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commit/galaxy-central: carlfeberhard: scatterplot: improved adj. for varying y-axis sizes; pack scripts
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/369a94139390/ changeset: 369a94139390 user: carlfeberhard date: 2012-10-02 21:36:56 summary: scatterplot: improved adj. for varying y-axis sizes; pack scripts affected #: 8 files diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/libs/underscore.js --- a/static/scripts/packed/libs/underscore.js +++ b/static/scripts/packed/libs/underscore.js @@ -1,1 +1,1 @@ -(function(){var w=this;var k=w._;var E={};var D=Array.prototype,g=Object.prototype,r=Function.prototype;var I=D.push,o=D.slice,y=D.concat,B=D.unshift,d=g.toString,j=g.hasOwnProperty;var M=D.forEach,q=D.map,F=D.reduce,c=D.reduceRight,b=D.filter,C=D.every,p=D.some,n=D.indexOf,l=D.lastIndexOf,u=Array.isArray,f=Object.keys,G=r.bind;var N=function(O){if(O instanceof N){return O}if(!(this instanceof N)){return new N(O)}this._wrapped=O};if(typeof exports!=="undefined"){if(typeof 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0}}));return{min:i.min(m),max:i.max(m)}}});return{CircsterView:b}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(i,k,j){var f=function(){this.initialize&&this.initialize.apply(this,arguments)};f.extend=Backbone.Model.extend;var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var e=Backbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var b=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=20;this.scale=1},render:function(){var v=this,s=this.dataset_arc_height,m=v.$el.width(),u=v.$el.height(),n=Math.min(m,u)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),t=this.model.get("tracks"),p=t.map(function(w,y){var z=n+y*(s+v.track_gap),x=(w.get("track_type")==="LineTrack"?g:h);return new x({track:w,track_index:y,radius_bounds:[z,z+s],genome:v.genome,total_gap:v.total_gap})});var q=k.select(v.$el[0]).append("svg").attr("width",m).attr("height",u).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){var w=k.event.scale;q.attr("transform","translate("+k.event.translate+") scale("+w+")");if(v.scale!==w){if(v.zoom_drag_timeout){clearTimeout(v.zoom_drag_timeout)}v.zoom_drag_timeout=setTimeout(function(){i.each(p,function(x){x.update_scale(w)})},400)}})).attr("transform","translate("+m/2+","+u/2+")").append("svg:g");i.each(p,function(w){w.render(q)});var r=n+t.length*(s+v.track_gap)+v.track_gap;var o=new a({track:new e(),track_index:t.length,radius_bounds:[r,r],genome:v.genome,total_gap:v.total_gap});o.render(q)}});var c=f.extend({initialize:function(m){this.options=m;this.options.bg_stroke="ccc";this.options.bg_fill="ccc";this.options.chroms_layout=this._chroms_layout();this.options.data_bounds=this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome));this.options.scale=1;this.options.parent_elt=null},render:function(q){this.options.parent_elt=q.append("g").attr("id","parent-"+this.options.track_index);var p=this.options.parent_elt;var o=this.options.chroms_layout,s=k.svg.arc().innerRadius(this.options.radius_bounds[0]).outerRadius(this.options.radius_bounds[1]),m=p.selectAll("g").data(o).enter().append("svg:g");m.append("path").attr("d",s).style("stroke",this.options.bg_stroke).style("fill",this.options.bg_fill).append("title").text(function(t){return t.data.chrom});this._render_data(p);var n=this.options.track.get("prefs"),r=n.block_color;if(!r){r=n.color}p.selectAll("path.chrom-data").style("stroke",r).style("fill",r)},update_scale:function(p){var o=this.options.scale;this.options.scale=p;if(p<=o){return}var n=this,m=new l();this.options.parent_elt.selectAll("path.chrom-data").filter(function(r,q){return m.is_visible(this)}).each(function(v,s){var u=k.select(this),r=u.attr("chrom"),t=n.options.genome.get_chrom_region(r),q=n.options.track.get("data_manager").get_more_detailed_data(t,"Coverage",0,p);$.when(q).then(function(z){u.remove();n._update_data_bounds();var y=i.find(n.options.chroms_layout,function(A){return A.data.chrom===r});var w=n.options.track.get("prefs"),x=w.block_color;if(!x){x=w.color}n._render_chrom_data(n.options.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_update_data_bounds:function(){this.options.data_bounds=this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome))},_render_data:function(p){var o=this,n=this.options.chroms_layout,m=this.options.track,s=m.get_genome_wide_data(this.options.genome),q=i.zip(n,s),r=i.map(q,function(t){var u=t[0],v=t[1];return o._render_chrom_data(p,u,v)});return p},_render_chrom_data:function(m,n,o){},_compute_path_data:function(m,n){},_chroms_layout:function(){var n=this.options.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.options.total_gap/n.length,o=i.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o}});var a=c.extend({initialize:function(m){this.options=m;this.options.bg_stroke="fff";this.options.bg_fill="fff";this.options.chroms_layout=this._chroms_layout()},_render_data:function(n){var m=n.selectAll("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom});m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0.08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(function(o){return o.data.chrom})}});var d=c.extend({_render_chrom_data:function(m,p,n){if(!n||typeof n==="string"||n.data.length===0){return null}var q=this._compute_path_data(p,n.data);var o=m.datum(n.data),r=o.append("path").attr("class","chrom-data").attr("chrom",p.data.chrom).attr("d",q);return r},_compute_path_data:function(o,p){var m=k.scale.linear().domain(this.options.data_bounds).range(this.options.radius_bounds);var q=k.scale.linear().domain([0,p.length]).range([o.startAngle,o.endAngle]);var n=k.svg.line.radial().interpolate("linear").radius(function(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.radial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius()).angle(n.angle())},get_data_bounds:function(m){}});var h=d.extend({get_data_bounds:function(n){var m=i.map(n,function(o){if(!o||typeof o==="string"){return 0}return o.max});return[0,(m&&typeof m!=="string"?i.max(m):0)]}});var g=d.extend({get_data_bounds:function(n){var m=i.flatten(i.map(n,function(o){if(o){return i.map(o.data,function(q){return q[1]})}else{return 0}}));return[i.min(m),i.max(m)]}});return{CircsterView:b}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(e){var h=this,g=10,f=12,d=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(null,i)}};this.log("new TwoVarScatterplot:",e);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,e);this.updateConfig=function(i){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(){this.svg.attr("width",this.config.width+(this.config.marginRight+this.config.marginLeft)).attr("height",this.config.height+(this.config.marginTop+this.config.marginBottom)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft,this.config.marginTop))};this.preprocessData=function(i){return i.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(i,j){this.xMin=this.config.xMin||d3.min(i);this.xMax=this.config.xMax||d3.max(i);this.yMin=this.config.yMin||d3.min(j);this.yMax=this.config.yMax||d3.max(j)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.log("xAxis:",this.xAxis);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));this.log("xLongestLabel:",this.xLongestLabel);if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);this.yLongestLabel=d3.max(_.map([this.yMin,this.yMax],function(j){return(String(j)).length}));this.log("yLongestLabel:",this.yLongestLabel);var i=this.yLongestLabel*g+(d);if(this.config.yAxisLabelBumpX>-(i)){this.config.yAxisLabelBumpX=-(i)}if(this.config.marginLeft<i){this.config.marginLeft=i+f;this.adjustChartDimensions()}this.log("this.config.yAxisLableBumpx, this.config.marginLeft:",this.config.yAxisLabelBumpX,this.config.marginLeft);this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel);this.log("yAxisLabel:",this.yAxisLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.log("vGridLines:",this.vGridLines);this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove();this.log("hGridLines:",this.hGridLines)};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l){var k=function(n,m){return h.xScale(i[m])};var j=function(n,m){return h.yScale(l[m])};this.datapoints=this.content.selectAll(".glyph").data(i);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",k).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",k).attr("cy",j).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove();this.log(this.datapoints,"glyphs rendered")};this.render=function(i,j){this.log("renderScatterplot",i.length,j.length,this.config);i=this.preprocessData(i);j=this.preprocessData(j);this.log("xCol len",i.length,"yCol len",j.length);this.setUpDomains(i,j);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,j)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</column>"}});e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);jQuery.ajax({url:e,dataType:"json",success:function(k){d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}))},error:function(m,k,l){alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file +define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return j.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(j,k){this.xMin=this.config.xMin||d3.min(j);this.xMax=this.config.xMax||d3.max(j);this.yMin=this.config.yMin||d3.min(k);this.yMax=this.config.yMax||d3.max(k)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(j,k){this.log("renderScatterplot",j.length,k.length,this.config);j=this.preprocessData(j);k=this.preprocessData(k);this.setUpDomains(j,k);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,k)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}));d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/sweepster.js --- a/static/scripts/packed/viz/sweepster.js +++ b/static/scripts/packed/viz/sweepster.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(o,f,n,h,g,d){var m=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(r){var q=this;this.get("tool").get("inputs").each(function(s){if(!s.get_samples()){return}s.on("change:min change:max change:num_samples",function(t){if(t.get("in_ptree")){q.set_tree_data()}},q);s.on("change:in_ptree",function(t){if(t.get("in_ptree")){q.add_param(t)}else{q.remove_param(t)}q.set_tree_data()},q)});if(r.config){_.each(r.config,function(t){var s=q.get("tool").get("inputs").find(function(u){return u.get("name")===t.name});q.add_param(s);s.set(t)})}},add_param:function(q){if(q.get("ptree_index")){return}q.set("in_ptree",true);q.set("ptree_index",this.get_tree_params().length)},remove_param:function(q){q.set("in_ptree",false);q.set("ptree_index",null);_(this.get_tree_params()).each(function(r,s){r.set("ptree_index",s+1)})},set_tree_data:function(){var r=_.map(this.get_tree_params(),function(t){return{param:t,samples:t.get_samples()}});var q=0,s=function(w,t){var y=w[t],x=y.param,v=x.get("label"),u=y.samples;if(w.length-1===t){return _.map(u,function(z){return{id:q++,name:z,param:x,value:z}})}return _.map(u,function(z){return{id:q++,name:z,param:x,value:z,children:s(w,t+1)}})};this.set("tree_data",{name:"Root",id:q++,children:(r.length!==0?s(r,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(q){return q.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(q,r){return q*r.get_samples().length},1)},get_node_settings:function(u){var s=this.get("tool").get_inputs_dict();var v=u.parent;if(v){while(v.depth!==0){s[v.param.get("name")]=v.value;v=v.parent}}var q=this,r=function(x,w){if(x.param){w[x.param.get("name")]=x.value}if(!x.children){return new m({inputs:q.get("tool").get("inputs"),values:w})}else{return _.flatten(_.map(x.children,function(y){return r(y,_.clone(w))}))}},t=r(u,s);if(!_.isArray(t)){t=[t]}return t},get_connected_nodes:function(s){var t=function(u){if(!u.children){return u}else{return _.flatten([u,_.map(u.children,function(v){return t(v)})])}};var r=[],q=s.parent;while(q){r.push(q);q=q.parent}return _.flatten([r,t(s)])},get_leaf:function(r){var s=this.get("tree_data"),q=function(t){return _.find(t,function(u){return r[u.param.get("name")]===u.value})};while(s.children){s=q(s.children)}return s},toJSON:function(){return this.get_tree_params().map(function(q){return{name:q.get("name"),min:q.get("min"),max:q.get("max"),num_samples:q.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:n.GenomeRegion}],initialize:function(q){if(q.track){var r=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},q.track);this.set("track",h.object_from_template(r,{},null))}},same_settings:function(q){var r=this.get("settings"),s=q.get("settings");for(var t in r){if(!s[t]||r[t]!==s[t]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=n.Visualization.extend({defaults:_.extend({},n.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:n.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(q){var r=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",r);this.set("parameter_tree",new p({tool:r,config:q.tree_config}))},add_track:function(q){this.get("tracks").add(q)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(q){this.canvas_manager=q.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var v=this.model.get("settings"),r=v.get("values"),t=$("<td/>").addClass("settings").appendTo(this.$el),s=$("<div/>").addClass("track-info").hide().appendTo(t);s.append($("<div/>").css("font-weight","bold").text("Track Settings"));v.get("inputs").each(function(x){s.append(x.get("label")+": "+r[x.get("name")]+"<br/>")});var q=this,w=$("<button/>").appendTo(s).text("Run on complete dataset").click(function(){s.toggle();q.trigger("run_on_dataset",v)});var u=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){s.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){q.$el.remove();$(".bs-tooltip").remove()}}]);t.prepend(u.$el);this.model.get("regions").each(function(){q.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var r=this,q=this.model.get("track"),t=this.model.get("regions"),s=this.$el.find("td.tile");if(!q){return}$.when(q.data_manager.data_is_ready()).then(function(u){t.each(function(x,w){var v=x.length()/r.TILE_LEN,z=1/v,y=r.model.get("mode");$.when(q.data_manager.get_data(x,y,v,{})).then(function(B){var A=r.canvas_manager.new_canvas();A.width=r.TILE_LEN;A.height=q.get_canvas_height(B,y,z,A.width);q.draw_tile(B,A.getContext("2d"),y,v,x,z);$(s[w]).empty().append(A)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(q){this.$el=q.tool_row;this.render()},render:function(){var r=this.model,v=r.get("type"),x=this.$el.find(".form-row-input"),t=null;x.find(":input").change(function(){r.set("value",$(this).val())});if(v==="number"){t=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(v==="select"){var s=_.map(this.$el.find("select option"),function(y){return $(y).val()}),u=s.join(", ");t=$(_.template(this.select_input_template,{options:u}))}}t.insertAfter(x);var q=this,w=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){r.set("in_ptree",true);x.hide();t.show();$(this).hide();q.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){r.set("in_ptree",false);t.hide();x.show();$(this).hide();q.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(w.$el);if(r.get("in_ptree")){x.hide();q.$el.find(".icon-button.plus-button").hide()}else{q.$el.find(".icon-button.toggle").hide();t.hide()}_.each(["min","max","num_samples"],function(y){t.find("."+y).change(function(){r.set(y,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(q){this.render()},render:function(){var s=new g.ToolFormView({model:this.model.get("tool")});s.render();this.$el.append(s.$el);var r=this,q=r.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(t){var u=new b({model:q.at(t),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(q){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var y=this.model.get_tree_params();if(!y.length){return}this.width=100*(2+y.length);this.height=15*this.model.get_num_leaves();var x=this;var w=o.layout.cluster().size([this.height,this.width-160]);var s=o.svg.diagonal().projection(function(z){return[z.y,z.x]});var q=w.nodes(this.model.get("tree_data"));var t=_.uniq(_.pluck(q,"y"));_.each(y,function(B,A){var z=t[A+1],C=$("#center").position().left;x.$el.append($("<div>").addClass("label").text(B.get("label")).css("left",z+C))});var r=o.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var v=r.selectAll("path.link").data(w.links(q)).enter().append("path").attr("class","link").attr("d",s);var u=r.selectAll("g.node").data(q).enter().append("g").attr("class","node").attr("transform",function(z){return"translate("+z.y+","+z.x+")"}).on("mouseover",function(A){var z=_.pluck(x.model.get_connected_nodes(A),"id");u.filter(function(B){return _.find(z,function(C){return C===B.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){u.style("fill","#000")});u.append("circle").attr("r",9);u.append("text").attr("dx",function(z){return z.children?-12:12}).attr("dy",3).attr("text-anchor",function(z){return z.children?"end":"start"}).text(function(z){return z.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(r){this.canvas_manager=new n.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var q=this;this.model.get("tracks").each(function(s){s.get("track").view=q});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var w=new k({model:this.model.get("parameter_tree")});$("#left").append(w.$el);var z=this,t=z.model.get("regions"),x=$("<tr/>").appendTo(this.track_collection_container);t.each(function(A){x.append($("<th>").text(A.toString()))});x.children().first().attr("colspan",2);var u=$("<div>").addClass("tiles");$("#right").append(u.append(this.track_collection_container));z.model.get("tracks").each(function(A){z.add_track(A)});var y=$(this.helpText).addClass("help"),v=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();y.remove()}}]);y.prepend(v.$el.css("float","right"));$("#center").append(y);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var s=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var r=["Squish","Pack"],q={};_.each(r,function(A){q[A]=function(){z.model.set("default_mode",A);z.model.get("tracks").each(function(B){B.set("mode",A)})}});make_popupmenu(s.$el.find(".chevron-expand"),q);s.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(s.$el)},run_tool_on_dataset:function(r){var q=this.model.get("tool"),t=q.get("name"),s=this.model.get("dataset");q.set_input_values(r.get("values"));$.when(q.rerun(s)).then(function(u){});show_modal("Running "+t+" on complete dataset",t+" is running on dataset '"+s.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(t){var r=this,s=this.model.get("parameter_tree");r.model.add_track(t);var q=new l({model:t,canvas_manager:r.canvas_manager});q.on("run_on_dataset",r.run_tool_on_dataset,r);r.track_collection_container.append(q.$el);q.$el.hover(function(){var v=s.get_leaf(t.get("settings").get("values"));var u=_.pluck(s.get_connected_nodes(v),"id");o.select(r.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(w){return _.find(u,function(x){return x===w.id})!==undefined}).style("fill","#f00")},function(){o.select(r.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return t},handle_node_clicks:function(){var q=this,r=this.model.get("parameter_tree"),t=this.model.get("regions"),s=o.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");s.on("click",function(z,w){var v=q.model.get("tool"),y=q.model.get("dataset"),x=r.get_node_settings(z),u=$.Deferred();if(x.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+q.model.get("tool").get("name")+" with "+x.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();u.resolve(false)}})}else{u.resolve(true)}$.when(u).then(function(A){if(!A){return}var B=_.map(x,function(C){var D=new c({settings:C,regions:t,mode:q.model.get("default_mode")});q.add_track(D);return D});_.each(B,function(D,C){setTimeout(function(){v.set_input_values(D.get("settings").get("values"));$.when(v.rerun(y,t)).then(function(F){var G=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},F.first().get("track_config")),E=h.object_from_template(G,q,null);E.data_manager.set("data_type","raw_data");E.prefs.block_color=q.block_color;E.prefs.reverse_strand_color=q.reverse_strand_color;D.set("track",E)})},C*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){if(!t.get_samples()){return}t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion}],initialize:function(r){if(r.track){var s=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(r){var s=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",s);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".bs-tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(w==="number"){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(w==="select"){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},G.first().get("track_config")),F=h.object_from_template(H,r,null);F.data_manager.set("data_type","raw_data");F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters","viz/trackster_ui"],function(ad,y,l,v,M,ab,i,q){var r=ad.extend;var R=l.get_random_color;var ae=function(af,ah,ag){$.ajax({url:af,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ai){show_modal("Select datasets for new tracks",ai,{Cancel:function(){hide_modal()},Add:function(){var aj=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var ak={data_type:"track_config",hda_ldda:"hda"},al=$(this).val();if($(this).attr("name")!=="id"){ak.hda_ldda="ldda"}aj[aj.length]=$.ajax({url:ah+"/"+al,data:ak,dataType:"json"})});$.when.apply($,aj).then(function(){var ak=(arguments[0] instanceof Array?$.map(arguments,function(al){return al[0]}):[arguments[0]]);ag(ak)});hide_modal()}})}})};var X=function(af){return("isResolved" in af)};var n={};var k=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this),aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){am=$(an.get(ao));if(at.offsetY<am.position().top&&!(am.hasClass("reference-track")||am.hasClass("intro"))){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};exports.moveable=m;var ac=16,H=9,E=20,B=100,J=12000,U=400,L=5000,x=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",a="Loading data...",W="Ready for display",S=10,I=20;function Y(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var s=function(ag,af,ai){if(!s.id_counter){s.id_counter=0}this.id=s.id_counter++;this.name=ai.name;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ai.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(aj){aj.stopPropagation()});var ah=this;this.container_div.hover(function(){ah.icons_div.show()},function(){ah.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};s.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".bs-tooltip").remove();af.remove()}}];r(s.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var af=this.view;this.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,al,ak,aj,af,ai){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",al).addClass("icon-button").addClass(ak).tooltip().click(function(){aj(ah)}).appendTo(this.icons_div);if(ai){this.action_icons[ag].hide()}},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend,ah.