset-body .prompt{font-weight:normal;color:#555} +.dataset.hda .dataset-body .prompt:after{content:':'} +.dataset.hda .dataset-body .dataset-summary{margin-bottom:8px}.dataset.hda .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.dataset.hda .dataset-body .dataset-summary .dataset-datatype,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.dataset.hda .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.dataset.hda .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset.hda .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.dataset.hda .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.dataset.hda .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset.hda .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.dataset.hda .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.dataset.hda .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.dataset.hda .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.dataset.hda .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.dataset.hda .dataset-body .dataset-actions .right{float:right}.dataset.hda .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.dataset.hda .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .tags-display .select2-container{min-width:0px}.dataset.hda .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.dataset.hda .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.dataset.hda .dataset-body .annotation-display .annotation:empty{height:22px} +.dataset.hda .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.dataset.hda .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.dataset.hda .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.dataset.hda .dataset-body .dataset-peek{margin-bottom:8px}.dataset.hda .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset.hda .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.dataset.hda .dataset-body .dataset-peek pre.peek table,.dataset.hda .dataset-body .dataset-peek pre.peek th,.dataset.hda .dataset-body .dataset-peek pre.peek tr,.dataset.hda .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.dataset.hda .icon-btn-group{display:inline-block}.dataset.hda .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.dataset.hda .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.dataset.hda .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.dataset.hda .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} .state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -269,7 +269,7 @@ } // ---------------------------------------------------------------------------- datasets -.dataset { +.dataset.hda { border: 1px solid @border-default-color; // body mixins @@ -512,7 +512,7 @@ } -.dataset .state-icon { +.dataset.hda .state-icon { .fa-icon; display: inline-block; vertical-align: middle; diff -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa -r 2b8e4f343a9abe4e936afec8a3d99bf8d9a01ef0 templates/webapps/galaxy/dataset/embed.mako --- a/templates/webapps/galaxy/dataset/embed.mako +++ b/templates/webapps/galaxy/dataset/embed.mako @@ -4,10 +4,10 @@ %><%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a> + <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk"></a> ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import tooltip"></a> - <a class="icon-button go-to-full-screen tooltip" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> + <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import"></a> + <a class="icon-button go-to-full-screen" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a></%def> https://bitbucket.org/galaxy/galaxy-central/commits/99beec4c3a33/ Changeset: 99beec4c3a33 User: carlfeberhard Date: 2014-02-05 22:18:33 Summary: merge Affected #: 3 files diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r 99beec4c3a338249ab661a7edc3e30ee115486e9 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1605,46 +1605,46 @@ .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-history-message{display:none;margin:0px 10px 0px 10px} .history-panel .tag-button{display:inline-block;height:20px;margin:2px 2px 0px 0px;border:1px solid grey;border-radius:3px 10px 10px 3px;padding:2px 4px 2px 4px;background-color:#EEE;line-height:13px}.history-panel .tag-button .tag-name{margin-right:2px} -.dataset{border:1px solid #bfbfbf}.dataset .vertical-spacing{margin-bottom:8px} -.dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.dataset .dataset-padding{padding:6px 10px 6px 8px} -.dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.dataset .help-text{font-weight:normal;color:#555} -.dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} -.dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset .dataset-primary-actions .icon-btn{margin-left:2px} -.dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.dataset .dataset-body .prompt{font-weight:normal;color:#555} -.dataset .dataset-body .prompt:after{content:':'} -.dataset .dataset-body .dataset-summary{margin-bottom:8px}.dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.dataset .dataset-body .dataset-summary .dataset-datatype,.dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset .dataset-body .dataset-summary .dataset-datatype .value,.dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} -.dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.dataset .dataset-body .dataset-actions .right{float:right}.dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset .dataset-body .tags-display .select2-container{min-width:0px}.dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.dataset .dataset-body .annotation-display .annotation:empty{height:22px} -.dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.dataset .dataset-body .dataset-peek{margin-bottom:8px}.dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.dataset .dataset-body .dataset-peek pre.peek table,.dataset .dataset-body .dataset-peek pre.peek th,.dataset .dataset-body .dataset-peek pre.peek tr,.dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.dataset .icon-btn-group{display:inline-block}.dataset .