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ag,af,ah){s.call(this,ag,af,ah);this.obj_type=ah.obj_type;this.drawables=[]};r(A.prototype,s.prototype,{unpack_drawables:function(ah){this.drawables=[];var ag;for(var af=0;af<ah.length;af++){ag=p(ah[af],this.view,this);this.add_drawable(ag)}},init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this;this.changed()},add_drawable_before:function(ah,af){this.changed();var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}this.changed()}return ai},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);ag.container=null;this.changed();return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var Q=function(ag,af,ai){r(ai,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ag,af,ai);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ai){this.unpack_drawables(ai.drawables)}if("filters" in ai){var ah=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ai.filters);ah.parent_div.replaceWith(this.filters_manager.parent_div);if(ai.filters.visible){this.setup_multitrack_filtering()}}};r(Q.prototype,s.prototype,A.prototype,{action_icons_def:[s.prototype.action_icons_def[0],s.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters();af._restore_filter_managers()}else{af.setup_multitrack_filtering();af.request_draw(true)}af.filters_manager.toggle()}},s.prototype.action_icons_def[2]],build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ah=this.drawables.length;if(ah===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ah===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ao,an,al,ar=true,aj=this.drawables[0].get_type(),af=0;for(ao=0;ao<ah;ao++){al=this.drawables[ao];if(al.get_type()!==aj){can_composite=false;break}if(al instanceof c){af++}}if(ar||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(af>1&&af===this.drawables.length){var at={},ag;al=this.drawables[0];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];at[ag.name]=[ag]}for(ao=1;ao<this.drawables.length;ao++){al=this.drawables[ao];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];if(ag.name in at){at[ag.name].push(ag)}}}this.filters_manager.remove_all();var ai,ak,am,ap;for(var aq in at){ai=at[aq];if(ai.length===af){ak=new i.NumberFilter({name:ai[0].name,index:ai[0].index});this.filters_manager.add_filter(ak)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].filters_manager=this.saved_filters_managers[af]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var af=0;af<this.drawables.length;af++){drawable=this.drawables[af];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var aj=[];for(var ag=0;ag<this.drawables.length;ag++){aj.push(this.drawables[ag].name)}var ah="Composite Track of "+this.drawables.length+" tracks ("+aj.join(", ")+")";var ai=new f(this.view,this.view,{name:ah,drawables:this.drawables});var af=this.container.replace_drawable(this,ai,true);ai.request_draw()},add_drawable:function(af){A.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){A.prototype.remove_drawable.call(this,af);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var af=r(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return af},request_draw:function(af,ah){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].request_draw(af,ah)}}});var aa=function(af){r(af,{obj_type:"View"});A.call(this,"View",af.container,af);this.chrom=null;this.vis_id=af.vis_id;this.dbkey=af.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ad.extend(aa.prototype,Backbone.Events);r(aa.prototype,A.prototype,{init:function(){this.requested_redraw=false;var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ae(add_datasets_url,add_track_async_url,function(aj){ad.each(aj,function(ak){af.add_drawable(p(ak,af,af))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus();af.nav_input.autocomplete({source:function(al,aj){var am=[],ak=$.map(af.get_drawables(),function(an){return an.data_manager.search_features(al.term).success(function(ao){am=am.concat(ao)})});$.when.apply($,ak).done(function(){aj($.map(am,function(an){return{label:an[0],value:an[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX)-af.container.offset().left,width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new Z(this,{content_div:this.top_labeltrack}));this.add_label_track(new Z(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){af.resize_window()},500)});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ag,ai,af,aj){if(this.timer){clearTimeout(this.timer)}if(aj){var ah=this;this.timer=setTimeout(function(){ah.trigger("navigate",ag+":"+ai+"-"+af)},500)}else{view.trigger("navigate",ag+":"+ai+"-"+af)}},update_location:function(af,ah){this.location_span.text(commatize(af)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ah));var ag=view.chrom_select.val();if(ag!==""){this.trigger_navigate(ag,view.low,view.high,true)}},load_chroms:function(ah){ah.num=x;var af=this,ag=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){return}if(aj.reference){af.add_label_track(new C(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+x+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+x+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){var ah=this;if(!ah.chrom_data){ah.load_chroms_deferred.then(function(){ah.change_chrom(ak,ag,am)});return}if(!ak||ak==="None"){return}if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-x});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+x});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}if(ah.reference_track){ah.reference_track.init()}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}else{ah.low=0;ah.high=ah.max_high}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ai){var af=this;var ah=af.high-af.low;if(af.low-ai<af.max_low){af.low=af.max_low;af.high=af.max_low+ah}else{if(af.high-ai>af.max_high){af.high=af.max_high;af.low=af.max_high-ah}else{af.high-=ai;af.low-=ai}}af.request_redraw();var ag=af.chrom_select.val();this.trigger_navigate(ag,af.low,af.high,true)},add_drawable:function(af){A.prototype.add_drawable.call(this,af);af.init();this.changed();this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){A.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ao){var al=this,ak=(ao?[ao]:al.drawables),ah;var ag;for(var aj=0;aj<ak.length;aj++){ag=ak[aj];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[aj][1]=af;al.tracks_to_be_redrawn[aj][2]=am}}if(!this.requested_redraw){requestAnimationFrame(function(){al._redraw(an)});this.requested_redraw=true}},_redraw:function(ap){this.requested_redraw=false;var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var t=function(ah,am,ai){this.track=ah;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ag=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params.push(new e(ag,at,ak,(ag in ai?ai[ag]:av),ao.min,ao.max))}else{if(aq==="select"){this.params.push(new O(ag,at,ak,(ag in ai?ai[ag]:av)))}else{console.log("WARNING: unrecognized tool parameter type:",ag,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("param-input").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);af.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()});if("visible" in ai&&ai.visible){this.parent_div.show()}};r(t.prototype,{update_params:function(){for(var af=0;af<this.params.length;af++){this.params[af].update_value()}},state_dict:function(){var ag={};for(var af=0;af<this.params.length;af++){ag[this.params[af].name]=this.params[af].value}ag.visible=this.parent_div.is(":visible");return ag},get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=ah});return af},get_param_values:function(){var af=[];this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var af=this;af.run({target_dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ak=this.track,ah=ag.tool_id+ak.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(ak.container===view){var aj=new Q(view,view,{name:this.name});var ai=ak.container.replace_drawable(ak,aj,false);aj.container_div.insertBefore(ak.view.content_div.children()[ai]);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);af=aj}else{af=ak.container}var al=new ak.constructor(view,af,{name:ah,hda_ldda:"hda"});al.init_for_tool_data();al.change_mode(ak.mode);al.set_filters_manager(ak.filters_manager.copy(al));al.update_icons();af.add_drawable(al);al.tiles_div.text("Starting job.");this.update_params();this.run(ag,al,function(am){al.set_dataset(new ab.Dataset(am));al.tiles_div.text("Running job.");al.init()})},run:function(af,ah,ai){af.inputs=this.get_param_values_dict();var ag=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(af),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(aj){return aj!=="pending"}});$.when(ag.go()).then(function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(z+aj.message)}else{ai(aj)}}})}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=$(ah);this.value=ai};r(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};r(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};r(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(an,aj){for(var ar=0;ar<an.length;ar++){ah=an[ar];if(ah.hidden){continue}var al="param_"+ar;var aw=ai.values[ah.key];var ay=$("<div class='form-row' />").appendTo(aj);ay.append($("<label />").attr("for",al).text(ah.label+":"));if(ah.type==="bool"){ay.append($('<input type="checkbox" />').attr("id",al).attr("name",al).attr("checked",aw))}else{if(ah.type==="text"){ay.append($('<input type="text"/>').attr("id",al).val(aw).click(function(){$(this).select()}))}else{if(ah.type==="select"){var au=$("<select />").attr("id",al);for(var ap=0;ap<ah.options.length;ap++){$("<option/>").text(ah.options[ap].label).attr("value",ah.options[ap].value).appendTo(au)}au.val(aw);ay.append(au)}else{if(ah.type==="color"){var ax=$("<div/>").appendTo(ay),at=$("<input />").attr("id",al).attr("name",al).val(aw).css("float","left").appendTo(ax).click(function(aA){$(".bs-tooltip").removeClass("in");var az=$(this).siblings(".bs-tooltip").addClass("in");az.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(az).height()/2)+($(this).height()/2)}).show();az.click(function(aB){aB.stopPropagation()});$(document).bind("click.color-picker",function(){az.hide();$(document).unbind("click.color-picker")});aA.stopPropagation()}),aq=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ax).attr("title","Set new random color").tooltip(),av=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(ax).hide(),am=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(av),ak=$("<div class='tooltip-arrow'></div>").appendTo(av),ao=$.farbtastic(am,{width:100,height:100,callback:at,color:aw});ax.append($("<div/>").css("clear","both"));(function(az){aq.click(function(){az.setColor(R())})})(ao)}else{ay.append($("<input />").attr("id",al).attr("name",al).val(aw))}}}}if(ah.help){ay.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange();this.track.changed()}}});var b=function(af,aj,ah,ag,ai){this.track=af;this.region=aj;this.low=aj.get("start");this.high=aj.get("end");this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag).height($(ag).attr("height"));this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(af,ak,ah,ag,ai,aj){b.call(this,af,ak,ah,ag,ai);this.max_val=aj};r(j.prototype,b.prototype);var P=function(ai,aq,aj,ah,al,at,am,au,ag,ap){b.call(this,ai,aq,aj,ah,al);this.mode=am;this.all_slotted=ag;this.feature_mapper=ap;this.has_icons=false;if(au){this.has_icons=true;var an=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:E-1,width:ah.width}).prependTo(this.html_elt);var ao=new y.GenomeRegion({chrom:ai.view.chrom,start:this.low,end:this.high}),ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ak.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()});af.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()})}};r(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)==="number"?Y(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(this).parents(".track-content").children(".overlay"));var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ag,af,ah){r(ah,{drag_handle_class:"draghandle"});s.call(this,ag,af,ah);this.dataset=new ab.Dataset({id:ah.dataset_id,hda_ldda:ah.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ah?ah.data_query_wait:L);this.data_manager=("data_manager" in ah?ah.data_manager:new y.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ah)||ah.resize){this.add_resize_handle()}}};r(g.prototype,s.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},s.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},s.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters()}else{af.filters_manager.init_filters()}af.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(af){var ai='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ah=ad.template(ai,{track:af});var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(){var am=$('select[name="regions"] option:selected').val(),ao,al=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),an=ad.map($(".bookmark"),function(ap){return new y.GenomeRegion({from_str:$(ap).children(".position").text()})});if(am==="cur"){ao=[al]}else{if(am==="bookmarks"){ao=an}else{ao=[al].concat(an)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:af.dataset_id,hda_ldda:af.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ao).toJSON())})},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ag()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ah,{No:ak,Yes:ag})}},s.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&s.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},on_resize:function(){},add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.tiles_div).css("height",aj);af.visible_height_px=(af.max_height_px===aj?0:aj);af.on_resize()}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.visible_height_px;af.changed()}).appendTo(af.container_div)},set_display_modes:function(ai,al){this.display_modes=ai;this.mode=(al?al:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ag=this,aj={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];aj[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.action_icons.mode_icon,aj)},build_action_icons:function(){s.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Z){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.content_div.css("height","auto");ag.tiles_div.children().remove();ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}var af=$.Deferred(),ah={hda_ldda:ag.hda_ldda,data_type:this.dataset_check_type,chrom:ag.view.chrom};$.getJSON(this.dataset.url(),ah,function(ai){if(!ai||ai==="error"||ai.kind==="error"){ag.container_div.addClass("error");ag.tiles_div.text(o);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ag.tiles_div.append(aj)}}else{if(ai==="no converter"){ag.container_div.addClass("error");ag.tiles_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ag.container_div.addClass("nodata");ag.tiles_div.text(F)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.tiles_div.html(w);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ai==="data"||ai.status==="data"){if(ai.valid_chroms){ag.valid_chroms=ai.valid_chroms;ag.update_icons()}ag.tiles_div.text(W);if(ag.view.chrom){ag.tiles_div.text("");ag.tiles_div.css("height",ag.visible_height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){af.resolve();ag.container_div.removeClass("nodata error pending");ag.request_draw()})}else{af.resolve()}}}}}}});this.update_icons();return af},predraw_init:function(){},get_drawables:function(){return this}});var N=function(ah,ag,ai){g.call(this,ah,ag,ai);var af=this;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new i.FiltersManager(this,("filters" in ai?ai.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ai&&ai.tool?new t(this,ai.tool,ai.tool_state):null);this.tile_cache=new y.Cache(S);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ai.mode){this.change_mode(ai.mode)}};r(N.prototype,s.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(af){$(".bs-tooltip").remove();af.slotters[af.view.resolution_px_b].max_rows*=2;af.request_draw(true)},hide:true}]),copy:function(af){var ag=this.to_dict();r(ag,{data_manager:this.data_manager});var ah=new this.constructor(this.view,af,ag);ah.change_mode(this.mode);ah.enabled=this.enabled;return ah},set_filters_manager:function(af){this.filters_manager=af;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show();af.action_icons.param_space_viz_icon.show()}else{af.action_icons.tools_icon.hide();af.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},before_draw:function(){},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),at=this.view.resolution_px_b,aj=this.view.resolution_b_px;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=(view.max_high-view.max_low)/ah;at=1/aj}this.before_draw();this.tiles_div.children().addClass("remove");var af=Math.floor(ao/(aj*U)),an=true,ar=[],al=function(au){return(au&&"track" in au)};while((af*U*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,this.tiles_div,at);if(al(ap)){ar.push(ap)}else{an=false}af+=1}if(!aq){this.tiles_div.children(".remove").removeClass("remove").remove()}var ai=this;if(an){this.tiles_div.children(".remove").remove();ai.postdraw_actions(ar,ah,at,aq)}},postdraw_actions:function(ah,ai,ak,af){var aj=false;for(var ag=0;ag<ah.length;ag++){if(ah[ag].has_icons){aj=true;break}}if(aj){for(var ag=0;ag<ah.length;ag++){tile=ah[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",E)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ai=this._get_tile_bounds(ax,av);if(!at){at={}}var az=(af?undefined:aq.tile_cache.get_elt(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ai,aq.mode,av,aq.data_url_extra_params);if(X(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ai,aq.mode,av,view.reference_track.data_url_extra_params);if(X(am)){ao=false}}if(ao){r(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ay=ai.get("start"),ag=ai.get("end"),ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ai,al,am);if(az!==undefined){aq.tile_cache.set_elt(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.visible_height_px},draw_tile:function(af,ag,ak,ai,aj,al,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.after_show_tile(ah)},after_show_tile:function(af){this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(af,ag){var ai=Math.floor(af*U*ag),aj=Math.ceil(U*ag),ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return new y.GenomeRegion({chrom:this.view.chrom,start:ai,end:ah})},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},can_subset:function(af){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ah,ai,ak,af){var ag=this;ag.normal_postdraw_actions(ah,ai,ak,af);ag.dataset_check_type="converted_datasets_state";ag.data_query_wait=L;var aj=new l.ServerStateDeferred({url:ag.dataset_state_url,url_params:{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},interval:ag.data_query_wait,success_fn:function(al){return al!=="pending"}});$.when(aj.go()).then(function(){ag.data_manager.set("data_type","data")});ag.postdraw_actions=ag.normal_postdraw_actions}}});var Z=function(ag,af){var ah={resize:false};g.call(this,ag,af,ah);this.container_div.addClass("label-track")};r(Z.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var f=function(ag,af,aj){N.call(this,ag,af,aj);this.drawables=[];this.left_offset=0;if("drawables" in aj){var ai;for(var ah=0;ah<aj.drawables.length;ah++){ai=aj.drawables[ah];this.drawables[ah]=p(ai,ag,null);if(ai.left_offset>this.left_offset){this.left_offset=ai.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};r(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(af){N.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].init())}var af=this;$.when.apply($,ah).then(function(){af.enabled=true;af.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:s.prototype.can_draw,draw_helper:function(ag,aw,aC,az,an,ap,ax){var av=this,aG=this._gen_tile_cache_key(aw,ap,aC),ak=this._get_tile_bounds(aC,az);if(!ax){ax={}}var aF=(ag?undefined:av.tile_cache.get_elt(aG));if(aF){av.show_tile(aF,an,ap);return aF}var ao=[],av,at=true,aA,aq;for(var aB=0;aB<this.drawables.length;aB++){av=this.drawables[aB];aA=av.data_manager.get_data(ak,av.mode,az,av.data_url_extra_params);if(X(aA)){at=false}ao.push(aA);aq=null;if(view.reference_track&&ap>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,av.mode,az,view.reference_track.data_url_extra_params);if(X(aq)){at=false}}ao.push(aq)}if(at){r(aA,ax.more_tile_data);this.tile_predraw_init();var aj=av.view.canvas_manager.new_canvas(),al=av._get_tile_bounds(aC,az),aD=ak.get("start"),ah=ak.get("end"),aE=0,aw=Math.ceil((ah-aD)*ap)+this.left_offset,au=0,ai=[],aB;var af=0;for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];var ar=av.mode;if(ar==="Auto"){ar=av.get_mode(aA);av.update_auto_mode(ar)}ai.push(ar);af=av.get_canvas_height(aA,ar,ap,aw);if(af>au){au=af}}aj.width=aw;aj.height=(ax.height?ax.height:au);aE=0;var ay=aj.getContext("2d");ay.translate(this.left_offset,0);ay.globalAlpha=0.5;ay.globalCompositeOperation="source-over";for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];aq=ao[aE+1];aF=av.draw_tile(aA,ay,ai[aB],az,ak,ap,aq)}this.tile_cache.set_elt(aG,aF);this.show_tile(aF,an,ap);return aF}var am=$.Deferred(),av=this;$.when.apply($,ao).then(function(){view.request_redraw(false,false,false,av);am.resolve()});return am},show_group:function(){var ai=new Q(this.view,this.container,{name:this.name}),af;for(var ah=0;ah<this.drawables.length;ah++){af=this.drawables[ah];af.update_icons();ai.add_drawable(af);af.container=ai;ai.content_div.append(af.container_div)}var ag=this.container.replace_drawable(this,ai,true);ai.request_draw()},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof h){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){N.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var C=function(af){N.call(this,af,{content_div:af.top_labeltrack},{resize:false});af.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};r(C.prototype,s.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:s.prototype.can_draw,draw_helper:function(aj,ah,af,ag,ak,al,ai){if(al>this.view.canvas_manager.char_width_px){return N.prototype.draw_helper.call(this,aj,ah,af,ag,ak,al,ai)}else{this.hide_contents();return null}},draw_tile:function(an,ao,aj,ai,al,ap){var ah=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){this.hide_contents();return}var ag=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var ak=0,am=an.length;ak<am;ak++){var af=Math.floor(ak*ap);ao.fillText(an[ak],af,10)}this.show_contents();return new b(ah,al,ai,ag,an)}this.hide_contents()}});var h=function(ah,ag,ai){var af=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:R()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(h.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.dataset.url(),{data_type:"data",stats:true,chrom:af.view.chrom,low:0,high:af.view.max_high,hda_ldda:af.hda_ldda},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min,al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div/>").text(Y(af.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_min_value(am)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+af.dataset_id+"_minval").prependTo(af.container_div),ai=$("<div/>").text(Y(af.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_max_value(am)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+af.dataset_id+"_maxval").prependTo(af.container_div)})},draw_tile:function(ao,am,ah,ag,aj,an){var af=am.canvas,ai=aj.get("start"),al=aj.get("end"),ak=new M.LinePainter(ao.data,ai,al,this.prefs,ah);ak.draw(am,af.width,af.height,an);return new b(this,aj,ag,af,ao.data)},can_subset:function(af){return false}});var u=function(ah,ag,ai){var af=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(u.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;this.tile_cache.clear();this.request_draw()},draw_tile:function(ap,an,ak,ai,ag,ao){var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new M.DiagonalHeatmapPainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this,ag,ai,ah,ap.data)}});var c=function(ai,ah,ak){var ag=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ai,ah,ak);var aj=R(),af=R([aj,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ak.prefs,onchange:function(){ag.set_name(ag.prefs.name);ag.tile_cache.clear();ag.set_painter_from_config();ag.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ak.hda_ldda;this.dataset_id=ak.dataset_id;this.original_dataset_id=ak.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};r(c.prototype,s.prototype,N.prototype,{set_dataset:function(af){this.dataset_id=af.get("id");this.hda_ldda=af.get("hda_ldda");this.dataset=af;this.data_manager.set("dataset",af)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(av,ap,ak,aj){N.prototype.postdraw_actions.call(this,av,aj);var ao=this,ar;if(ao.mode==="Coverage"){var ag=-1;for(ar=0;ar<av.length;ar++){var aq=av[ar].max_val;if(aq>ag){ag=aq}}for(ar=0;ar<av.length;ar++){var ax=av[ar];if(ax.max_val!==ag){ax.html_elt.remove();ao.draw_helper(true,ap,ax.index,ax.resolution,ax.html_elt.parent(),ak,{more_tile_data:{max:ag}})}}}if(ao.filters_manager){var al=ao.filters_manager.filters;for(var au=0;au<al.length;au++){al[au].update_ui_elt()}var aw=false,af,am;for(ar=0;ar<av.length;ar++){if(av[ar].data.length){af=av[ar].data[0];for(var au=0;au<al.length;au++){am=al[au];if(am.applies_to(af)&&am.min!==am.max){aw=true;break}}}}if(ao.filters_available!==aw){ao.filters_available=aw;if(!ao.filters_available){ao.filters_manager.hide()}ao.update_icons()}}this.container_div.find(".yaxislabel").remove();var ai=av[0];if(ai instanceof j){var an=(this.prefs.histogram_max?this.prefs.histogram_max:ai.max_val),ah=$("<div/>").text(an).make_text_editable({num_cols:12,on_finish:function(ay){$(".bs-tooltip").remove();var ay=parseFloat(ay);ao.prefs.histogram_max=(!isNaN(ay)?ay:null);ao.tile_cache.clear();ao.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ah)}if(ai instanceof P){var at=true;for(ar=0;ar<av.length;ar++){if(!av[ar].all_slotted){at=false;break}}if(!at){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(af){var af;if(this.mode==="Auto"){if(af==="no_detail"){af="feature spans"}else{if(af==="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (v.FeatureSlotter)(aj,ai,B,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>J){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Coverage"){return this.summary_draw_height}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ac,ah.get_required_height(ai,ag))}},draw_tile:function(ap,au,ar,av,ai,am,ah){var at=this,ag=au.canvas,aB=ai.get("start"),af=ai.get("end"),aj=this.left_offset;if(ar==="summary_tree"||ar==="Coverage"){var aD=new M.SummaryTreePainter(ap,aB,af,this.prefs);aD.draw(au,ag.width,ag.height,am);return new j(at,ai,av,ag,ap.data,ap.max)}var al=[],aq=this.slotters[am].slots;all_slotted=true;if(ap.data){var an=this.filters_manager.filters;for(var aw=0,ay=ap.data.length;aw<ay;aw++){var ak=ap.data[aw];var ax=false;var ao;for(var aA=0,aF=an.length;aA<aF;aA++){ao=an[aA];ao.update_attrs(ak);if(!ao.keep(ak)){ax=true;break}}if(!ax){al.push(ak);if(!(ak[0] in aq)){all_slotted=false}}}}var aE=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aC=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aD=new (this.painter)(al,aB,af,this.prefs,ar,aE,aC,ah);var az=null;au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";if(ap.data){az=aD.draw(au,ag.width,ag.height,am,aq);az.translation=-aj}return new P(at,ai,av,ag,ap.data,am,ar,ap.message,all_slotted,az)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(ag==="Coverage"){return af.dataset_type==="summary_tree"}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(af){if(af.dataset_type==="summary_tree"||af.message||af.extra_info==="no_detail"){return false}return true}});var T=function(ag,af,ah){c.call(this,ag,af,ah);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:R()},{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}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};r(T.prototype,s.prototype,N.prototype,c.prototype);var V=function(ah,ag,aj){c.call(this,ah,ag,aj);var ai=R(),af=R([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:aj.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};r(V.prototype,s.prototype,N.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:T,ReadTrack:V,CompositeTrack:f,DrawableGroup:Q};var p=function(ah,ag,af){if("copy" in ah){return ah.copy(af)}else{var ai=ah.obj_type;if(!ai){ai=ah.track_type}return new d[ai](ag,af,ah)}};return{View:aa,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:u,ReadTrack:V,VcfTrack:T,CompositeTrack:f,object_from_template:p,add_datasets:ae}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=w;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+w+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+w+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-w});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+w});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new e(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new aa.Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};q(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};q(j.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.after_show_tile(ag)},after_show_tile:function(ae){this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{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}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 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"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"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")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=s.level+1}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -61,8 +61,9 @@ */ function TwoVarScatterplot( config ){ var plot = this, - GUESS_AT_SVG_CHAR_WIDTH = 10, - GUESS_AT_SVG_CHAR_HEIGHT = 12, + TICK_LINE_AND_PADDING = 10, + GUESS_AT_SVG_CHAR_WIDTH = 7, + GUESS_AT_SVG_CHAR_HEIGHT = 10, PADDING = 8, X_LABEL_TOO_LONG_AT = 5; @@ -135,16 +136,23 @@ this.log( 'built svg:', d3.selectAll( 'svg' ) ); - this.adjustChartDimensions = function(){ + this.adjustChartDimensions = function( top, right, bottom, left ){ + top = top || 0; + right = right || 0; + bottom = bottom || 0; + left = left || 0; this.svg - .attr( "width", this.config.width + ( this.config.marginRight + this.config.marginLeft ) ) - .attr( "height", this.config.height + ( this.config.marginTop + this.config.marginBottom ) ) + .attr( "width", this.config.width + ( this.config.marginRight + right ) + + ( this.config.marginLeft + left ) ) + .attr( "height", this.config.height + ( this.config.marginTop + top ) + + ( this.config.marginBottom + bottom ) ) // initial is hidden - show it .style( 'display', 'block' ); // move content group away from margins + //TODO: allow top, right axis this.content = this.svg.select( "g.content" ) - .attr( "transform", this.translateStr( this.config.marginLeft, this.config.marginTop ) ); + .attr( "transform", this.translateStr( this.config.marginLeft + left, this.config.marginTop + top ) ); }; // ........................................................ data and scales @@ -208,29 +216,38 @@ .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - //this.log( 'yAxis:', this.yAxis ); + this.log( 'yAxis:', this.yAxis ); - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick - this.yLongestLabel = d3.max( _.map( [ this.yMin, this.yMax ], - function( number ){ return ( String( number ) ).length; } ) ); - this.log( 'yLongestLabel:', this.yLongestLabel ); + // get the tick labels for the y axis + var yTickLabels = this.yAxis.selectAll( 'text' ).filter( function( e, i ){ return i !== 0; } ); + //this.log( 'yTickLabels:', yTickLabels ); - //TODO: ugh ... so clumsy - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick - var neededY = this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH + ( PADDING ); + // get the longest label length (or 0 if no labels) + this.yLongestLabel = d3.max( + //NOTE: d3 returns an nested array - use the plain array inside ([0]) + yTickLabels[0].map( function( e, i ){ + return ( d3.select( e ).text() ).length; + }) + ) || 0; + //this.log( 'yLongestLabel:', this.yLongestLabel ); + //TODO: lose the guessing if possible + var neededY = TICK_LINE_AND_PADDING + ( this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH ) + + PADDING + GUESS_AT_SVG_CHAR_HEIGHT; + //this.log( 'neededY:', neededY ); // increase width for yLongerStr, increase margin for y //TODO??: (or transform each number: 2k) - if( this.config.yAxisLabelBumpX > -( neededY ) ){ - this.config.yAxisLabelBumpX = -( neededY ); + this.config.yAxisLabelBumpX = -( neededY - GUESS_AT_SVG_CHAR_HEIGHT ); + if( this.config.marginLeft < neededY ){ + var adjusting = ( neededY ) - this.config.marginLeft; + adjusting = ( adjusting < 0 )?( 0 ):( adjusting ); + this.log( 'adjusting:', adjusting ); + + // update dimensions, translations + this.adjustChartDimensions( 0, 0, 0, adjusting ); } - if( this.config.marginLeft < neededY ){ - this.config.marginLeft = neededY + GUESS_AT_SVG_CHAR_HEIGHT; - // update dimensions, translations - this.adjustChartDimensions(); - } - this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', - this.config.yAxisLabelBumpX, this.config.marginLeft ); + //this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', + // this.config.yAxisLabelBumpX, this.config.marginLeft ); this.yAxisLabel// = yAxis.select( 'text#y-axis-label' ) .attr( 'x', this.config.yAxisLabelBumpX ) @@ -367,7 +384,7 @@ * */ var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ - logger : console, + //logger : console, tagName : 'form', className : 'scatterplot-settings-form', @@ -444,12 +461,10 @@ message = message || ''; this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); this.$el.find( 'div#loading-indicator' ).show( 'fast' ); - console.debug( 'showing:', this.$el.find( 'div#loading-indicator' ), message ); }, hideLoadingIndicator : function(){ this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); - console.debug( 'hiding:', this.$el.find( 'div#loading-indicator' ) ); }, renderScatterplot : function(){ diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -60,9 +60,15 @@ stroke: black; shape-rendering: crispEdges; } + svg .axis text { + font-family: monospace; + font-size: 12px; +} + +svg #x-axis-label, svg #y-axis-label { font-family: sans-serif; - font-size: 12px; + font-size: 10px; } svg .glyph { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from 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commit/galaxy-central: carlfeberhard: scatterplot: loading indicators; api/datasets: minor cleanup;
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/80251cd7f94d/ changeset: 80251cd7f94d user: carlfeberhard date: 2012-10-02 19:24:26 summary: scatterplot: loading indicators; api/datasets: minor cleanup; affected #: 4 files diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -102,6 +102,7 @@ "column index (%d) must be less" % ( column ) + " than the number of columns: %d" % ( self.original_dataset.metadata.columns ) ) + #print columns, start_val, max_vals, skip_comments, kwargs # alter meta by column_selectors (if any) diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -187,7 +187,6 @@ # Return data. data = None data_provider = trans.app.data_provider_registry.get_data_provider( trans, raw=True, original_dataset=dataset ) - print 'data_provider:', data_provider if isinstance( data_provider, ColumnDataProvider ): data = data_provider.get_data( **kwargs ) diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -181,12 +181,11 @@ this.xAxis// = content.select( 'g#x-axis' ) .attr( 'transform', this.translateStr( 0, this.config.height ) ) .call( this.xAxisFn ); - this.log( 'xAxis:', this.xAxis ); + //this.log( 'xAxis:', this.xAxis ); - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick this.xLongestLabel = d3.max( _.map( [ this.xMin, this.xMax ], function( number ){ return ( String( number ) ).length; } ) ); - this.log( 'xLongestLabel:', this.xLongestLabel ); + //this.log( 'xLongestLabel:', this.xLongestLabel ); if( this.xLongestLabel >= X_LABEL_TOO_LONG_AT ){ //TODO: adjust ticks when tick labels are long - move odds down and extend tick line @@ -199,7 +198,7 @@ .attr( 'y', this.config.xAxisLabelBumpY ) .attr( 'text-anchor', 'middle' ) .text( this.config.xLabel ); - this.log( 'xAxisLabel:', this.xAxisLabel ); + //this.log( 'xAxisLabel:', this.xAxisLabel ); }; this.setUpYAxis = function(){ @@ -209,8 +208,9 @@ .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - this.log( 'yAxis:', this.yAxis ); + //this.log( 'yAxis:', this.yAxis ); + //TODO: this isn't reliable with -/+ ranges - better to go thru each tick this.yLongestLabel = d3.max( _.map( [ this.yMin, this.yMax ], function( number ){ return ( String( number ) ).length; } ) ); this.log( 'yLongestLabel:', this.yLongestLabel ); @@ -219,7 +219,7 @@ //TODO: this isn't reliable with -/+ ranges - better to go thru each tick var neededY = this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH + ( PADDING ); - // increase width for xLongerStr, increase margin for y + // increase width for yLongerStr, increase margin for y //TODO??: (or transform each number: 2k) if( this.config.yAxisLabelBumpX > -( neededY ) ){ this.config.yAxisLabelBumpX = -( neededY ); @@ -238,7 +238,7 @@ .attr( 'text-anchor', 'middle' ) .attr( 'transform', this.rotateStr( -90, this.config.yAxisLabelBumpX, this.config.height / 2 ) ) .text( this.config.yLabel ); - this.log( 'yAxisLabel:', this.yAxisLabel ); + //this.log( 'yAxisLabel:', this.yAxisLabel ); }; // ........................................................ grid lines @@ -261,7 +261,7 @@ // remove unneeded (less ticks) this.vGridLines.exit().remove(); - this.log( 'vGridLines:', this.vGridLines ); + //this.log( 'vGridLines:', this.vGridLines ); // HORIZONTAL this.hGridLines = this.content.selectAll( 'line.h-grid-line' ) @@ -277,7 +277,7 @@ .attr( 'y2', this.yScale ); this.hGridLines.exit().remove(); - this.log( 'hGridLines:', this.hGridLines ); + //this.log( 'hGridLines:', this.hGridLines ); }; // ........................................................ data points @@ -332,7 +332,7 @@ .style( "fill-opacity", 0 ) .remove(); - this.log( this.datapoints, 'glyphs rendered' ); + //this.log( this.datapoints, 'glyphs rendered' ); }; this.render = function( xCol, yCol ){ @@ -343,11 +343,11 @@ //TODO: ^^ isn't necessarily true with current ColumnDataProvider xCol = this.preprocessData( xCol ); yCol = this.preprocessData( yCol ); - this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); + //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); //TODO: compute min, max on server. this.setUpDomains( xCol, yCol ); - this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); this.setUpScales(); this.adjustChartDimensions(); @@ -367,9 +367,11 @@ * */ var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ - //logger : console, + logger : console, tagName : 'form', - className : 'scatterplot-settings-form', + className : 'scatterplot-settings-form', + + loadingIndicatorImagePath : ( galaxy_paths.get( 'image_path' ) + '/loading_large_white_bg.gif' ), events : { 'click #render-button' : 'renderScatterplot' @@ -397,6 +399,7 @@ var view = this, html = '', columnHtml = ''; + // build column select controls for each x, y (based on name if available) // ugh...hafta preprocess this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' ); @@ -408,10 +411,16 @@ if( view.dataset.metadata_column_names ){ name = view.dataset.metadata_column_names[ index ]; } - columnHtml += '<option value="' + index + '">' + name + '</column>'; + columnHtml += '<option value="' + index + '">' + name + '</option>'; } }); + // loading indicator - initially hidden + html += '<div id="loading-indicator" style="display: none;">'; + html += '<img class="loading-img" src=' + this.loadingIndicatorImagePath + ' />'; + html += '<span class="loading-message"></span>'; + html += '</div>'; + // column selector containers html += '<div id="x-column-input">'; html += '<label for="">Data column for X: </label><select name="x-column">' + columnHtml + '</select>'; @@ -430,6 +439,18 @@ this.$el.find( '#render-button' ); return this; }, + + showLoadingIndicator : function( message ){ + message = message || ''; + this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); + this.$el.find( 'div#loading-indicator' ).show( 'fast' ); + console.debug( 'showing:', this.$el.find( 'div#loading-indicator' ), message ); + }, + + hideLoadingIndicator : function(){ + this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); + console.debug( 'hiding:', this.$el.find( 'div#loading-indicator' ) ); + }, renderScatterplot : function(){ // parse the column values for both @@ -462,19 +483,23 @@ }); this.log( 'url:', url ); + this.showLoadingIndicator( 'Fetching data...' ); jQuery.ajax({ url : url, dataType : 'json', success : function( response ){ //TODO: server sends back an endpoint, cache for next pagination request + view.showLoadingIndicator( 'Rendering...' ); view.endpoint = response.endpoint; view.plot.render( // pull apart first two regardless of number of columns _.map( response.data, function( columns ){ return columns[0]; } ), _.map( response.data, function( columns ){ return columns[1]; } ) ); + view.hideLoadingIndicator(); }, error : function( xhr, status, error ){ + view.hideLoadingIndicator(); alert( 'ERROR:' + status + '\n' + error ); } }); diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -37,12 +37,14 @@ max-width: 256px; } -#chart-settings-form [value=Draw] { - float: right; +#chart-holder { + overflow: auto; } -#chart-holder { - overflow: auto; +#chart-settings-form #loading-indicator .loading-message { + margin-left: 16px; + font-style: italic; + color: grey; } svg .grid-line { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for viewing a tool shed repository README in a changeset revision older than the tip.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/00681c35d987/ changeset: 00681c35d987 user: greg date: 2012-10-02 17:36:20 summary: Fix for viewing a tool shed repository README in a changeset revision older than the tip. affected #: 3 files diff -r fb35591b0273945610917c178255674bba0f9a21 -r 00681c35d987cde2200ff94c7f5510c594c904fd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1043,15 +1043,6 @@ if name == config_file: return os.path.abspath( os.path.join( root, name ) ) return None -def get_config_from_repository( app, config_file, repository, changeset_revision, dir, install_dir=None ): - """Return config_filename if it exists in some changeset of the repository using only the repository and changeset_revision.""" - if install_dir is None: - install_dir = repository.repo_path( app ) - repo_files_dir = os.path.join( install_dir, repository.name ) - repo = hg.repository( get_configured_ui(), repo_files_dir ) - ctx = get_changectx_for_changeset( repo, changeset_revision ) - config = get_config( config_file, repo, ctx, dir ) - return config def get_configured_ui(): # Configure any desired ui settings. _ui = ui.ui() @@ -1140,6 +1131,13 @@ if deleted: return 'DELETED' return None +def get_file_from_changeset_revision( app, repository, repo_files_dir, changeset_revision, file_name, dir ): + """Return file_name from the received changeset_revision of the repository manifest.""" + stripped_file_name = strip_path( file_name ) + repo = hg.repository( get_configured_ui(), repo_files_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + named_tmp_file = get_named_tmpfile_from_ctx( ctx, file_name, dir ) + return named_tmp_file def get_list_of_copied_sample_files( repo, ctx, dir ): """ Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy diff -r fb35591b0273945610917c178255674bba0f9a21 -r 00681c35d987cde2200ff94c7f5510c594c904fd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -624,10 +624,7 @@ status = 'error' else: tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) - try: - shutil.rmtree( work_dir ) - except: - pass + remove_dir( work_dir ) trans.app.config.tool_data_path = original_tool_data_path # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) @@ -685,6 +682,12 @@ return True # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed. return False +def remove_dir( dir ): + if os.path.exists( dir ): + try: + shutil.rmtree( dir ) + except: + pass def reset_all_metadata_on_repository( trans, id, **kwd ): def reset_all_tool_versions( trans, id, repo ): changeset_revisions = [] @@ -799,11 +802,7 @@ changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None - if os.path.exists( work_dir ): - try: - shutil.rmtree( work_dir ) - except: - pass + remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. clean_repository_metadata( trans, id, changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. diff -r fb35591b0273945610917c178255674bba0f9a21 -r 00681c35d987cde2200ff94c7f5510c594c904fd lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,8 +9,8 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents -from galaxy.util.shed_util import get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk +from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision +from galaxy.util.shed_util import get_repository_file_contents, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path from galaxy.util.shed_util import to_html_escaped, translate_string, update_repository, url_join @@ -2184,9 +2184,32 @@ repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) metadata = repository_metadata.metadata if metadata and 'readme' in metadata: - f = open( metadata[ 'readme' ], 'r' ) - raw_text = f.read() - f.close() + readme_file = str( metadata[ 'readme' ] ) + repo_files_dir = repository.repo_path + try: + f = open( readme_file, 'r' ) + raw_text = f.read() + f.close() + except IOError: + work_dir = tempfile.mkdtemp() + try: + manifest_readme_file = get_file_from_changeset_revision( trans.app, + repository, + repo_files_dir, + changeset_revision, + readme_file, + work_dir ) + f = open( manifest_readme_file, 'r' ) + raw_text = f.read() + f.close() + remove_dir( work_dir ) + except Exception, e: + raw_text = "Error locating and reading this repository's README file '%s': %s" % ( readme_file, str( e ) ) + log.debug( raw_text ) + remove_dir( work_dir ) + except Exception, e: + raw_text = "Error locating and reading this repository's README file '%s': %s" % ( readme_file, str( e ) ) + log.debug( raw_text ) readme_text = translate_string( raw_text, to_html=True ) else: readme_text = '' 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.