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.dataset.hda{border:1px solid #bfbfbf}.dataset.hda .vertical-spacing{margin-bottom:8px} +.dataset.hda .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.dataset.hda .dataset-padding{padding:6px 10px 6px 8px} +.dataset.hda [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.dataset.hda .help-text{font-weight:normal;color:#555} +.dataset.hda .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.dataset.hda .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.dataset.hda .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.dataset.hda .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset.hda .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.dataset.hda .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.dataset.hda .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.dataset.hda .dataset-primary-actions .icon-btn{margin-left:2px} +.dataset.hda .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset.hda .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.dataset.hda .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.dataset.hda .dataset-body .prompt{font-weight:normal;color:#555} +.dataset.hda .dataset-body .prompt:after{content:':'} +.dataset.hda .dataset-body .dataset-summary{margin-bottom:8px}.dataset.hda .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.dataset.hda .dataset-body .dataset-summary .dataset-datatype,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.dataset.hda .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.dataset.hda .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset.hda .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.dataset.hda .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.dataset.hda .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset.hda .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.dataset.hda .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.dataset.hda .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.dataset.hda .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.dataset.hda .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.dataset.hda .dataset-body .dataset-actions .right{float:right}.dataset.hda .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.dataset.hda .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .tags-display .select2-container{min-width:0px}.dataset.hda .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.dataset.hda .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.dataset.hda .dataset-body .annotation-display .annotation:empty{height:22px} +.dataset.hda .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.dataset.hda .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.dataset.hda .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.dataset.hda .dataset-body .dataset-peek{margin-bottom:8px}.dataset.hda .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset.hda .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.dataset.hda .dataset-body .dataset-peek pre.peek table,.dataset.hda .dataset-body .dataset-peek pre.peek th,.dataset.hda .dataset-body .dataset-peek pre.peek tr,.dataset.hda .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.dataset.hda .icon-btn-group{display:inline-block}.dataset.hda .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.dataset.hda .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.dataset.hda .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.dataset.hda .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} .state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r 99beec4c3a338249ab661a7edc3e30ee115486e9 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -269,7 +269,7 @@ } // ---------------------------------------------------------------------------- datasets -.dataset { +.dataset.hda { border: 1px solid @border-default-color; // body mixins @@ -512,7 +512,7 @@ } -.dataset .state-icon { +.dataset.hda .state-icon { .fa-icon; display: inline-block; vertical-align: middle; diff -r 0a8336ad8d4df064abcaa286814527ee8bbde34f -r 99beec4c3a338249ab661a7edc3e30ee115486e9 templates/webapps/galaxy/dataset/embed.mako --- a/templates/webapps/galaxy/dataset/embed.mako +++ b/templates/webapps/galaxy/dataset/embed.mako @@ -4,10 +4,10 @@ %><%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a> + <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk"></a> ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import tooltip"></a> - <a class="icon-button go-to-full-screen tooltip" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> + <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import"></a> + <a class="icon-button go-to-full-screen" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Feb '14