1 0

commit/galaxy-central: jgoecks: Circster: show more data when zoomed in.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fb35591b0273/ changeset: fb35591b0273 user: jgoecks date: 2012-10-02 17:17:22 summary: Circster: show more data when zoomed in. affected #: 2 files diff -r 0445cd851094b8bad61d2a96f399538f74e5db03 -r fb35591b0273945610917c178255674bba0f9a21 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -30,8 +30,7 @@ /** * A label track. */ -// FIXME: merge with tracks.js LabelTrack -var LabelTrack = Backbone.Model.extend({ +var CircsterLabelTrack = Backbone.Model.extend({ defaults: { prefs: { color: '#ccc' @@ -51,6 +50,7 @@ this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; this.label_arc_height = 20; + this.scale = 1; }, render: function() { @@ -63,7 +63,23 @@ init_radius_start = Math.min(width, height) / 2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) - (this.label_arc_height + this.track_gap), - tracks = this.model.get('tracks'); + tracks = this.model.get('tracks'), + + // Create a renderer for each track in the visualiation. + track_renderers = tracks.map(function(track, index) { + var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), + track_renderer_class = (track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackRenderer : + CircsterSummaryTreeTrackRenderer ); + + return new track_renderer_class({ + track: track, + track_index: index, + radius_bounds: [radius_start, radius_start + dataset_arc_height], + genome: self.genome, + total_gap: self.total_gap + }); + }); // Set up SVG element. var svg = d3.select(self.$el[0]) @@ -74,78 +90,41 @@ // Set up zooming, dragging. .append('svg:g') .call(d3.behavior.zoom().on('zoom', function() { - // Do zoom. + // Do zoom, drag. + var scale = d3.event.scale; svg.attr("transform", "translate(" + d3.event.translate + ")" + - " scale(" + d3.event.scale + ")"); + " scale(" + scale + ")"); - // Update visible elements with more data. - var utils = new SVGUtils(), - tracks_and_chroms_to_update = {}; - - tracks.each(function(t) { - tracks_and_chroms_to_update[t.id] = []; - }); - - d3.selectAll('path.chrom-data').filter(function(d, i) { - return utils.is_visible(this, svg); - }).each(function(d, i) { - var elt_data = $.data(this, 'chrom_data'); - tracks_and_chroms_to_update[elt_data.track.id].push(elt_data.chrom); - }); - - /* - _.each(_.pairs(tracks_and_chroms_to_update), function(track_and_chroms) { - var track = tracks.get(track_and_chroms[0]) - chroms = track_and_chroms[1]; - - _.each(chroms, function(chr_name) { - var chr_region = self.genome.get_chrom_region(chr_name), - data_deferred = track.get('data_manager').get_more_detailed_data(chr_region, 'Coverage', 0, d3.event.scale); - - $.when(data_deferred).then(function(data) { - console.log("got more detailed data", data); - }) - }) - - - }); - - // TODO: update tracks and chroms. - console.log(tracks_and_chroms_to_update); - */ + // Propagate scale changes to renderers. + if (self.scale !== scale) { + // Use timeout to wait for zooming/dragging to stop before rendering more detail. + if (self.zoom_drag_timeout) { + clearTimeout(self.zoom_drag_timeout); + } + self.zoom_drag_timeout = setTimeout(function() { + // Render more detail in tracks' visible elements. + _.each(track_renderers, function(renderer) { + renderer.update_scale(scale); + }); + }, 400); + } })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g'); // -- Render each dataset in the visualization. -- - tracks.each(function(track, index) { - var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), - track_renderer_class = (track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackRenderer : - CircsterSummaryTreeTrackRenderer ); - - var track_renderer = new track_renderer_class({ - track: track, - track_index: index, - radius_start: radius_start, - radius_end: radius_start + dataset_arc_height, - genome: self.genome, - total_gap: self.total_gap - }); - - track_renderer.render(svg); - + _.each(track_renderers, function(renderer) { + renderer.render(svg); }); // -- Render chromosome labels. -- var radius_start = init_radius_start + tracks.length * (dataset_arc_height + self.track_gap) + self.track_gap; var chrom_labels_track = new CircsterLabelTrackRenderer({ - track: new LabelTrack(), + track: new CircsterLabelTrack(), track_index: tracks.length, - radius_start: radius_start, - radius_end: radius_start, + radius_bounds: [radius_start, radius_start], genome: self.genome, total_gap: self.total_gap }); @@ -154,27 +133,38 @@ } }); -var CircsterTrackRenderer = Base.extend( { +/** + * Renders a track in a Circster visualization. + */ +var CircsterTrackRenderer = Base.extend({ + + /* ----------------------- Public Methods ------------------------- */ initialize: function(options) { this.options = options; this.options.bg_stroke = 'ccc'; this.options.bg_fill = 'ccc'; + this.options.chroms_layout = this._chroms_layout(); + this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + this.options.scale = 1; + this.options.parent_elt = null; }, - render: function(svg) { + /** + * Render track's data by adding SVG elements to parent. + */ + render: function(parent) { // Create track group element. - var track_group_elt = svg.append("g").attr("id", "parent-" + this.options.track_index); + this.options.parent_elt = parent.append("g").attr("id", "parent-" + this.options.track_index); + var track_parent_elt = this.options.parent_elt; // Render background arcs. - var genome_arcs = this._chroms_layout(), - radius_start = this.options.radius_start, - radius_end = this.options.radius_end, + var genome_arcs = this.options.chroms_layout, arc_gen = d3.svg.arc() - .innerRadius(radius_start) - .outerRadius(radius_end), + .innerRadius(this.options.radius_bounds[0]) + .outerRadius(this.options.radius_bounds[1]), - chroms_elts = track_group_elt.selectAll('g') + chroms_elts = track_parent_elt.selectAll('g') .data(genome_arcs).enter().append('svg:g'); // Draw arcs. @@ -185,16 +175,112 @@ .append("title").text(function(d) { return d.data.chrom; }); // Render track data. - this.render_data(track_group_elt); + this._render_data(track_parent_elt); // Apply prefs. var prefs = this.options.track.get('prefs'), block_color = prefs.block_color; if (!block_color) { block_color = prefs.color; } - track_group_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); }, /** + * Update renderer scale. This fetches more data if scale is increased. + */ + update_scale: function(new_scale) { + // -- Update scale and return if new scale is less than old scale. -- + + var old_scale = this.options.scale; + this.options.scale = new_scale; + if (new_scale <= old_scale) { + return; + } + + // -- Scale increased, so render visible data with more detail. -- + + var self = this, + utils = new SVGUtils(); + + // Select all chrom data and filter to operate on those that are visible. + this.options.parent_elt.selectAll('path.chrom-data').filter(function(d, i) { + return utils.is_visible(this); + }).each(function(d, i) { + // Now operating on a single path element representing chromosome data. + var path_elt = d3.select(this), + chrom = path_elt.attr('chrom'), + chrom_region = self.options.genome.get_chrom_region(chrom), + + // Get more detailde data for chrom. + data_deferred = self.options.track.get('data_manager').get_more_detailed_data(chrom_region, 'Coverage', 0, new_scale); + + // When more data is available, use new data to redraw path. + $.when(data_deferred).then(function(data) { + // Remove current data path. + path_elt.remove(); + + // Update data bounds with new data. + self._update_data_bounds(); + + // Find chromosome arc to draw data on. + var chrom_arc = _.find(self.options.chroms_layout, function(layout) { + return layout.data.chrom === chrom; + }); + + // Add new data path and apply preferences. + var prefs = self.options.track.get('prefs'), + block_color = prefs.block_color; + if (!block_color) { block_color = prefs.color; } + self._render_chrom_data(self.options.parent_elt, chrom_arc, data).style('stroke', block_color).style('fill', block_color); + }); + }); + + return self; + }, + + /* ----------------------- Internal Methods ------------------------- */ + + /** + * Update data bounds. + */ + _update_data_bounds: function() { + this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + + // TODO: transition all paths to use the new data bounds. + }, + + /** + * Render data as elements attached to svg. + */ + _render_data: function(svg) { + var self = this, + chrom_arcs = this.options.chroms_layout, + track = this.options.track, + genome_wide_data = track.get_genome_wide_data(this.options.genome), + + // Merge chroms layout with data. + layout_and_data = _.zip(chrom_arcs, genome_wide_data), + + // Render each chromosome's data. + chroms_data_layout = _.map(layout_and_data, function(chrom_info) { + var chrom_arc = chrom_info[0], + data = chrom_info[1]; + return self._render_chrom_data(svg, chrom_arc, data); + }); + + return svg; + }, + + /** + * Render a chromosome data and attach elements to svg. + */ + _render_chrom_data: function(svg, chrom_arc, data) {}, + + /** + * Returns data for creating a path for the given data using chrom_arc and data bounds. + */ + _compute_path_data: function(chrom_arc, data) {}, + + /** * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle * separated by gaps. */ @@ -211,42 +297,6 @@ return arc; }); return chrom_arcs; - }, - - /** - * Render chromosome data and attach elements to svg. - */ - render_chrom_data: function(svg, chrom_arc, data, inner_radius, outer_radius, max) { - }, - - /** - * Render data as elements attached to svg. - */ - render_data: function(svg) { - var self = this, - chrom_arcs = this._chroms_layout(), - track = this.options.track, - r_start = this.options.radius_start, - r_end = this.options.radius_end, - - genome_wide_data = track.get_genome_wide_data(this.options.genome), - - // Merge chroms layout with data. - layout_and_data = _.zip(chrom_arcs, genome_wide_data), - - // Get min, max in data. - bounds = this.get_bounds(genome_wide_data), - - // Do dataset layout for each chromosome's data using pie layout. - chroms_data_layout = _.map(layout_and_data, function(chrom_info) { - var chrom_arc = chrom_info[0], - data = chrom_info[1]; - return self.render_chrom_data(svg, chrom_arc, data, - r_start, r_end, - bounds.min, bounds.max); - }); - - return chroms_data_layout; } }); @@ -259,18 +309,19 @@ this.options = options; this.options.bg_stroke = 'fff'; this.options.bg_fill = 'fff'; + this.options.chroms_layout = this._chroms_layout(); }, /** * Render labels. */ - render_data: function(svg) { + _render_data: function(svg) { // Add chromosome label where it will fit; an alternative labeling mechanism // would be nice for small chromosomes. var chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') - .attr('id', function(d) { return 'label-' + d.data.chrom; }) + .attr('id', function(d) { return 'label-' + d.data.chrom; }); chrom_arcs.append("svg:text") .filter(function(d) { @@ -295,46 +346,56 @@ * Renders quantitative data with the form [x, value] and assumes data is equally spaced across * chromosome. Attachs a dict with track and chrom name information to DOM element. */ - render_quantitative_data: function(svg, chrom_arc, data, inner_radius, outer_radius, min, max) { + _render_chrom_data: function(svg, chrom_arc, chrom_data) { + // If no chrom data, return null. + if (!chrom_data || typeof chrom_data === "string" || chrom_data.data.length === 0) { + return null; + } + + var path_data = this._compute_path_data(chrom_arc, chrom_data.data); + + // Render data. + var parent = svg.datum(chrom_data.data), + path = parent.append('path') + .attr('class', 'chrom-data') + .attr('chrom', chrom_arc.data.chrom) + .attr('d', path_data); + + return path; + }, + + /** + * Returns data for creating a path for the given data using chrom_arc, radius bounds, and data bounds. + */ + _compute_path_data: function(chrom_arc, data) { // Radius scaler. var radius = d3.scale.linear() - .domain([min, max]) - .range([inner_radius, outer_radius]); + .domain(this.options.data_bounds) + .range(this.options.radius_bounds); // Scaler for placing data points across arc. var angle = d3.scale.linear() .domain([0, data.length]) .range([chrom_arc.startAngle, chrom_arc.endAngle]); + // Use line generator to create area. var line = d3.svg.line.radial() .interpolate("linear") .radius(function(d) { return radius(d[1]); }) .angle(function(d, i) { return angle(i); }); - var area = d3.svg.area.radial() + return d3.svg.area.radial() .interpolate(line.interpolate()) .innerRadius(radius(0)) .outerRadius(line.radius()) .angle(line.angle()); - - // Render data. - var parent = svg.datum(data), - path = parent.append("path") - .attr("class", "chrom-data") - .attr("d", area); - - // Attach dict with track and chrom info for path. - $.data(path[0][0], "chrom_data", { - track: this.options.track, - chrom: chrom_arc.data.chrom - }); }, /** - * Returns an object with min, max attributes denoting the minimum and maximum + * Returns an array with two values denoting the minimum and maximum * values for the track. */ - get_bounds: function() {} + get_data_bounds: function(data) {} }); @@ -342,29 +403,14 @@ * Layout for summary tree data in a circster visualization. */ var CircsterSummaryTreeTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ - - /** - * Renders a chromosome's data. - */ - render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { - // If no chrom data, return null. - if (!chrom_data || typeof chrom_data === "string") { - return null; - } - return this.render_quantitative_data(svg, chrom_arc, chrom_data.data, inner_radius, outer_radius, min, max); - }, - - get_bounds: function(data) { + get_data_bounds: function(data) { // Get max across data. var max_data = _.map(data, function(d) { if (!d || typeof d === 'string') { return 0; } return d.max; }); - return { - min: 0, - max: (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) - }; + return [ 0, (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) ]; } }); @@ -372,18 +418,8 @@ * Layout for BigWig data in a circster visualization. */ var CircsterBigWigTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ - - /** - * Renders a chromosome's data. - */ - render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { - var data = chrom_data.data; - if (data.length === 0) { return; } - return this.render_quantitative_data(svg, chrom_arc, data, inner_radius, outer_radius, min, max); - }, - - get_bounds: function(data) { + get_data_bounds: function(data) { // Set max across dataset by extracting all values, flattening them into a // single array, and getting the min and max. var values = _.flatten( _.map(data, function(d) { @@ -398,13 +434,11 @@ } }) ); - return { - min: _.min(values), - max: _.max(values) - }; + return [ _.min(values), _.max(values) ]; } }); +// Module exports. return { CircsterView: CircsterView }; diff -r 0445cd851094b8bad61d2a96f399538f74e5db03 -r fb35591b0273945610917c178255674bba0f9a21 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -356,7 +356,7 @@ extra_params.num_samples = cur_data.data.length * detail_multiplier; } else if (cur_data.dataset_type === 'summary_tree') { - extra_params.level = cur_data.level + 1; + extra_params.level = Math.min(cur_data.level - 1, 2); } return this.load_data(region, mode, resolution, extra_params); 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: inithello: Import missing utility methods from the admin controller.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0445cd851094/ changeset: 0445cd851094 user: inithello date: 2012-10-02 16:30:38 summary: Import missing utility methods from the admin controller. affected #: 1 file diff -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c -r 0445cd851094b8bad61d2a96f399538f74e5db03 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -11,6 +11,7 @@ from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH from galaxy.util.shed_util import load_tool_from_config, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * +from galaxy.web.base.controllers.admin import * from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.model.item_attrs import UsesItemRatings 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: greg: Fixes for tool shed features broken due to the elimination of the ability to use the webapp param.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c3a9547df6f1/ changeset: c3a9547df6f1 user: greg date: 2012-10-02 15:47:06 summary: Fixes for tool shed features broken due to the elimination of the ability to use the webapp param. affected #: 33 files diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -138,8 +138,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() @@ -260,7 +259,7 @@ tool_shed_repository, self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) # Get the tool_versions from the tool shed for each tool in the installed change set. - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) response = urllib2.urlopen( url ) text = response.read() diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -30,7 +30,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager' % \ + url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) try: response = urllib2.urlopen( url ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -34,7 +34,7 @@ log.info( 'Transfer job restarter shutting down...' ) def check_for_update( self, repository ): tool_shed_url = get_url_from_repository_tool_shed( self.app, repository ) - url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager' % \ + url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) try: response = urllib2.urlopen( url ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -297,7 +297,7 @@ # tag for any tool in the repository. break return can_generate_dependency_metadata -def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files, webapp='galaxy' ): +def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make sure the files exist. @@ -602,7 +602,7 @@ tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, webapp='galaxy' ): + resetting_all_metadata_on_repository=False, updating_installed_repository=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's @@ -695,7 +695,7 @@ if not valid: invalid_file_tups.append( ( name, error_message ) ) else: - invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: @@ -1115,7 +1115,7 @@ return manifest_ctx, ctx_file return None, None def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): - url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( name, owner, changeset_revision ) ) + url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() response.close() diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -69,7 +69,7 @@ columns = [ UserLoginColumn( "Email", key="email", - link=( lambda item: dict( operation="information", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="information", id=item.id ) ), attach_popup=True, filterable="advanced" ), UserNameColumn( "User Name", @@ -93,18 +93,18 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Create new user", - dict( controller='admin', action='users', operation='create', webapp="community" ) ) + dict( controller='admin', action='users', operation='create' ) ) ] operations = [ grids.GridOperation( "Manage Roles and Groups", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="manage_roles_and_groups_for_user" ) ), + url_args=dict( action="manage_roles_and_groups_for_user" ) ), grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False, - url_args=dict( webapp="community", action="reset_user_password" ) ) + url_args=dict( action="reset_user_password" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), @@ -119,8 +119,7 @@ return trans.user class RoleListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): return role.name @@ -156,7 +155,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), attach_popup=True, filterable="advanced" ), DescriptionColumn( "Description", @@ -183,24 +182,24 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new role", - dict( controller='admin', action='roles', operation='create', webapp="community" ) ) + dict( controller='admin', action='roles', operation='create' ) ) ] operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="rename_role" ) ), + url_args=dict( action="rename_role" ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="mark_role_deleted" ) ), + url_args=dict( action="mark_role_deleted" ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="undelete_role" ) ), + url_args=dict( action="undelete_role" ) ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="purge_role" ) ) ] + url_args=dict( action="purge_role" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -213,8 +212,7 @@ return query.filter( model.Role.type != model.Role.types.PRIVATE ) class GroupListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, group ): return group.name @@ -242,7 +240,7 @@ columns = [ NameColumn( "Name", #key="name", - link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), attach_popup=True #filterable="advanced" ), @@ -262,24 +260,24 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new group", - dict( controller='admin', action='groups', operation='create', webapp="community" ) ) + dict( controller='admin', action='groups', operation='create' ) ) ] operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="rename_group" ) ), + url_args=dict( action="rename_group" ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="mark_group_deleted" ) ), + url_args=dict( action="mark_group_deleted" ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="undelete_group" ) ), + url_args=dict( action="undelete_group" ) ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="purge_group" ) ) ] + url_args=dict( action="purge_group" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -294,12 +292,12 @@ # Override the NameColumn to include an Edit link columns[ 0 ] = CategoryListGrid.NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id ) ), model_class=model.Category, attach_popup=False ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create' ) ) ] class AdminRepositoryListGrid( RepositoryListGrid ): @@ -377,9 +375,7 @@ NameColumn( "Name", key="name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository_revision", - id=item.id, - webapp="community" ) ), + link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), attach_popup=True ), RevisionColumn( "Revision", attach_popup=False ), @@ -716,7 +712,6 @@ "repository" ) ) trans.response.send_redirect( web.url_for( controller='admin', action='browse_repository_metadata', - webapp='community', message=util.sanitize_text( message ), status=status ) ) else: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -612,8 +612,7 @@ repo_files_dir, tool_config_filename, tool, - sample_files, - webapp='community' ) + sample_files ) if invalid_files_and_errors_tups: message2 = generate_message_for_invalid_tools( invalid_files_and_errors_tups, repository, @@ -753,8 +752,7 @@ relative_install_dir=repo_dir, repository_files_dir=work_dir, resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - webapp='community' ) + updating_installed_repository=False ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -829,8 +827,7 @@ relative_install_dir=repo_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='community' ) + updating_installed_repository=False ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -49,7 +49,7 @@ columns = [ NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="repositories_by_category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_category", id=item.id ) ), attach_popup=False ), DescriptionColumn( "Description", key="Category.description", @@ -87,7 +87,7 @@ columns = [ CategoryListGrid.NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id, webapp="galaxy" ) ), + link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ), attach_popup=False ), CategoryListGrid.DescriptionColumn( "Description", key="Category.description", @@ -136,7 +136,7 @@ rval = '<ul>' if repository.categories: for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s&webapp=community">%s</a></li>' \ + rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' \ % ( trans.security.encode_id( rca.category.id ), rca.category.name ) else: rval += '<li>not set</li>' @@ -173,8 +173,7 @@ NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", key="description", @@ -187,7 +186,7 @@ attach_popup=False ), UserColumn( "Owner", model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), grids.CommunityRatingColumn( "Average Rating", key="rating" ), @@ -231,15 +230,14 @@ RepositoryListGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + id=item.id ) ), attach_popup=False ), RepositoryListGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), RepositoryListGrid.UserColumn( "Owner", model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ), @@ -254,7 +252,7 @@ condition=( lambda item: not item.deleted ), async_compatible=False ) ] global_actions = [ - grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) ) + grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) ] class WritableRepositoryListGrid( RepositoryListGrid ): @@ -285,7 +283,7 @@ rval = '<ul>' if repository.categories: for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s&webapp=galaxy">%s</a></li>' \ + rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>' \ % ( trans.security.encode_id( rca.category.id ), rca.category.name ) else: rval += '<li>not set</li>' @@ -372,9 +370,7 @@ default_sort_key = "Repository.name" columns = [ NameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", attach_popup=False ), @@ -414,9 +410,7 @@ columns = [ col for col in MatchedRepositoryListGrid.columns ] # Override the NameColumn columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="galaxy" ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ) class RepositoryController( BaseUIController, ItemRatings ): @@ -481,7 +475,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) cntrller = params.get( 'cntrller', 'repository' ) is_admin = trans.user_is_admin() invalid_tools_dict = odict() @@ -514,15 +507,12 @@ return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, - webapp=webapp, message=message, status=status ) @web.expose def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. - if 'webapp' not in kwd: - kwd[ 'webapp' ] = get_webapp( trans, **kwd ) if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": @@ -606,7 +596,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) @@ -619,7 +608,6 @@ metadata=metadata, commit_message=commit_message, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -631,7 +619,7 @@ if 'f-free-text-search' in kwd: if kwd[ 'f-free-text-search' ] == 'All': # The user performed a search, then clicked the "x" to eliminate the search criteria. - new_kwd = dict( webapp='galaxy' ) + new_kwd = {} return self.valid_category_list_grid( trans, **new_kwd ) # Since we are searching valid repositories and not categories, redirect to browse_valid_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: @@ -656,7 +644,6 @@ return self.valid_category_list_grid( trans, **kwd ) @web.expose def browse_valid_repositories( self, trans, **kwd ): - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if 'f-free-text-search' in kwd: if 'f-Category.name' in kwd: @@ -676,7 +663,6 @@ latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', - webapp=webapp, repository_id=repository_id, changeset_revision=latest_installable_changeset_revision ) ) elif operation == "valid_repositories_by_category": @@ -700,12 +686,10 @@ if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', - webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', - webapp=webapp, repository_id=repository_id ) self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", url_args=url_args, @@ -745,10 +729,7 @@ shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) @web.expose def check_for_updates( self, trans, **kwd ): - """ - Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' UpdateManager, the value of 'webapp' - will be 'update_manager'. - """ + """Handle a request from a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -757,14 +738,13 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = get_webapp( trans, **kwd ) repository = get_repository_by_name_and_owner( trans, name, owner ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) # Default to the current changeset revision. update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) latest_changeset_revision = changeset_revision - from_update_manager = webapp == 'update_manager' + from_update_manager = kwd.get( 'from_update_manager', False ) if from_update_manager: update = 'true' no_update = 'false' @@ -923,7 +903,6 @@ message = "Repository '%s' has been created." % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', - webapp='community', message=message, id=trans.security.encode_id( repository.id ) ) ) return trans.fill_template( '/webapps/community/repository/create_repository.mako', @@ -939,7 +918,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository, tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) @@ -952,12 +930,11 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) except Exception, e: message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %s." % str( e ) - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -996,7 +973,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -1012,7 +988,7 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): + if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' @@ -1048,16 +1024,16 @@ if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': # Our initial request originated from a Galaxy instance. global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_categories', webapp=webapp ) ), + dict( controller='repository', action='browse_valid_categories' ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), + dict( controller='repository', action='find_tools' ) ), grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + dict( controller='repository', action='find_workflows' ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) + install_url_args = dict( controller='repository', action='find_tools' ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) @@ -1071,7 +1047,6 @@ status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_tools.mako', - webapp=webapp, tool_id=self.__stringify( tool_ids ), tool_name=self.__stringify( tool_names ), tool_version=self.__stringify( tool_versions ), @@ -1083,7 +1058,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -1099,7 +1073,7 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): + if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' @@ -1136,17 +1110,16 @@ ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples - # Render the list view - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': # Our initial request originated from a Galaxy instance. global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + dict( controller='repository', action='browse_valid_repositories' ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), + dict( controller='repository', action='find_tools' ) ), grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + dict( controller='repository', action='find_workflows' ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp ) + install_url_args = dict( controller='repository', action='find_workflows' ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) @@ -1163,7 +1136,6 @@ workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_workflows.mako', - webapp=webapp, workflow_name=self.__stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, @@ -1234,8 +1206,7 @@ return '' @web.expose def get_tool_dependencies( self, trans, **kwd ): - # Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' InstallManager, the value of 'webapp' - # will be 'install_manager'. + """Handle a request from a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1244,14 +1215,14 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = get_webapp( trans, **kwd ) repository = get_repository_by_name_and_owner( trans, name, owner ) for downloadable_revision in repository.downloadable_revisions: if downloadable_revision.changeset_revision == changeset_revision: break metadata = downloadable_revision.metadata tool_dependencies = metadata.get( 'tool_dependencies', '' ) - if webapp == 'install_manager': + from_install_manager = kwd.get( 'from_install_manager', False ) + if from_install_manager: if tool_dependencies: return tool_shed_encode( tool_dependencies ) return '' @@ -1450,7 +1421,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) - webapp = get_webapp( trans, **kwd ) repository_clone_url = generate_clone_url( trans, repository_id ) repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) @@ -1461,8 +1431,7 @@ repository.repo_path, tool_config, tool, - [], - webapp=webapp ) + [] ) if invalid_file_tups: message = generate_message_for_invalid_tools( invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) elif error_message: @@ -1474,12 +1443,11 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - webapp=webapp, message=message, status='error' ) except Exception, e: message = "Exception thrown attempting to display tool: %s." % str( e ) - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -1535,7 +1503,6 @@ if user.email in repository.email_alerts: email_alert_repositories.append( repository ) return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", - webapp='community', new_repo_alert_check_box=new_repo_alert_check_box, email_alert_repositories=email_alert_repositories, message=message, @@ -1573,7 +1540,6 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, - webapp='community', message=message, status='error' ) ) if description != repository.description: @@ -1713,8 +1679,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - if 'webapp' not in kwd: - kwd[ 'webapp' ] = 'community' if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "receive email alerts": @@ -1753,7 +1717,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1776,7 +1739,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, metadata=metadata, - webapp=webapp, message=message, status=status ) @web.expose @@ -2218,7 +2180,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) - webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) metadata = repository_metadata.metadata @@ -2236,7 +2197,6 @@ changeset_revision=changeset_revision, readme_text=readme_text, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -2245,7 +2205,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) - webapp = get_webapp( trans, **kwd ) repo = hg.repository( get_configured_ui(), repository.repo_path ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) @@ -2307,7 +2266,6 @@ changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -2315,7 +2273,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) @@ -2376,7 +2333,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -19,7 +19,7 @@ class UploadController( BaseUIController ): @web.expose - @web.require_login( 'upload', use_panels=True, webapp='community' ) + @web.require_login( 'upload', use_panels=True ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -161,7 +161,6 @@ action='browse_repository', id=repository_id, commit_message='Deleted selected files', - webapp='community', message=message, status=status ) ) else: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -141,7 +141,6 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) - webapp = kwd.get( 'webapp', 'community' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -152,11 +151,10 @@ repository_metadata_id=repository_metadata_id, workflow_name=workflow_name, metadata=repository_metadata, - webapp=webapp, message=message, status=status ) @web.expose - def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): + def generate_workflow_image( self, trans, repository_metadata_id, workflow_name ): repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision @@ -388,7 +386,6 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) - webapp = kwd.get( 'webapp', 'community' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -404,8 +401,8 @@ to_file.write( to_json_string( workflow_data ) ) return open( tmp_fname ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ - ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s' % \ + ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ) ) return trans.response.send_redirect( url ) return trans.response.send_redirect( web.url_for( controller='workflow', action='view_workflow', diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -65,7 +65,7 @@ key="name", link=( lambda item: iff( item.status in [ model.ToolShedRepository.installation_status.CLONING ], None, - dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), + dict( operation="manage_repository", id=item.id ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -410,7 +410,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s&webapp=galaxy' % ( galaxy_url ) ) + url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -419,7 +419,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako', - webapp='galaxy', message=message, status='error' ) @web.expose @@ -429,7 +428,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @@ -507,14 +506,14 @@ def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s&webapp=galaxy' % galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s&webapp=galaxy' % galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) def generate_tool_path( self, repository_clone_url, changeset_revision ): """ @@ -676,7 +675,7 @@ trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) url = url_join( tool_shed_url, - '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -731,8 +730,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -806,7 +804,7 @@ # Send a request to the tool shed to install the repository. tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s&webapp=galaxy' % \ + 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision, @@ -1030,7 +1028,7 @@ changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. url = url_join( tool_shed_url, - 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % \ + 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \ ( repository_ids, changeset_revisions ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1175,7 +1173,7 @@ repo_info_tuple = repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple url = url_join( tool_shed_url, - 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \ ( name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1350,7 +1348,7 @@ # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. url = url_join( tool_shed_url, - 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -1413,7 +1411,7 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True ) if metadata and 'readme' in metadata: url = url_join( tool_shed_url, - 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1448,8 +1446,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) repository.metadata = metadata_dict trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1506,7 +1503,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -1625,8 +1622,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - webapp='galaxy' ) + updating_installed_repository=True ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision @@ -1676,7 +1672,6 @@ changeset_revision=repository.changeset_revision, readme_text=readme_text, is_malicious=is_malicious, - webapp='galaxy', message=message, status=status ) @web.expose @@ -1685,7 +1680,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) repository_metadata = repository.metadata tool_metadata = {} diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1026,7 +1026,6 @@ """ url = kwd.get( 'url', '' ) workflow_text = kwd.get( 'workflow_text', '' ) - webapp = get_webapp( trans, **kwd ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) import_button = kwd.get( 'import_button', False ) @@ -1056,8 +1055,8 @@ import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. - workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&open_for_url=true' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ) ) response = urllib2.urlopen( workflow_url ) workflow_text = response.read() response.close() @@ -1137,7 +1136,7 @@ for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '/', qualified=True ), webapp ) + url = '%s/repository/find_tools?galaxy_url=%s' % ( shed_url, url_for( '/', qualified=True ) ) if missing_tool_tups: url += '&tool_id=' for missing_tool_tup in missing_tool_tups: @@ -1155,7 +1154,6 @@ action = 'index' return trans.response.send_redirect( web.url_for( controller='admin', action=action, - webapp='galaxy', message=message, status=status ) ) else: @@ -1164,8 +1162,8 @@ if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. message = "Workflow <b>%s</b> imported successfully." % workflow.name - url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) + url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&message=%s' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), message ) return trans.response.send_redirect( url ) elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository. diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -48,19 +48,19 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories', webapp='community' )}">Reset selected metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}">Reset selected metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin', webapp='community' )}">Browse invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin' )}">Browse invalid tools</a></div></div></div> @@ -70,7 +70,7 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories' )}">Manage categories</a></div></div></div> @@ -81,13 +81,13 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='users' )}">Manage users</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups' )}">Manage groups</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles' )}">Manage roles</a></div></div></div> @@ -95,7 +95,7 @@ Statistics </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}">View shed statistics</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics' )}">View shed statistics</a></div></div></div> @@ -104,7 +104,7 @@ <%def name="center_panel()"><% - center_url = h.url_for( action='center', webapp='community' ) + center_url = h.url_for( action='center' ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ b/templates/webapps/community/admin/statistics.mako @@ -7,7 +7,7 @@ <div class="toolForm"><div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> - <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}" method="post" > + <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics' )}" method="post" ><div class="form-row"><table class="grid"><tr> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -64,10 +64,10 @@ </%def> ## Repositories tab. - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index', webapp='community' ) )} + ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )} ## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index', webapp='community' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} + ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} ## Help tab. <% @@ -85,9 +85,9 @@ ## User tabs. <% # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login', webapp='community' ), "galaxy_main" ] ] + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='community' ), "galaxy_main" ] ) + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedout-only" visible = ( trans.user == None ) tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) @@ -101,12 +101,12 @@ if app.config.remote_user_logout_href: menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='community' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) + logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='community' ), "galaxy_main" ] ) + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/common/view_readme.mako --- a/templates/webapps/community/common/view_readme.mako +++ b/templates/webapps/community/common/view_readme.mako @@ -3,7 +3,7 @@ <%namespace file="/webapps/community/common/common.mako" import="render_readme" /><% - if webapp == 'community': + if trans.webapp.name == 'community': is_admin = trans.user_is_admin() is_new = repository.is_new can_contact_owner = trans.user and trans.user != repository.user @@ -22,43 +22,43 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'community': + %if trans.webapp.name == 'community': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %else: %if cntrller=='repository': - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Preview tools for install</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ) )}">Preview tools for install</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -50,10 +50,10 @@ </div><div class="toolSectionBody"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows', webapp='community' )}">Search for workflows</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></div> %endif @@ -62,7 +62,7 @@ All Repositories </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div> %if trans.user: <div class="toolSectionPad"></div> @@ -70,20 +70,20 @@ My Repositories and Tools </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own', webapp='community' )}">Repositories I own</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own' )}">Repositories I own</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories', webapp='community' )}">My writable repositories</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories' )}">My writable repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository', webapp='community' )}">My invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a></div><div class="toolSectionPad"></div><div class="toolSectionTitle"> Available Actions </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository', webapp='community' )}">Create new repository</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a></div> %else: <div class="toolSectionPad"></div> @@ -91,7 +91,7 @@ Available Actions </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to create a repository</a> + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a></div> %endif </div> @@ -102,9 +102,9 @@ <%def name="center_panel()"><% if trans.app.config.require_login and not trans.user: - center_url = h.url_for( controller='user', action='login', message=message, status=status, webapp='community' ) + center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status, webapp='community' ) + center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ b/templates/webapps/community/repository/browse_invalid_tools.mako @@ -20,7 +20,7 @@ <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %><tr><td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> ${invalid_tool_config} </a></td> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -65,23 +65,23 @@ <br/><br/><ul class="manage-table-actions"> %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False )"><% from galaxy.tool_shed.encoding_util import tool_shed_encode %> %if metadata or can_set_metadata: <p/> @@ -184,10 +184,10 @@ <tr><td><div style="float:left;" class="menubutton split popup" id="tool-${index}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_dict[ 'name' ]}</a> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_dict[ 'name' ]}</a></div><div popupmenu="tool-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], webapp=webapp )}">View tool metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> @@ -232,7 +232,7 @@ %for invalid_tool_config in invalid_tool_configs: <tr><td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> ${invalid_tool_config} </a></td> @@ -274,7 +274,7 @@ %><tr><td> - <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">${workflow_name}</a> + <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">${workflow_name}</a></td><td> %if steps: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/contact_owner.mako --- a/templates/webapps/community/repository/contact_owner.mako +++ b/templates/webapps/community/repository/contact_owner.mako @@ -31,26 +31,26 @@ <br/><br/><ul class="manage-table-actions"> %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/find_tools.mako --- a/templates/webapps/community/repository/find_tools.mako +++ b/templates/webapps/community/repository/find_tools.mako @@ -10,11 +10,11 @@ %><%inherit file="${inherit(context)}"/> -%if webapp == 'galaxy': +%if trans.webapp.name == 'galaxy': <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></li></ul> %endif @@ -32,7 +32,7 @@ strings if these types of search strings are entered in more than one field. </div><div style="clear: both"></div> - <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" > + <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" ><div class="form-row"><label>Tool id:</label><input name="tool_id" type="textfield" value="${tool_id}" size="40"/> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/find_workflows.mako --- a/templates/webapps/community/repository/find_workflows.mako +++ b/templates/webapps/community/repository/find_workflows.mako @@ -10,11 +10,11 @@ %><%inherit file="${inherit(context)}"/> -%if webapp == 'galaxy': +%if trans.webapp.name == 'galaxy': <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a></li> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a></li> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a></ul> %endif @@ -30,7 +30,7 @@ Comma-separated strings may be entered to expand search criteria. </div><div style="clear: both"></div> - <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}" method="post" > + <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows' )}" method="post" ><div style="clear: both"></div><div class="form-row"><label>Workflow name:</label> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -42,30 +42,30 @@ <br/><br/><ul class="manage-table-actions"> %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_reset_all_metadata: - <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ), webapp='community' )}">Reset all repository metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ) )}">Reset all repository metadata</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -276,7 +276,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp='community' )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -303,7 +303,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp='community' )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> %endif </div> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -36,15 +36,15 @@ <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></ul> @@ -79,4 +79,4 @@ </div></div><p/> -${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata )} diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -72,29 +72,29 @@ <br/><br/><ul class="manage-table-actions"> %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -121,46 +121,46 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'galaxy': + %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="tool_shed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -50,13 +50,13 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif </div></ul> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -45,24 +45,24 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_changeset.mako --- a/templates/webapps/community/repository/view_changeset.mako +++ b/templates/webapps/community/repository/view_changeset.mako @@ -46,27 +46,27 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -11,8 +11,8 @@ can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = webapp == 'community' and not is_new - can_view_change_log = webapp == 'community' and not is_new + can_browse_contents = trans.webapp.name == 'community' and not is_new + can_view_change_log = trans.webapp.name == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -37,44 +37,44 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'community': + %if trans.webapp.name == 'community': %if is_new and can_upload: - <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a></li> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif %else: - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %endif </ul> @@ -87,7 +87,7 @@ <div class="toolForm"><div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" > + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><% if changeset_revision == repository.tip: @@ -117,7 +117,7 @@ <div class="form-row"><label>Name:</label> %if can_browse_contents: - <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${repository.name}</a> + <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${repository.name}</a> %else: ${repository.name} %endif @@ -132,7 +132,7 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${revision_label}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: ${revision_label} %endif @@ -157,7 +157,7 @@ %endif </div></div> -${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata )} %if repository.categories: <p/><div class="toolForm"> @@ -172,12 +172,12 @@ </div></div> %endif -%if webapp == 'community' and trans.user and trans.app.config.smtp_server: +%if trans.webapp.name == 'community' and trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"><div class="toolFormTitle">Notification on update</div><div class="toolFormBody"> - <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" > + <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><label>Receive email alerts:</label> ${alerts_check_box.get_html()} @@ -214,7 +214,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp=webapp )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -241,7 +241,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp=webapp )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> %endif </div> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -12,10 +12,10 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = webapp == 'community' and not is_new + can_browse_contents = trans.webapp.name == 'community' and not is_new can_rate = repository.user != trans.user can_manage = is_admin or repository.user == trans.user - can_view_change_log = webapp == 'community' and not is_new + can_view_change_log = trans.webapp.name == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -34,43 +34,43 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'galaxy': + %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="tool_shed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -126,7 +126,7 @@ </div><div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_metadata_dict[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_metadata_dict[ 'name' ]}</a><div style="clear: both"></div></div> %if 'description' in tool_metadata_dict: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -7,7 +7,7 @@ from galaxy.web.framework.helpers import time_ago from galaxy.tool_shed.encoding_util import tool_shed_encode - in_tool_shed = webapp == 'community' + in_tool_shed = trans.webapp.name == 'community' is_admin = trans.user_is_admin() is_new = repository.is_new can_manage = is_admin or trans.user == repository.user @@ -34,8 +34,8 @@ %><%inherit file="${inherit(context)}"/> -<%def name="render_workflow( repository_metadata_id, workflow_name, webapp )"> - <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp ) %> +<%def name="render_workflow( repository_metadata_id, workflow_name )"> + <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> @@ -43,32 +43,32 @@ <ul class="manage-table-actions"> %if in_tool_shed: %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -80,14 +80,14 @@ %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">Import workflow to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li></div><li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="toolshed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %endif </ul> @@ -105,4 +105,4 @@ </div><br clear="left"/> -${render_workflow( repository_metadata_id, workflow_name, webapp )} +${render_workflow( repository_metadata_id, workflow_name )} diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/user/manage_email_alerts.mako --- a/templates/webapps/community/user/manage_email_alerts.mako +++ b/templates/webapps/community/user/manage_email_alerts.mako @@ -4,10 +4,10 @@ <br/><br/><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository', webapp=webapp )}">Manage repository alerts</a> + <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository' )}">Manage repository alerts</a></li><li> - <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository', webapp=webapp )}">User preferences</a> + <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository' )}">User preferences</a></li></ul> @@ -17,7 +17,7 @@ <div class="toolForm"><div class="toolFormTitle">Email alerts for new repositories</div> - <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts', webapp=webapp )}" method="post" > + <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts' )}" method="post" ><div class="form-row"><label>New repository alert:</label> ${new_repo_alert_check_box.get_html()} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix some UI framework issues.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4bdb9214efd6/ changeset: 4bdb9214efd6 user: jgoecks date: 2012-10-02 04:53:21 summary: Fix some UI framework issues. affected #: 3 files diff -r 55e7d7008efee2c5622f2505612265a9593ae992 -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 static/scripts/libs/underscore.js --- a/static/scripts/libs/underscore.js +++ b/static/scripts/libs/underscore.js @@ -1,7 +1,10 @@ -// Underscore.js 1.4.0 -// http://underscorejs.org +// Underscore.js 1.3.1 // (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. -// Underscore may be freely distributed under the MIT license. +// Underscore is freely distributable under the MIT license. +// Portions of Underscore are inspired or borrowed from Prototype, +// Oliver Steele's Functional, and John Resig's Micro-Templating. +// For all details and documentation: +// http://documentcloud.github.com/underscore (function() { @@ -21,9 +24,7 @@ var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; // Create quick reference variables for speed access to core prototypes. - var push = ArrayProto.push, - slice = ArrayProto.slice, - concat = ArrayProto.concat, + var slice = ArrayProto.slice, unshift = ArrayProto.unshift, toString = ObjProto.toString, hasOwnProperty = ObjProto.hasOwnProperty; @@ -45,11 +46,7 @@ nativeBind = FuncProto.bind; // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { - if (obj instanceof _) return obj; - if (!(this instanceof _)) return new _(obj); - this._wrapped = obj; - }; + var _ = function(obj) { return new wrapper(obj); }; // Export the Underscore object for **Node.js**, with // backwards-compatibility for the old `require()` API. If we're in @@ -65,7 +62,7 @@ } // Current version. - _.VERSION = '1.4.0'; + _.VERSION = '1.3.1'; // Collection Functions // -------------------- @@ -74,11 +71,12 @@ // Handles objects with the built-in `forEach`, arrays, and raw objects. // Delegates to **ECMAScript 5**'s native `forEach` if available. var each = _.each = _.forEach = function(obj, iterator, context) { + if (obj == null) return; if (nativeForEach && obj.forEach === nativeForEach) { obj.forEach(iterator, context); } else if (obj.length === +obj.length) { for (var i = 0, l = obj.length; i < l; i++) { - if (iterator.call(context, obj[i], i, obj) === breaker) return; + if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return; } } else { for (var key in obj) { @@ -93,10 +91,12 @@ // Delegates to **ECMAScript 5**'s native `map` if available. _.map = _.collect = function(obj, iterator, context) { var results = []; + if (obj == null) return results; if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context); each(obj, function(value, index, list) { results[results.length] = iterator.call(context, value, index, list); }); + if (obj.length === +obj.length) results.length = obj.length; return results; }; @@ -104,6 +104,7 @@ // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available. _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) { var initial = arguments.length > 2; + if (obj == null) obj = []; if (nativeReduce && obj.reduce === nativeReduce) { if (context) iterator = _.bind(iterator, context); return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator); @@ -124,26 +125,14 @@ // Delegates to **ECMAScript 5**'s native `reduceRight` if available. _.reduceRight = _.foldr = function(obj, iterator, memo, context) { var initial = arguments.length > 2; + if (obj == null) obj = []; if (nativeReduceRight && obj.reduceRight === nativeReduceRight) { if (context) iterator = _.bind(iterator, context); - return arguments.length > 2 ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); + return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); } - var length = obj.length; - if (length !== +length) { - var keys = _.keys(obj); - length = keys.length; - } - each(obj, function(value, index, list) { - index = keys ? keys[--length] : --length; - if (!initial) { - memo = obj[index]; - initial = true; - } else { - memo = iterator.call(context, memo, obj[index], index, list); - } - }); - if (!initial) throw new TypeError('Reduce of empty array with no initial value'); - return memo; + var reversed = _.toArray(obj).reverse(); + if (context && !initial) iterator = _.bind(iterator, context); + return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator); }; // Return the first value which passes a truth test. Aliased as `detect`. @@ -163,6 +152,7 @@ // Aliased as `select`. _.filter = _.select = function(obj, iterator, context) { var results = []; + if (obj == null) return results; if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context); each(obj, function(value, index, list) { if (iterator.call(context, value, index, list)) results[results.length] = value; @@ -173,6 +163,7 @@ // Return all the elements for which a truth test fails. _.reject = function(obj, iterator, context) { var results = []; + if (obj == null) return results; each(obj, function(value, index, list) { if (!iterator.call(context, value, index, list)) results[results.length] = value; }); @@ -183,13 +174,13 @@ // Delegates to **ECMAScript 5**'s native `every` if available. // Aliased as `all`. _.every = _.all = function(obj, iterator, context) { - iterator || (iterator = _.identity); var result = true; + if (obj == null) return result; if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context); each(obj, function(value, index, list) { if (!(result = result && iterator.call(context, value, index, list))) return breaker; }); - return !!result; + return result; }; // Determine if at least one element in the object matches a truth test. @@ -198,6 +189,7 @@ var any = _.some = _.any = function(obj, iterator, context) { iterator || (iterator = _.identity); var result = false; + if (obj == null) return result; if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context); each(obj, function(value, index, list) { if (result || (result = iterator.call(context, value, index, list))) return breaker; @@ -205,10 +197,11 @@ return !!result; }; - // Determine if the array or object contains a given value (using `===`). - // Aliased as `include`. - _.contains = _.include = function(obj, target) { + // Determine if a given value is included in the array or object using `===`. + // Aliased as `contains`. + _.include = _.contains = function(obj, target) { var found = false; + if (obj == null) return found; if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1; found = any(obj, function(value) { return value === target; @@ -220,7 +213,7 @@ _.invoke = function(obj, method) { var args = slice.call(arguments, 2); return _.map(obj, function(value) { - return (_.isFunction(method) ? method : value[method]).apply(value, args); + return (_.isFunction(method) ? method || value : value[method]).apply(value, args); }); }; @@ -229,25 +222,9 @@ return _.map(obj, function(value){ return value[key]; }); }; - // Convenience version of a common use case of `filter`: selecting only objects - // with specific `key:value` pairs. - _.where = function(obj, attrs) { - if (_.isEmpty(attrs)) return []; - return _.filter(obj, function(value) { - for (var key in attrs) { - if (attrs[key] !== value[key]) return false; - } - return true; - }); - }; - // Return the maximum element or (element-based computation). - // Can't optimize arrays of integers longer than 65,535 elements. - // See: https://bugs.webkit.org/show_bug.cgi?id=80797 _.max = function(obj, iterator, context) { - if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { - return Math.max.apply(Math, obj); - } + if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj); if (!iterator && _.isEmpty(obj)) return -Infinity; var result = {computed : -Infinity}; each(obj, function(value, index, list) { @@ -259,9 +236,7 @@ // Return the minimum element (or element-based computation). _.min = function(obj, iterator, context) { - if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { - return Math.min.apply(Math, obj); - } + if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj); if (!iterator && _.isEmpty(obj)) return Infinity; var result = {computed : Infinity}; each(obj, function(value, index, list) { @@ -273,107 +248,81 @@ // Shuffle an array. _.shuffle = function(obj) { - var rand; - var index = 0; - var shuffled = []; - each(obj, function(value) { - rand = _.random(index++); - shuffled[index - 1] = shuffled[rand]; - shuffled[rand] = value; + var shuffled = [], rand; + each(obj, function(value, index, list) { + if (index == 0) { + shuffled[0] = value; + } else { + rand = Math.floor(Math.random() * (index + 1)); + shuffled[index] = shuffled[rand]; + shuffled[rand] = value; + } }); return shuffled; }; - // An internal function to generate lookup iterators. - var lookupIterator = function(value) { - return _.isFunction(value) ? value : function(obj){ return obj[value]; }; - }; - // Sort the object's values by a criterion produced by an iterator. - _.sortBy = function(obj, value, context) { - var iterator = lookupIterator(value); + _.sortBy = function(obj, iterator, context) { return _.pluck(_.map(obj, function(value, index, list) { return { value : value, - index : index, criteria : iterator.call(context, value, index, list) }; }).sort(function(left, right) { - var a = left.criteria; - var b = right.criteria; - if (a !== b) { - if (a > b || a === void 0) return 1; - if (a < b || b === void 0) return -1; - } - return left.index < right.index ? -1 : 1; + var a = left.criteria, b = right.criteria; + return a < b ? -1 : a > b ? 1 : 0; }), 'value'); }; - // An internal function used for aggregate "group by" operations. - var group = function(obj, value, context, behavior) { + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = function(obj, val) { var result = {}; - var iterator = lookupIterator(value); + var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; }; each(obj, function(value, index) { - var key = iterator.call(context, value, index, obj); - behavior(result, key, value); + var key = iterator(value, index); + (result[key] || (result[key] = [])).push(value); }); return result; }; - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = function(obj, value, context) { - return group(obj, value, context, function(result, key, value) { - (_.has(result, key) ? result[key] : (result[key] = [])).push(value); - }); - }; - - // Counts instances of an object that group by a certain criterion. Pass - // either a string attribute to count by, or a function that returns the - // criterion. - _.countBy = function(obj, value, context) { - return group(obj, value, context, function(result, key, value) { - if (!_.has(result, key)) result[key] = 0; - result[key]++; - }); - }; - - // Use a comparator function to figure out the smallest index at which - // an object should be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iterator, context) { - iterator = iterator == null ? _.identity : lookupIterator(iterator); - var value = iterator.call(context, obj); + // Use a comparator function to figure out at what index an object should + // be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iterator) { + iterator || (iterator = _.identity); var low = 0, high = array.length; while (low < high) { - var mid = (low + high) >>> 1; - iterator.call(context, array[mid]) < value ? low = mid + 1 : high = mid; + var mid = (low + high) >> 1; + iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid; } return low; }; // Safely convert anything iterable into a real, live array. - _.toArray = function(obj) { - if (!obj) return []; - if (obj.length === +obj.length) return slice.call(obj); - return _.values(obj); + _.toArray = function(iterable) { + if (!iterable) return []; + if (iterable.toArray) return iterable.toArray(); + if (_.isArray(iterable)) return slice.call(iterable); + if (_.isArguments(iterable)) return slice.call(iterable); + return _.values(iterable); }; // Return the number of elements in an object. _.size = function(obj) { - return (obj.length === +obj.length) ? obj.length : _.keys(obj).length; + return _.toArray(obj).length; }; // Array Functions // --------------- // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head` and `take`. The **guard** check - // allows it to work with `_.map`. - _.first = _.head = _.take = function(array, n, guard) { + // values in the array. Aliased as `head`. The **guard** check allows it to work + // with `_.map`. + _.first = _.head = function(array, n, guard) { return (n != null) && !guard ? slice.call(array, 0, n) : array[0]; }; - // Returns everything but the last entry of the array. Especially useful on + // Returns everything but the last entry of the array. Especcialy useful on // the arguments object. Passing **n** will return all the values in // the array, excluding the last N. The **guard** check allows it to work with // `_.map`. @@ -391,12 +340,12 @@ } }; - // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. - // Especially useful on the arguments object. Passing an **n** will return - // the rest N values in the array. The **guard** + // Returns everything but the first entry of the array. Aliased as `tail`. + // Especially useful on the arguments object. Passing an **index** will return + // the rest of the values in the array from that index onward. The **guard** // check allows it to work with `_.map`. - _.rest = _.tail = _.drop = function(array, n, guard) { - return slice.call(array, (n == null) || guard ? 1 : n); + _.rest = _.tail = function(array, index, guard) { + return slice.call(array, (index == null) || guard ? 1 : index); }; // Trim out all falsy values from an array. @@ -404,21 +353,13 @@ return _.filter(array, function(value){ return !!value; }); }; - // Internal implementation of a recursive `flatten` function. - var flatten = function(input, shallow, output) { - each(input, function(value) { - if (_.isArray(value)) { - shallow ? push.apply(output, value) : flatten(value, shallow, output); - } else { - output.push(value); - } - }); - return output; - }; - // Return a completely flattened version of an array. _.flatten = function(array, shallow) { - return flatten(array, shallow, []); + return _.reduce(array, function(memo, value) { + if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value)); + memo[memo.length] = value; + return memo; + }, []); }; // Return a version of the array that does not contain the specified value(s). @@ -429,28 +370,28 @@ // Produce a duplicate-free version of the array. If the array has already // been sorted, you have the option of using a faster algorithm. // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iterator, context) { - var initial = iterator ? _.map(array, iterator, context) : array; - var results = []; - var seen = []; - each(initial, function(value, index) { - if (isSorted ? (!index || seen[seen.length - 1] !== value) : !_.contains(seen, value)) { - seen.push(value); - results.push(array[index]); + _.uniq = _.unique = function(array, isSorted, iterator) { + var initial = iterator ? _.map(array, iterator) : array; + var result = []; + _.reduce(initial, function(memo, el, i) { + if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) { + memo[memo.length] = el; + result[result.length] = array[i]; } - }); - return results; + return memo; + }, []); + return result; }; // Produce an array that contains the union: each distinct element from all of // the passed-in arrays. _.union = function() { - return _.uniq(concat.apply(ArrayProto, arguments)); + return _.uniq(_.flatten(arguments, true)); }; // Produce an array that contains every item shared between all the - // passed-in arrays. - _.intersection = function(array) { + // passed-in arrays. (Aliased as "intersect" for back-compat.) + _.intersection = _.intersect = function(array) { var rest = slice.call(arguments, 1); return _.filter(_.uniq(array), function(item) { return _.every(rest, function(other) { @@ -462,8 +403,8 @@ // Take the difference between one array and a number of other arrays. // Only the elements present in just the first array will remain. _.difference = function(array) { - var rest = concat.apply(ArrayProto, slice.call(arguments, 1)); - return _.filter(array, function(value){ return !_.contains(rest, value); }); + var rest = _.flatten(slice.call(arguments, 1)); + return _.filter(array, function(value){ return !