05 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce8a3e4414e6/ Changeset: ce8a3e4414e6 Branch: next-stable User: dan Date: 2014-02-05 21:48:36 Summary: Fix minor display bug in show_params. Affected #: 1 file diff -r 8e2fab723bca8ce5eac70d1bef2cb127897eae81 -r ce8a3e4414e6ea4e761d3b40b66541e8c53471fa templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -141,9 +141,9 @@ % if params_objects and tool: ${ inputs_recursive( tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages ) } %elif params_objects is None: - <tr><td colspan="2">Unable to load parameters.</td></tr> + <tr><td colspan="3">Unable to load parameters.</td></tr> % else: - <tr><td colspan="2">No parameters.</td></tr> + <tr><td colspan="3">No parameters.</td></tr> % endif </tbody></table> https://bitbucket.org/galaxy/galaxy-central/commits/0a8336ad8d4d/ Changeset: 0a8336ad8d4d User: dan Date: 2014-02-05 21:48:36 Summary: Fix minor display bug in show_params. Affected #: 1 file diff -r 58f73c96431bdd701c0bdf656d0f0f0d14c456e4 -r 0a8336ad8d4df064abcaa286814527ee8bbde34f templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -141,9 +141,9 @@ % if params_objects and tool: ${ inputs_recursive( tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages ) } %elif params_objects is None: - <tr><td colspan="2">Unable to load parameters.</td></tr> + <tr><td colspan="3">Unable to load parameters.</td></tr> % else: - <tr><td colspan="2">No parameters.</td></tr> + <tr><td colspan="3">No parameters.</td></tr> % endif </tbody></table> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Feb '14

05 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8e2fab723bca/ Changeset: 8e2fab723bca Branch: next-stable User: dan Date: 2014-02-05 19:44:32 Summary: Update GenomeSpace import tools to use current working directory instead of __new_file_path__ for extrafiles created using multiple outputs technique. Should resolve issue on our public servers where only the first selected file was being imported to the history. Affected #: 2 files diff -r c77d83fe4c3e37d07c241bb1f76064a3d0b7f149 -r 8e2fab723bca8ce5eac70d1bef2cb127897eae81 tools/genomespace/genomespace_file_browser.py --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -166,7 +166,7 @@ while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) - output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) ) + output_filename = os.path.join( os.getcwd(), 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) ) metadata_dict = dict( type = 'new_primary_dataset', base_dataset_id = dataset_id, diff -r c77d83fe4c3e37d07c241bb1f76064a3d0b7f149 -r 8e2fab723bca8ce5eac70d1bef2cb127897eae81 tools/genomespace/genomespace_importer.py --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -189,7 +189,7 @@ while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) - target_output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) + target_output_filename = os.path.join( os.getcwd(), 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) shutil.move( output_filename, target_output_filename ) metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset', base_dataset_id = base_dataset_id, https://bitbucket.org/galaxy/galaxy-central/commits/58f73c96431b/ Changeset: 58f73c96431b User: dan Date: 2014-02-05 19:44:32 Summary: Update GenomeSpace import tools to use current working directory instead of __new_file_path__ for extrafiles created using multiple outputs technique. Should resolve issue on our public servers where only the first selected file was being imported to the history. Affected #: 2 files diff -r 47990c9bd4d8003e0ba619d73c1022646f3bc973 -r 58f73c96431bdd701c0bdf656d0f0f0d14c456e4 tools/genomespace/genomespace_file_browser.py --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -166,7 +166,7 @@ while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) - output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) ) + output_filename = os.path.join( os.getcwd(), 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) ) metadata_dict = dict( type = 'new_primary_dataset', base_dataset_id = dataset_id, diff -r 47990c9bd4d8003e0ba619d73c1022646f3bc973 -r 58f73c96431bdd701c0bdf656d0f0f0d14c456e4 tools/genomespace/genomespace_importer.py --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -189,7 +189,7 @@ while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) - target_output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) + target_output_filename = os.path.join( os.getcwd(), 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) shutil.move( output_filename, target_output_filename ) metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset', base_dataset_id = base_dataset_id, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Visualizations API: properly return visualization model id from update; Visualizations MVC: bring setConfig into line with Backbone API
by commits-noreply＠bitbucket.org 05 Feb '14