_.include(rest, value); }); }; // Zip together multiple lists into a single array -- elements that share @@ -472,27 +413,10 @@ var args = slice.call(arguments); var length = _.max(_.pluck(args, 'length')); var results = new Array(length); - for (var i = 0; i < length; i++) { - results[i] = _.pluck(args, "" + i); - } + for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i); return results; }; - // Converts lists into objects. Pass either a single array of `[key, value]` - // pairs, or two parallel arrays of the same length -- one of keys, and one of - // the corresponding values. - _.object = function(list, values) { - var result = {}; - for (var i = 0, l = list.length; i < l; i++) { - if (values) { - result[list[i]] = values[i]; - } else { - result[list[i][0]] = list[i][1]; - } - } - return result; - }; - // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**), // we need this function. Return the position of the first occurrence of an // item in an array, or -1 if the item is not included in the array. @@ -500,25 +424,23 @@ // If the array is large and already in sort order, pass `true` // for **isSorted** to use binary search. _.indexOf = function(array, item, isSorted) { - var i = 0, l = array.length; + if (array == null) return -1; + var i, l; if (isSorted) { - if (typeof isSorted == 'number') { - i = (isSorted < 0 ? Math.max(0, l + isSorted) : isSorted); - } else { - i = _.sortedIndex(array, item); - return array[i] === item ? i : -1; - } + i = _.sortedIndex(array, item); + return array[i] === item ? i : -1; } - if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item, isSorted); - for (; i < l; i++) if (array[i] === item) return i; + if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item); + for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i; return -1; }; // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available. - _.lastIndexOf = function(array, item, fromIndex) { - if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item, fromIndex); - var i = (fromIndex != null ? fromIndex : array.length); - while (i--) if (array[i] === item) return i; + _.lastIndexOf = function(array, item) { + if (array == null) return -1; + if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item); + var i = array.length; + while (i--) if (i in array && array[i] === item) return i; return -1; }; @@ -592,7 +514,7 @@ // it with the arguments supplied. _.delay = function(func, wait) { var args = slice.call(arguments, 2); - return setTimeout(function(){ return func.apply(null, args); }, wait); + return setTimeout(function(){ return func.apply(func, args); }, wait); }; // Defers a function, scheduling it to run after the current call stack has @@ -604,46 +526,39 @@ // Returns a function, that, when invoked, will only be triggered at most once // during a given window of time. _.throttle = function(func, wait) { - var context, args, timeout, throttling, more, result; + var context, args, timeout, throttling, more; var whenDone = _.debounce(function(){ more = throttling = false; }, wait); return function() { context = this; args = arguments; var later = function() { timeout = null; - if (more) { - result = func.apply(context, args); - } + if (more) func.apply(context, args); whenDone(); }; if (!timeout) timeout = setTimeout(later, wait); if (throttling) { more = true; } else { - throttling = true; - result = func.apply(context, args); + func.apply(context, args); } whenDone(); - return result; + throttling = true; }; }; // Returns a function, that, as long as it continues to be invoked, will not // be triggered. The function will be called after it stops being called for - // N milliseconds. If `immediate` is passed, trigger the function on the - // leading edge, instead of the trailing. - _.debounce = function(func, wait, immediate) { - var timeout, result; + // N milliseconds. + _.debounce = function(func, wait) { + var timeout; return function() { var context = this, args = arguments; var later = function() { timeout = null; - if (!immediate) result = func.apply(context, args); + func.apply(context, args); }; - var callNow = immediate && !timeout; clearTimeout(timeout); timeout = setTimeout(later, wait); - if (callNow) result = func.apply(context, args); - return result; }; }; @@ -654,9 +569,7 @@ return function() { if (ran) return memo; ran = true; - memo = func.apply(this, arguments); - func = null; - return memo; + return memo = func.apply(this, arguments); }; }; @@ -665,8 +578,7 @@ // conditionally execute the original function. _.wrap = function(func, wrapper) { return function() { - var args = [func]; - push.apply(args, arguments); + var args = [func].concat(slice.call(arguments, 0)); return wrapper.apply(this, args); }; }; @@ -688,9 +600,7 @@ _.after = function(times, func) { if (times <= 0) return func(); return function() { - if (--times < 1) { - return func.apply(this, arguments); - } + if (--times < 1) { return func.apply(this, arguments); } }; }; @@ -708,23 +618,7 @@ // Retrieve the values of an object's properties. _.values = function(obj) { - var values = []; - for (var key in obj) if (_.has(obj, key)) values.push(obj[key]); - return values; - }; - - // Convert an object into a list of `[key, value]` pairs. - _.pairs = function(obj) { - var pairs = []; - for (var key in obj) if (_.has(obj, key)) pairs.push([key, obj[key]]); - return pairs; - }; - - // Invert the keys and values of an object. The values must be serializable. - _.invert = function(obj) { - var result = {}; - for (var key in obj) if (_.has(obj, key)) result[obj[key]] = key; - return result; + return _.map(obj, _.identity); }; // Return a sorted list of the function names available on the object. @@ -747,26 +641,6 @@ return obj; }; - // Return a copy of the object only containing the whitelisted properties. - _.pick = function(obj) { - var copy = {}; - var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); - each(keys, function(key) { - if (key in obj) copy[key] = obj[key]; - }); - return copy; - }; - - // Return a copy of the object without the blacklisted properties. - _.omit = function(obj) { - var copy = {}; - var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); - for (var key in obj) { - if (!_.contains(keys, key)) copy[key] = obj[key]; - } - return copy; - }; - // Fill in a given object with default properties. _.defaults = function(obj) { each(slice.call(arguments, 1), function(source) { @@ -791,16 +665,19 @@ return obj; }; - // Internal recursive comparison function for `isEqual`. - var eq = function(a, b, aStack, bStack) { + // Internal recursive comparison function. + function eq(a, b, stack) { // Identical objects are equal. `0 === -0`, but they aren't identical. // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal. if (a === b) return a !== 0 || 1 / a == 1 / b; // A strict comparison is necessary because `null == undefined`. if (a == null || b == null) return a === b; // Unwrap any wrapped objects. - if (a instanceof _) a = a._wrapped; - if (b instanceof _) b = b._wrapped; + if (a._chain) a = a._wrapped; + if (b._chain) b = b._wrapped; + // Invoke a custom `isEqual` method if one is provided. + if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b); + if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a); // Compare `[[Class]]` names. var className = toString.call(a); if (className != toString.call(b)) return false; @@ -830,15 +707,14 @@ if (typeof a != 'object' || typeof b != 'object') return false; // Assume equality for cyclic structures. The algorithm for detecting cyclic // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - var length = aStack.length; + var length = stack.length; while (length--) { // Linear search. Performance is inversely proportional to the number of // unique nested structures. - if (aStack[length] == a) return bStack[length] == b; + if (stack[length] == a) return true; } // Add the first object to the stack of traversed objects. - aStack.push(a); - bStack.push(b); + stack.push(a); var size = 0, result = true; // Recursively compare objects and arrays. if (className == '[object Array]') { @@ -848,24 +724,20 @@ if (result) { // Deep compare the contents, ignoring non-numeric properties. while (size--) { - if (!(result = eq(a[size], b[size], aStack, bStack))) break; + // Ensure commutative equality for sparse arrays. + if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break; } } } else { - // Objects with different constructors are not equivalent, but `Object`s - // from different frames are. - var aCtor = a.constructor, bCtor = b.constructor; - if (aCtor !== bCtor && !(_.isFunction(aCtor) && (aCtor instanceof aCtor) && - _.isFunction(bCtor) && (bCtor instanceof bCtor))) { - return false; - } + // Objects with different constructors are not equivalent. + if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false; // Deep compare objects. for (var key in a) { if (_.has(a, key)) { // Count the expected number of properties. size++; // Deep compare each member. - if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break; + if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break; } } // Ensure that both objects contain the same number of properties. @@ -877,20 +749,18 @@ } } // Remove the first object from the stack of traversed objects. - aStack.pop(); - bStack.pop(); + stack.pop(); return result; - }; + } // Perform a deep comparison to check if two objects are equal. _.isEqual = function(a, b) { - return eq(a, b, [], []); + return eq(a, b, []); }; // Is a given array, string, or object empty? // An "empty" object has no enumerable own-properties. _.isEmpty = function(obj) { - if (obj == null) return true; if (_.isArray(obj) || _.isString(obj)) return obj.length === 0; for (var key in obj) if (_.has(obj, key)) return false; return true; @@ -898,7 +768,7 @@ // Is a given value a DOM element? _.isElement = function(obj) { - return !!(obj && obj.nodeType === 1); + return !!(obj && obj.nodeType == 1); }; // Is a given value an array? @@ -912,36 +782,35 @@ return obj === Object(obj); }; - // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp. - each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) { - _['is' + name] = function(obj) { - return toString.call(obj) == '[object ' + name + ']'; - }; - }); - - // Define a fallback version of the method in browsers (ahem, IE), where - // there isn't any inspectable "Arguments" type. + // Is a given variable an arguments object? + _.isArguments = function(obj) { + return toString.call(obj) == '[object Arguments]'; + }; if (!_.isArguments(arguments)) { _.isArguments = function(obj) { return !!(obj && _.has(obj, 'callee')); }; } - // Optimize `isFunction` if appropriate. - if (typeof (/./) !== 'function') { - _.isFunction = function(obj) { - return typeof obj === 'function'; - }; - } - - // Is a given object a finite number? - _.isFinite = function(obj) { - return _.isNumber(obj) && isFinite(obj); + // Is a given value a function? + _.isFunction = function(obj) { + return toString.call(obj) == '[object Function]'; }; - // Is the given value `NaN`? (NaN is the only number which does not equal itself). + // Is a given value a string? + _.isString = function(obj) { + return toString.call(obj) == '[object String]'; + }; + + // Is a given value a number? + _.isNumber = function(obj) { + return toString.call(obj) == '[object Number]'; + }; + + // Is the given value `NaN`? _.isNaN = function(obj) { - return _.isNumber(obj) && obj != +obj; + // `NaN` is the only value for which `===` is not reflexive. + return obj !== obj; }; // Is a given value a boolean? @@ -949,6 +818,16 @@ return obj === true || obj === false || toString.call(obj) == '[object Boolean]'; }; + // Is a given value a date? + _.isDate = function(obj) { + return toString.call(obj) == '[object Date]'; + }; + + // Is the given value a regular expression? + _.isRegExp = function(obj) { + return toString.call(obj) == '[object RegExp]'; + }; + // Is a given value equal to null? _.isNull = function(obj) { return obj === null; @@ -959,8 +838,7 @@ return obj === void 0; }; - // Shortcut function for checking if an object has a given property directly - // on itself (in other words, not on a prototype). + // Has own property? _.has = function(obj, key) { return hasOwnProperty.call(obj, key); }; @@ -981,65 +859,20 @@ }; // Run a function **n** times. - _.times = function(n, iterator, context) { + _.times = function (n, iterator, context) { for (var i = 0; i < n; i++) iterator.call(context, i); }; - // Return a random integer between min and max (inclusive). - _.random = function(min, max) { - if (max == null) { - max = min; - min = 0; - } - return min + (0 | Math.random() * (max - min + 1)); + // Escape a string for HTML interpolation. + _.escape = function(string) { + return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/'); }; - // List of HTML entities for escaping. - var entityMap = { - escape: { - '&': '&', - '<': '<', - '>': '>', - '"': '"', - "'": ''', - '/': '/' - } - }; - entityMap.unescape = _.invert(entityMap.escape); - - // Regexes containing the keys and values listed immediately above. - var entityRegexes = { - escape: new RegExp('[' + _.keys(entityMap.escape).join('') + ']', 'g'), - unescape: new RegExp('(' + _.keys(entityMap.unescape).join('|') + ')', 'g') - }; - - // Functions for escaping and unescaping strings to/from HTML interpolation. - _.each(['escape', 'unescape'], function(method) { - _[method] = function(string) { - if (string == null) return ''; - return ('' + string).replace(entityRegexes[method], function(match) { - return entityMap[method][match]; - }); - }; - }); - - // If the value of the named property is a function then invoke it; - // otherwise, return it. - _.result = function(object, property) { - if (object == null) return null; - var value = object[property]; - return _.isFunction(value) ? value.call(object) : value; - }; - - // Add your own custom functions to the Underscore object. + // Add your own custom functions to the Underscore object, ensuring that + // they're correctly added to the OOP wrapper as well. _.mixin = function(obj) { each(_.functions(obj), function(name){ - var func = _[name] = obj[name]; - _.prototype[name] = function() { - var args = [this._wrapped]; - push.apply(args, arguments); - return result.call(this, func.apply(_, args)); - }; + addToWrapper(name, _[name] = obj[name]); }); }; @@ -1062,72 +895,41 @@ // When customizing `templateSettings`, if you don't want to define an // interpolation, evaluation or escaping regex, we need one that is // guaranteed not to match. - var noMatch = /(.)^/; + var noMatch = /.^/; - // Certain characters need to be escaped so that they can be put into a - // string literal. - var escapes = { - "'": "'", - '\\': '\\', - '\r': 'r', - '\n': 'n', - '\t': 't', - '\u2028': 'u2028', - '\u2029': 'u2029' + // Within an interpolation, evaluation, or escaping, remove HTML escaping + // that had been previously added. + var unescape = function(code) { + return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'"); }; - var escaper = /\\|'|\r|\n|\t|\u2028|\u2029/g; - // JavaScript micro-templating, similar to John Resig's implementation. // Underscore templating handles arbitrary delimiters, preserves whitespace, // and correctly escapes quotes within interpolated code. - _.template = function(text, data, settings) { - settings = _.defaults({}, settings, _.templateSettings); - - // Combine delimiters into one regular expression via alternation. - var matcher = new RegExp([ - (settings.escape || noMatch).source, - (settings.interpolate || noMatch).source, - (settings.evaluate || noMatch).source - ].join('|') + '|$', 'g'); - - // Compile the template source, escaping string literals appropriately. - var index = 0; - var source = "__p+='"; - text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { - source += text.slice(index, offset) - .replace(escaper, function(match) { return '\\' + escapes[match]; }); - source += - escape ? "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'" : - interpolate ? "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'" : - evaluate ? "';\n" + evaluate + "\n__p+='" : ''; - index = offset + match.length; - }); - source += "';\n"; - - // If a variable is not specified, place data values in local scope. - if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; - - source = "var __t,__p='',__j=Array.prototype.join," + - "print=function(){__p+=__j.call(arguments,'');};\n" + - source + "return __p;\n"; - - try { - var render = new Function(settings.variable || 'obj', '_', source); - } catch (e) { - e.source = source; - throw e; - } - - if (data) return render(data, _); - var template = function(data) { - return render.call(this, data, _); + _.template = function(str, data) { + var c = _.templateSettings; + var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' + + 'with(obj||{}){__p.push(\'' + + str.replace(/\\/g, '\\\\') + .replace(/'/g, "\\'") + .replace(c.escape || noMatch, function(match, code) { + return "',_.escape(" + unescape(code) + "),'"; + }) + .replace(c.interpolate || noMatch, function(match, code) { + return "'," + unescape(code) + ",'"; + }) + .replace(c.evaluate || noMatch, function(match, code) { + return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('"; + }) + .replace(/\r/g, '\\r') + .replace(/\n/g, '\\n') + .replace(/\t/g, '\\t') + + "');}return __p.join('');"; + var func = new Function('obj', '_', tmpl); + if (data) return func(data, _); + return function(data) { + return func.call(this, data, _); }; - - // Provide the compiled function source as a convenience for precompilation. - template.source = 'function(' + (settings.variable || 'obj') + '){\n' + source + '}'; - - return template; }; // Add a "chain" function, which will delegate to the wrapper. @@ -1135,15 +937,29 @@ return _(obj).chain(); }; - // OOP + // The OOP Wrapper // --------------- + // If Underscore is called as a function, it returns a wrapped object that // can be used OO-style. This wrapper holds altered versions of all the // underscore functions. Wrapped objects may be chained. + var wrapper = function(obj) { this._wrapped = obj; }; + + // Expose `wrapper.prototype` as `_.prototype` + _.prototype = wrapper.prototype; // Helper function to continue chaining intermediate results. - var result = function(obj) { - return this._chain ? _(obj).chain() : obj; + var result = function(obj, chain) { + return chain ? _(obj).chain() : obj; + }; + + // A method to easily add functions to the OOP wrapper. + var addToWrapper = function(name, func) { + wrapper.prototype[name] = function() { + var args = slice.call(arguments); + unshift.call(args, this._wrapped); + return result(func.apply(_, args), this._chain); + }; }; // Add all of the Underscore functions to the wrapper object. @@ -1152,35 +968,32 @@ // Add all mutator Array functions to the wrapper. each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { var method = ArrayProto[name]; - _.prototype[name] = function() { - var obj = this._wrapped; - method.apply(obj, arguments); - if ((name == 'shift' || name == 'splice') && obj.length === 0) delete obj[0]; - return result.call(this, obj); + wrapper.prototype[name] = function() { + var wrapped = this._wrapped; + method.apply(wrapped, arguments); + var length = wrapped.length; + if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0]; + return result(wrapped, this._chain); }; }); // Add all accessor Array functions to the wrapper. each(['concat', 'join', 'slice'], function(name) { var method = ArrayProto[name]; - _.prototype[name] = function() { - return result.call(this, method.apply(this._wrapped, arguments)); + wrapper.prototype[name] = function() { + return result(method.apply(this._wrapped, arguments), this._chain); }; }); - _.extend(_.prototype, { + // Start chaining a wrapped Underscore object. + wrapper.prototype.chain = function() { + this._chain = true; + return this; + }; - // Start chaining a wrapped Underscore object. - chain: function() { - this._chain = true; - return this; - }, - - // Extracts the result from a wrapped and chained object. - value: function() { - return this._wrapped; - } - - }); + // Extracts the result from a wrapped and chained object. + wrapper.prototype.value = function() { + return this._wrapped; + }; }).call(this); diff -r 55e7d7008efee2c5622f2505612265a9593ae992 -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -3,8 +3,8 @@ * genomic visualization. */ -define(["libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], - function(d3, util, visualization, tracks, tools, data) { +define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], + function(_, d3, util, visualization, tracks, tools, data) { /** * A collection of tool input settings. Object is useful for keeping a list of settings diff -r 55e7d7008efee2c5622f2505612265a9593ae992 -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,7 +1,7 @@ define( ["libs/underscore", "viz/visualization", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters", "mvc/data", - "viz/trackster/filters", "viz/trackster_ui" ], - function( _, visualization, util, slotting, painters, data, filters_mod, trackster_ui_mod ) { + "viz/trackster/filters" ], + function( _, visualization, util, slotting, painters, data, filters_mod ) { var extend = _.extend; var get_random_color = util.get_random_color; 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: afgane: Fix workflow API imports
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/55e7d7008efe/ changeset: 55e7d7008efe user: afgane date: 2012-10-02 03:03:00 summary: Fix workflow API imports affected #: 1 file diff -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 -r 55e7d7008efee2c5622f2505612265a9593ae992 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -8,9 +8,10 @@ from sqlalchemy import desc from galaxy import util from galaxy import web -from galaxy.tools.parameters import visit_input_values, DataToolParameter +from galaxy import model +from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue from galaxy.web.base.controller import BaseAPIController, url_for -from galaxy.workflow.modules import module_factory +from galaxy.workflow.modules import module_factory, ToolModule from galaxy.jobs.actions.post import ActionBox from galaxy.model.item_attrs import UsesAnnotations @@ -344,7 +345,7 @@ def _workflow_from_dict( self, trans, data, source=None ): """ - RPARK: copied from galaxy.web.controllers.workflows.py + RPARK: copied from galaxy.webapps.galaxy.controllers.workflows.py Creates a workflow from a dict. Created workflow is stored in the database and returned. """ # Put parameters in workflow mode @@ -388,7 +389,7 @@ # Stick this in the step temporarily step.temp_input_connections = step_dict['input_connections'] # Save step annotation. - annotation = step_dict[ 'annotation' ] + #annotation = step_dict[ 'annotation' ] #if annotation: #annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) # ------------------------------------------ # @@ -398,7 +399,7 @@ # Unpack and add post-job actions. post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], + model.PostJobAction( pja_dict[ 'action_type' ], step, pja_dict[ 'output_name' ], pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps 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: fixes and improvements to (alt)history - now renders history controls; fix to popupmenu parent parameter; pack scripts
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3164ba737fd4/ changeset: 3164ba737fd4 user: carlfeberhard date: 2012-10-02 00:25:35 summary: fixes and improvements to (alt)history - now renders history controls; fix to popupmenu parent parameter; pack scripts affected #: 19 files diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -173,11 +173,19 @@ states = states.split( "," ) for encoded_id, state in zip( ids, states ): try: + # assume encoded and decode to int id = int( trans.app.security.decode_id( encoded_id ) ) except: + # fallback to non-encoded id id = int( encoded_id ) + + # fetch new data for that id data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) + + # if the state has changed, if data.state != state: + + # find out if we need to force a refresh on this data job_hda = data while job_hda.copied_from_history_dataset_association: job_hda = job_hda.copied_from_history_dataset_association @@ -187,12 +195,15 @@ if tool: force_history_refresh = tool.force_history_refresh if not job_hda.visible: - force_history_refresh = True + force_history_refresh = True + + # add the new state html for the item, the refresh option and the new state, map to the id rval[encoded_id] = { "state": data.state, "html": unicode( trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ), 'utf-8' ), "force_history_refresh": force_history_refresh } + return rval @web.json diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -196,7 +196,7 @@ } }); // locate the element with the id corresponding to the menu's popupmenu attr - var box = $( "#" + menu.attr( 'popupmenu' ) ); + var box = $( parent ).find( "#" + menu.attr( 'popupmenu' ) ); // For menus with clickable link text, make clicking on the link go through instead // of activating the popup menu diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -69,6 +69,72 @@ } }; +// ============================================================================= +/** Global string localization object (and global short form alias) + * set with either: + * GalaxyLocalization.setLocalizedString( original, localized ) + * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) + * get with either: + * _l( original ) + */ +//TODO: move to Galaxy.Localization (maybe galaxy.base.js) +var GalaxyLocalization = jQuery.extend({}, { + aliasName : '_l', + localizedStrings : {}, + + setLocalizedString : function( str_or_obj, localizedString ){ + // pass in either two strings (english, translated) or an obj (map) of english : translated attributes + //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); + var self = this; + + // DRY non-duplicate assignment function + var setStringIfNotDuplicate = function( original, localized ){ + // do not set if identical - strcmp expensive but should only happen once per page per word + if( original !