05 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47990c9bd4d8/ Changeset: 47990c9bd4d8 User: carlfeberhard Date: 2014-02-05 18:36:11 Summary: Visualizations API: properly return visualization model id from update; Visualizations MVC: bring setConfig into line with Backbone API Affected #: 3 files diff -r 6af6d838db509c1ce90a885d15a6e2cda2ef1e87 -r 47990c9bd4d8003e0ba619d73c1022646f3bc973 lib/galaxy/webapps/galaxy/api/visualizations.py --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -176,8 +176,11 @@ or ( dbkey != visualization.latest_revision.dbkey ) or ( util.json.to_json_string( config ) != util.json.to_json_string( latest_config ) ) ): revision = self.add_visualization_revision( trans, visualization, config, title, dbkey ) - #TODO: need to somehow get what changed here? - rval = { 'id' : revision.id } + rval = { 'id' : id, 'revision' : revision.id } + + #TODO: allow updating vis title & slug + #visualization.title = title + #trans.sa_session.flush() except ( ItemAccessibilityException, ItemDeletionException ), exception: trans.response.status = 403 diff -r 6af6d838db509c1ce90a885d15a6e2cda2ef1e87 -r 47990c9bd4d8003e0ba619d73c1022646f3bc973 static/scripts/mvc/visualization/visualization-model.js --- a/static/scripts/mvc/visualization/visualization-model.js +++ b/static/scripts/mvc/visualization/visualization-model.js @@ -1,24 +1,6 @@ //define([ //], function(){ -//function saveVis( title, config ){ -// var xhr = jQuery.ajax( '/api/visualizations', { -// type : 'POST', -// data : { -// type : 'scatterplot', -// title : title, -// config : JSON.stringify( config ) -// } -// }); -// xhr.fail( function( xhr, status, message ){ -// console.debug( jQuery.makeArray( arguments ) ); -// console.error( 'Error saving visualization:', xhr.responseJSON.error ); -// }); -// return xhr.then( function( saveInfo ){ -// return saveInfo; -// }); -//} - //============================================================================== /** @class Model for a saved Galaxy visualization. * @@ -36,21 +18,13 @@ /** default attributes for a model */ defaults : { - //id : null, - //type : null, - //title : null, - //dbkey : null, - //user_id : null, - //slug : null, - //revisions : [], - //latest_revision : null - - //(this is unusual in that visualizations don't have configs, revisions do) - //config : {} + config : {} }, - url : function(){ - return galaxy_config.root + 'api/visualizations'; + /** override urlRoot to handle presence/absence of galaxy_config */ + urlRoot : function(){ + var apiUrl = '/api/visualizations'; + return (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root + apiUrl ):( apiUrl )); }, /** Set up the model, determine if accessible, bind listeners @@ -58,27 +32,39 @@ */ initialize : function( data ){ this.log( this + '.initialize', data, this.attributes ); + + // munge config sub-object here since bbone won't handle defaults with this + if( _.isObject( data.config ) && _.isObject( this.defaults.config ) ){ + _.defaults( data.config, this.defaults.config ); + } + this._setUpListeners(); }, /** set up any event listeners */ _setUpListeners : function(){ + //this.on( 'change', function(){ + // console.info( 'change:', arguments ); + //}); }, // ........................................................................ config - setConfig: function( config ){ - var oldConfig = this.get( 'config' ); - // extend if already exists (and clone in order to trigger change) - if( _.isObject( oldConfig ) ){ - config = _.extend( _.clone( oldConfig ), config ); + /** override set to properly allow update and trigger change when setting the sub-obj 'config' */ + set: function( key, val ){ + //TODO: validate config is object + if( key === 'config' ){ + var oldConfig = this.get( 'config' ); + // extend if already exists (is this correct behavior? no way to eliminate keys or reset entirely) + // clone in order to trigger change (diff. obj ref) + if( _.isObject( oldConfig ) ){ + val = _.extend( _.clone( oldConfig ), val ); + } } - this.set( 'config', config ); + Backbone.Model.prototype.set.call( this, key, val ); return this; }, - // ........................................................................ common queries - // ........................................................................ ajax // ........................................................................ misc /** String representation */ toString : function(){ diff -r 6af6d838db509c1ce90a885d15a6e2cda2ef1e87 -r 47990c9bd4d8003e0ba619d73c1022646f3bc973 static/scripts/packed/mvc/visualization/visualization-model.js --- a/static/scripts/packed/mvc/visualization/visualization-model.js +++ b/static/scripts/packed/mvc/visualization/visualization-model.js @@ -1,1 +1,1 @@ -var Visualization=Backbone.Model.extend(LoggableMixin).extend({defaults:{},url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(a){this.log(this+".initialize",a,this.attributes);this._setUpListeners()},_setUpListeners:function(){},setConfig:function(b){var a=this.get("config");if(_.isObject(a)){b=_.extend(_.clone(a),b)}this.set("config",b);return this},toString:function(){var a=this.get("id")||"";if(this.get("title")){a+=":"+this.get("title")}return"Visualization("+a+")"}});var VisualizationCollection=Backbone.Collection.extend(LoggableMixin).extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(b,a){a=a||{}},set:function(c,a){var b=this;c=_.map(c,function(e){var f=b.get(e.id);if(!f){return e}var d=f.toJSON();_.extend(d,e);return d});Backbone.Collection.prototype.set.call(this,c,a)},toString:function(){return(["VisualizationCollection(",[this.historyId,this.length].join(),")"].join(""))}}); \ No newline at end of file +var Visualization=Backbone.Model.extend(LoggableMixin).extend({defaults:{config:{}},urlRoot:function(){var a="/api/visualizations";return((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root+a):(a))},initialize:function(a){this.log(this+".initialize",a,this.attributes);if(_.isObject(a.config)&&_.isObject(this.defaults.config)){_.defaults(a.config,this.defaults.config)}this._setUpListeners()},_setUpListeners:function(){},set:function(b,c){if(b==="config"){var a=this.get("config");if(_.isObject(a)){c=_.extend(_.clone(a),c)}}Backbone.Model.prototype.set.call(this,b,c);return this},toString:function(){var a=this.get("id")||"";if(this.get("title")){a+=":"+this.get("title")}return"Visualization("+a+")"}});var VisualizationCollection=Backbone.Collection.extend(LoggableMixin).extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(b,a){a=a||{}},set:function(c,a){var b=this;c=_.map(c,function(e){var f=b.get(e.id);if(!f){return e}var d=f.toJSON();_.extend(d,e);return d});Backbone.Collection.prototype.set.call(this,c,a)},toString:function(){return(["VisualizationCollection(",[this.historyId,this.length].join(),")"].join(""))}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: PageServingPluginManager: allow additional common paths to be added to each plugin's TemplateLookup and allow configuration of these paths; Visualizations Framework: add common/templates, readme, and configuration of same
by commits-noreply＠bitbucket.org 05 Feb '14

05 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6af6d838db50/ Changeset: 6af6d838db50 User: carlfeberhard Date: 2014-02-05 17:55:13 Summary: PageServingPluginManager: allow additional common paths to be added to each plugin's TemplateLookup and allow configuration of these paths; Visualizations Framework: add common/templates, readme, and configuration of same Affected #: 3 files diff -r 9c4a45cd38e6fd6122698db67689c7aaacd0adac -r 6af6d838db509c1ce90a885d15a6e2cda2ef1e87 config/plugins/visualizations/additional_template_paths.xml --- /dev/null +++ b/config/plugins/visualizations/additional_template_paths.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<paths> + <path>common/templates</path> +</paths> diff -r 9c4a45cd38e6fd6122698db67689c7aaacd0adac -r 6af6d838db509c1ce90a885d15a6e2cda2ef1e87 config/plugins/visualizations/common/templates/README.txt --- /dev/null +++ b/config/plugins/visualizations/common/templates/README.txt @@ -0,0 +1,8 @@ +Common templates for visualization plugins +========================================== + +Placing Mako templates in this directory will allow them to be properly +inherited and imported in plugin directories. E.g. if you have a template file +in this directory named 'config_utils.mako', you can import it in your plugin +templates using: + <%namespace name="config_utils" file="config_utils.mako" /> diff -r 9c4a45cd38e6fd6122698db67689c7aaacd0adac -r 6af6d838db509c1ce90a885d15a6e2cda2ef1e87 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -374,6 +374,8 @@ DEFAULT_TEMPLATE_COLLECTION_SIZE = 10 #: default encoding of plugin templates DEFAULT_TEMPLATE_ENCODING = 'utf-8' + #: name of files to search for additional template lookup directories + additional_template_paths_config_filename = 'additional_template_paths.xml' def __init__( self, app, base_url, template_cache_dir=None, **kwargs ): """ @@ -389,9 +391,42 @@ """ self.base_url = base_url self.template_cache_dir = template_cache_dir + self.additional_template_paths = [] super( PageServingPluginManager, self ).__init__( app, **kwargs ) + def load_configuration( self ): + """ + Load framework wide configuration, including: + additional template lookup directories + """ + for directory in self.directories: + possible_path = os.path.join( directory, self.additional_template_paths_config_filename ) + if os.path.exists( possible_path ): + added_paths = self.parse_additional_template_paths( possible_path, directory ) + self.additional_template_paths.extend( added_paths ) + + def parse_additional_template_paths( self, config_filepath, base_directory ): + """ + Parse an XML config file at `config_filepath` for template paths + (relative to `base_directory`) to add to each plugin's template lookup. + + Allows having a set of common templates for import/inheritance in + plugin templates. + + :type config_filepath: string + :param config_filepath: filesystem path to the config file + :type base_directory: string + :param base_directory: path prefixed to new, relative template paths + """ + additional_paths = [] + xml_tree = util.parse_xml( config_filepath ) + paths_list = xml_tree.getroot() + for rel_path_elem in paths_list.findall( 'path' ): + if rel_path_elem.text is not None: + additional_paths.append( os.path.join( base_directory, rel_path_elem.text ) ) + return additional_paths + def is_plugin( self, plugin_path ): """ Determines whether the given filesystem path contains a plugin. @@ -518,7 +553,11 @@ """ if not plugin.serves_templates: return None - template_lookup = self._create_mako_template_lookup( self.template_cache_dir, plugin.template_path ) + template_lookup_paths = plugin.template_path + if self.additional_template_paths: + template_lookup_paths = [ template_lookup_paths ] + self.additional_template_paths + #log.debug( 'template_lookup_paths: %s', template_lookup_paths ) + template_lookup = self._create_mako_template_lookup( self.template_cache_dir, template_lookup_paths ) return template_lookup def _create_mako_template_lookup( self, cache_dir, paths, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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