== localized ){ + self.localizedStrings[ original ] = localized; + } + }; + + if( jQuery.type( str_or_obj ) === "string" ){ + setStringIfNotDuplicate( str_or_obj, localizedString ); + + } else if( jQuery.type( str_or_obj ) === "object" ){ + jQuery.each( str_or_obj, function( key, val ){ + //console.debug( 'key=>val', key, '=>', val ); + // could recurse here but no reason + setStringIfNotDuplicate( key, val ); + }); + + } else { + throw( 'Localization.setLocalizedString needs either a string or object as the first argument,' + + ' given: ' + str_or_obj ); + } + }, + + localize : function( strToLocalize ){ + //console.debug( this + '.localize:', strToLocalize ); + // return the localized version if it's there, the strToLocalize if not + var retStr = strToLocalize; + if( _.has( this.localizedStrings, strToLocalize ) ){ + //console.debug( 'found' ); + retStr = this.localizedStrings[ strToLocalize ]; + } + //console.debug( 'returning:', retStr ); + return retStr; + }, + + toString : function(){ return 'GalaxyLocalization'; } +}); + +// global localization alias +window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; + +//TEST: setLocalizedString( string, string ), _l( string ) +//TEST: setLocalizedString( hash ), _l( string ) +//TEST: setLocalizedString( string === string ), _l( string ) +//TEST: _l( non assigned string ) + + //============================================================================== /** diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -6,71 +6,47 @@ Backbone.js implementation of history panel TODO: - replicate then refactor (could be the wrong order) + meta: + require.js + convert function comments to jsDoc style, complete comments + move inline styles into base.less + watch the magic strings + watch your globals - fix: - tags - annotations - _render_displayApps - _render_downloadButton - widget building (popupmenu, etc.) - history.mako js: updater, etc. - have info bodies prev. opened, redisplay on refresh + all: + add classes, ids on empty divs + incorporate relations? + events (local/ui and otherwise) + have info bodies prev. opened, redisplay on refresh + transfer history.mako js: + updater, etc. + create viz icon + trackster + scatterplot + phylo-viz + on ready: + delete function + check_transfer_status (running->ok) + quota meter update + + historyItemView: + poly HistoryItemView (and HistoryView?) on: for_editing, display_structured, trans.user + don't draw body until it's first unhide event + HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) + move visualizations menu + include phyloviz - don't draw body until it's first unhide event - all history.mako js -> this - HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) - History (meta controls : collapse all, rename, annotate, etc. - see history.js.120823.bak) - events (local/ui and otherwise) - HistoryCollection: (collection of History: 'Saved Histories') + History: + renaming broken + tags rendering broken (url?) + annotation (url?) + meta controls : collapse all, rename, annotate, etc. + + collection: + show_deleted, show_hidden (thru js - no refresh) + - ?move IconButtonViews -> templates? - - convert function comments to jsDoc style, complete comments - collection -> show_deleted, show_hidden - poly HistoryItemView on: for_editing, display_structured, trans.user - incorporate relations? - localization - template helper {{#local}} calls _l() - - move inline styles into base.less - add classes, ids on empty divs - watch the magic strings ============================================================================= */ - -//============================================================================== -// jq plugin? -//?? into template? I dunno: need to handle variadic keys, remove empty attrs (href="") -//TODO: not happy with this (a 4th rendering/templating system!?) or it being global -function linkHTMLTemplate( config, tag ){ - // Create an anchor (or any tag) using any config params passed in - //NOTE!: send class attr as 'classes' to avoid res. keyword collision (jsLint) - if( !config ){ return '<a></a>'; } - tag = tag || 'a'; - - var template = [ '<' + tag ]; - for( key in config ){ - var val = config[ key ]; - if( val === '' ){ continue; } - switch( key ){ - case 'text': continue; - case 'classes': - // handle keyword class which is also an HTML attr name - key = 'class'; - val = ( config.classes.join )?( config.classes.join( ' ' ) ):( config.classes ); - //note: lack of break (fall through) - default: - template.push( [ ' ', key, '="', val, '"' ].join( '' ) ); - } - } - template.push( '>' ); - if( 'text' in config ){ template.push( config.text ); } - template.push( '</' + tag + '>' ); - - return template.join( '' ); -} - -//============================================================================== //TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted var HistoryItem = BaseModel.extend( LoggableMixin ).extend({ // a single HDA model @@ -292,7 +268,6 @@ var deleteBtnData = { title : 'Delete', href : this.model.get( 'delete_url' ), - target : 'galaxy_main', id : 'historyItemDeleter-' + this.model.get( 'id' ), icon_class : 'delete' }; @@ -329,8 +304,7 @@ var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), view = this; _.each( buttonRenderingFuncs, function( fn ){ - var render_return = fn.call( view ); - primaryActionButtons.append( render_return ); + primaryActionButtons.append( fn.call( view ) ); }); return primaryActionButtons; }, @@ -342,8 +316,7 @@ // return either: a single download icon-button (if there are no meta files) // or a popupmenu with links to download assoc. meta files (if there are meta files) var downloadLinkHTML = HistoryItemView.templates.downloadLinks( this.model.toJSON() ); - this.log( '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); - + //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); return $( downloadLinkHTML ); }, @@ -447,7 +420,7 @@ // ................................................................................ other elements _render_tagArea : function(){ - if( this.model.get( 'retag_url' ) ){ return null; } + if( !this.model.get( 'retag_url' ) ){ return null; } //TODO: move to mvc/tags.js return $( HistoryItemView.templates.tagArea( this.model.toJSON() ) ); }, @@ -464,14 +437,14 @@ var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ - this.log( this + 'display_types:', this.model.get( 'display_types' ) ); + //this.log( this + 'display_types:', this.model.get( 'display_types' ) ); //TODO:?? does this ever get used? displayAppsDiv.append( HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_types }) ); } if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ - this.log( this + 'display_apps:', this.model.get( 'display_apps' ) ); + //this.log( this + 'display_apps:', this.model.get( 'display_apps' ) ); displayAppsDiv.append( HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_apps }) ); @@ -655,9 +628,10 @@ // Show or hide tag area; if showing tag area and it's empty, fill it. if( tagArea.is( ":hidden" ) ){ - if( !tagElt.html() ){ + if( !jQuery.trim( tagElt.html() ) ){ // Need to fill tag element. $.ajax({ + //TODO: the html from this breaks a couple of times url: this.model.get( 'ajax_get_tag_url' ), error: function() { alert( "Tagging failed" ); }, success: function(tag_elt_html) { @@ -688,7 +662,7 @@ // Show or hide annotation area; if showing annotation area and it's empty, fill it. if ( annotationArea.is( ":hidden" ) ){ - if( !annotationElem.html() ){ + if( !jQuery.trim( annotationElem.html() ) ){ // Need to fill annotation element. $.ajax({ url: this.model.get( 'ajax_get_annotation_url' ), @@ -762,6 +736,7 @@ //============================================================================== var History = BaseModel.extend( LoggableMixin ).extend({ + //TODO: bind change events from items and collection to this (itemLengths, states) // uncomment this out see log messages //logger : console, @@ -770,7 +745,8 @@ defaults : { id : '', name : '', - state : '', + state : '', + //TODO:?? change these to a list of encoded ids? state_details : { discarded : 0, empty : 0, @@ -781,15 +757,51 @@ running : 0, setting_metadata: 0, upload : 0 - } + }, + + // maybe security issues... + userIsAdmin : false, + userRoles : [], + //TODO: hardcoded + + //TODO: wire this to items + itemsLength : 0, + showDeleted : false, + showHidden : false, + + diskSize : 0, + deleted : false, + + // tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), + // tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") + tags : [], + annotation : null, + message : null, + quotaMsg : false, + + baseURL : null, + hideDeletedURL : null, + hideHiddenURL : null, + tagURL : null, + annotateURL : null }, initialize : function( data, history_datasets ){ - this.log( this + '.initialize', data, history_datasets ); + //this.log( this + '.initialize', data, history_datasets ); this.items = new HistoryCollection(); }, + toJSON : function(){ + // unfortunately, bb doesn't call 'get' to form the JSON meaning computed vals from get aren't used, so... + // a simple example of override and super call + var json = Backbone.Model.prototype.toJSON.call( this ); + json.itemsLength = this.items.length; + //this.log( this + '.json:', json ); + return json; + }, + loadDatasetsAsHistoryItems : function( datasets ){ + //TODO: add via ajax - multiple datasets at once // adds the given dataset/Item data to historyItems // and updates this.state based on their states //pre: datasets is a list of objs @@ -799,12 +811,12 @@ stateDetails = this.get( 'state_details' ); _.each( datasets, function( dataset, index ){ - self.log( 'loading dataset: ', dataset, index ); + //self.log( 'loading dataset: ', dataset, index ); // create an item sending along the history_id as well var historyItem = new HistoryItem( _.extend( dataset, { history_id: selfID } ) ); - self.log( 'as History:', historyItem ); + //self.log( 'as History:', historyItem ); self.items.add( historyItem ); // add item's state to running totals in stateDetails @@ -864,28 +876,42 @@ // direct attachment to existing element el : 'body.historyPage', - initialize : function(){ - this.log( this + '.initialize' ); + initialize : function(){ + this.log( this + '.initialize:', this ); this.itemViews = []; var parent = this; this.model.items.each( function( item ){ var itemView = new HistoryItemView({ model: item }); parent.itemViews.push( itemView ); }); - //itemViews.reverse(); }, - render : function(){ - this.log( this + '.render' ); + render : function(){ + this.$el.append( HistoryView.templates.historyPanel( this.model.toJSON() ) ); + this.log( this + ' rendered from template:', this.$el ); - // render to temp, move all at once, remove temp holder + // set up aliases + this.itemsDiv = this.$el.find( '#' + this.model.get( 'id' ) + '-datasets' ); + + //TODO: set up widgets, tooltips, etc. + + if( this.model.items.length ){ + // render to temp, move all at once, remove temp holder + var tempDiv = this._render_items(); + this.itemsDiv.append( tempDiv.children() ); + tempDiv.remove(); + } + }, + + _render_items : function(){ + var div = $( '<div/>' ), + view = this; //NOTE!: render in reverse (newest on top) via prepend (instead of append) - var tempDiv = $( '<div/>' ); - _.each( this.itemViews, function( view ){ - tempDiv.prepend( view.render() ); + _.each( this.itemViews, function( itemView ){ + view.log( view + '.render_items:', itemView ); + div.prepend( itemView.render() ); }); - this.$el.append( tempDiv.children() ); - tempDiv.remove(); + return div; }, toString : function(){ @@ -893,6 +919,13 @@ return 'HistoryView(' + nameString + ')'; } }); +//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ +HistoryView.templates = CompiledTemplateLoader.getTemplates({ + 'history-templates.html' : { + historyPanel : 'template-history-historyPanel' + } +}); + //============================================================================== diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -157,79 +157,10 @@ } }); -// ============================================================================= -/** Global string localization object (and global short form alias) - * set with either: - * GalaxyLocalization.setLocalizedString( original, localized ) - * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) - * get with either: - * _l( original ) - */ -//TODO: move to Galaxy.Localization -var GalaxyLocalization = jQuery.extend({}, { - aliasName : '_l', - localizedStrings : {}, - - setLocalizedString : function( str_or_obj, localizedString ){ - // pass in either two strings (english, translated) or an obj (map) of english : translated attributes - //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); - var self = this; - - // DRY non-duplicate assignment function - var setStringIfNotDuplicate = function( original, localized ){ - // do not set if identical - strcmp expensive but should only happen once per page per word - if( original !== localized ){ - self.localizedStrings[ original ] = localized; - } - }; - - if( jQuery.type( str_or_obj ) === "string" ){ - setStringIfNotDuplicate( str_or_obj, localizedString ); - - } else if( jQuery.type( str_or_obj ) === "object" ){ - jQuery.each( str_or_obj, function( key, val ){ - //console.debug( 'key=>val', key, '=>', val ); - // could recurse here but no reason - setStringIfNotDuplicate( key, val ); - }); - - } else { - throw( 'Localization.setLocalizedString needs either a string or object as the first argument,' + - ' given: ' + str_or_obj ); - } - }, - - localize : function( strToLocalize ){ - //console.debug( this + '.localize:', strToLocalize ); - // return the localized version if it's there, the strToLocalize if not - // try/catch cheaper than if in - try { - //var localized = this.localizedStrings[ strToLocalize ]; - //return localized; - return this.localizedStrings[ strToLocalize ]; - } catch( err ){ - //TODO??: potentially problematic catch all - //console.error( err ); - return strToLocalize; - } - }, - - toString : function(){ return 'GalaxyLocalization'; } -}); -// global localization alias -window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; -//TEST: setLocalizedString( string, string ), _l( string ) -//TEST: setLocalizedString( hash ), _l( string ) -//TEST: setLocalizedString( string === string ), _l( string ) -//TEST: _l( non assigned string ) -// ============================================================================= -/** UI icon-button (Backbone.View only - no model) - * - */ @@ -239,8 +170,3 @@ - - - - - diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var 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HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){var e=d.call(a);b.append(e)});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());this.log("_render_downloadButton, downloadLinkHTML:",a);return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){this.log(this+"display_types:",this.model.get("display_types"));a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){this.log(this+"display_apps:",this.model.get("display_apps"));a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}}); \ No newline at end of file +var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(c){a.log(a+".render_items:",c);b.prepend(c.render())});return b},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates=CompiledTemplateLoader.getTemplates({"history-templates.html":{historyPanel:"template-history-historyPanel"}}); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){try{return this.localizedStrings[b]}catch(a){return b}},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}}); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/helpers-common-templates.js --- a/static/scripts/packed/templates/compiled/helpers-common-templates.js +++ b/static/scripts/packed/templates/compiled/helpers-common-templates.js @@ -1,1 +1,1 @@ -Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){a+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">"+((c.enabled)?("</a>"):("</span>"));return a}); \ No newline at end of file +Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"});Handlebars.registerHelper("local",function(a){return _l(a.fn(this))});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){a+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">"+((c.enabled)?("</a>"):("</span>"));return a}); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.meta_download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_download_url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(p,o){return'\n<a href="" title="Download" class="icon-button disk tooltip"></a>\n'}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.meta_download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_download_url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(s,r){var p="",q,o;p+='\n<a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n';return p}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="';K=A.tagURL;if(K){M=K.call(O,{hash:{}})}else{M=O.tagURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="';K=A.annotateURL;if(K){M=K.call(O,{hash:{}})}else{M=O.annotateURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n </div>\n ';return L}function q(L,K){return"Edit history tags"}function m(L,K){return"Edit history annotation"}function I(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideDeletedURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideDeletedURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function H(L,K){return"hide deleted"}function G(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+'</div>\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n \n ";return L}function D(O,N){var L="",M,K;L+='\n <div id="history-size">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function p(O,N){var L="",M,K;L+="\n";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}if(M||M===0){L+=M}L+="\n";return L}function l(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}if(L||L===0){return L}else{return""}}function j(L,K){return"You are currently viewing a deleted history!"}function i(N,M){var K="",L;K+="\n";K+='\n<div style="margin: 0px 5px 10px 5px">\n\n <div id="history-tag-area" style="display: none">\n <b>Tags:</b>\n ';K+="\n ";K+='\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';L=N.annotation;L=A["if"].call(N,L,{hash:{},inverse:y.program(27,g,M),fn:y.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n</div>\n";return K}function h(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function g(L,K){return"\n <em>Describe or add notes to history</em>\n "}function d(O,N){var L="",M,K;L+='\n<div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n</div>\n";return L}function z(L,K){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n '}function x(O,N){var L="",M,K;L+='\n<div id="';K=A.id;if(K){M=K.call(O,{hash:{}})}else{M=O.id;M=typeof M===f?M():M}L+=e(M)+'-datasets" class="history-datasets-list">\n ';L+="\n</div>\n\n";return L}function w(O,N){var L="",M,K;L+='\n<div class="infomessagesmall" id="emptyHistoryMessage">\n';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}if(M||M===0){L+=M}L+="\n</div>\n";return L}function v(L,K){return"Your history is empty. Click 'Get Data' on the left pane to start"}B+='<div id="top-links" class="historyLinks">\n <a title="';n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}if(o||o===0){B+=o}B+='" class="icon-button arrow-circle tooltip" href="';n=A.baseURL;if(n){o=n.call(C,{hash:{}})}else{o=C.baseURL;o=typeof o===f?o():o}B+=e(o)+"\"></a>\n <a title='";n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}if(o||o===0){B+=o}B+="' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n ";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(5,r,J)});if(o||o===0){B+=o}B+='\n</div>\n<div class="clear"></div>\n\n';B+="\n";o=C.showDeleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(10,I,J)});if(o||o===0){B+=o}B+="\n\n";o=C.showHidden;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(13,G,J)});if(o||o===0){B+=o}B+="\n\n";B+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.program(18,D,J),fn:y.program(16,E,J)});if(o||o===0){B+=o}B+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n';o=C.deleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(20,p,J)});if(o||o===0){B+=o}B+="\n\n";B+="\n";B+="\n";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(24,i,J)});if(o||o===0){B+=o}B+="\n\n";o=C.message;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(29,d,J)});if(o||o===0){B+=o}B+='\n\n<div id="quota-message-container">\n ';o=C.over_quota;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(31,z,J)});if(o||o===0){B+=o}B+="\n</div>\n\n";o=C.itemsLength;o=A["if"].call(C,o,{hash:{},inverse:y.program(35,w,J),fn:y.program(33,x,J)});if(o||o===0){B+=o}return B})})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/tool_search.js --- a/static/scripts/packed/templates/compiled/tool_search.js +++ b/static/scripts/packed/templates/compiled/tool_search.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<input type="text" name="query" value="';g=d.search_hint_string;if(g){c=g.call(l,{hash:{}})}else{c=l.search_hint_string;c=typeof c===f?c():c}h+=i(c)+'" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<a id="search-clear-btn" class="icon-button cross-circle tooltip" title="clear search (esc)"></a>\n<img src="';g=d.spinner_url;if(g){c=g.call(l,{hash:{}})}else{c=l.spinner_url;c=typeof c===f?c():c}h+=i(c)+'" id="search-spinner" class="search-spinner"/>';return h})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<input type="text" name="query" value="';g=d.search_hint_string;if(g){c=g.call(l,{hash:{}})}else{c=l.search_hint_string;c=typeof c===f?c():c}h+=i(c)+'" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<a id="search-clear-btn" class="tooltip" title="clear search (esc)"></a>\n<img src="';g=d.spinner_url;if(g){c=g.call(l,{hash:{}})}else{c=l.spinner_url;c=typeof c===f?c():c}h+=i(c)+'" id="search-spinner" class="search-spinner"/>';return h})})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/common-templates.html --- a/static/scripts/templates/common-templates.html +++ b/static/scripts/templates/common-templates.html @@ -14,6 +14,15 @@ }); </script> +<script type="text/javascript" class="helper-common" id="helper-local"> +/** Calls _l (from base-mvc.js) to localize strings (if poosible) + * This helper is specifically for localization within templates + */ +Handlebars.registerHelper( 'local', function( options ){ + return _l( options.fn( this ) ); +}); +</script> + <script type="text/template" class="template-common" id="template-warningmessagesmall"> {{! renders a warning in a (mostly css) highlighted, iconned warning box }} <div class="warningmessagesmall"><strong>{{{ warning }}}</strong></div> diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/compiled/helpers-common-templates.js --- a/static/scripts/templates/compiled/helpers-common-templates.js +++ b/static/scripts/templates/compiled/helpers-common-templates.js @@ -8,6 +8,12 @@ Handlebars.registerHelper( 'warningmessagesmall', function( options ){ return '<div class="warningmessagesmall"><strong>' + options.fn( this ) + '</strong></div>' }); +/** Calls _l (from base-mvc.js) to localize strings (if poosible) + * This helper is specifically for localization within templates + */ +Handlebars.registerHelper( 'local', function( options ){ + return _l( options.fn( this ) ); +}); /** Renders a glx style icon-button (see IconButton in mvc/ui.js) * can be used in either of the following ways: * within a template: {{> iconButton buttonData}} diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/templates/compiled/template-history-downloadLinks.js @@ -45,8 +45,13 @@ function program4(depth0,data) { - - return "\n<a href=\"\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n";} + var buffer = "", stack1, foundHelper; + buffer += "\n<a href=\""; + foundHelper = helpers.download_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n"; + return buffer;} stack1 = depth0.meta_files; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)}); diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/compiled/template-history-historyPanel.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -0,0 +1,272 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; + +function program1(depth0,data) { + + + return "refresh";} + +function program3(depth0,data) { + + + return "collapse all";} + +function program5(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n <a id=\"history-tag\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\""; + foundHelper = helpers.tagURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.tagURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\""; + foundHelper = helpers.annotateURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.annotateURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></a>\n </div>\n "; + return buffer;} +function program6(depth0,data) { + + + return "Edit history tags";} + +function program8(depth0,data) { + + + return "Edit history annotation";} + +function program10(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"historyLinks\">\n <a href=\""; + foundHelper = helpers.hideDeletedURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.hideDeletedURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n</div>\n"; + return buffer;} +function program11(depth0,data) { + + + return "hide deleted";} + +function program13(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"historyLinks\">\n <a href=\""; + foundHelper = helpers.hideHiddenURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.hideHiddenURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n</div>\n"; + return buffer;} +function program14(depth0,data) { + + + return "hide hidden";} + +function program16(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; + foundHelper = helpers.diskSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\" title=\"Click to rename history\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n \n "; + return buffer;} + +function program18(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-size\">"; + foundHelper = helpers.diskSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n "; + return buffer;} + +function program20(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program21(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} +function program22(depth0,data) { + + + return "You are currently viewing a deleted history!";} + +function program24(depth0,data) { + + var buffer = "", stack1; + buffer += "\n"; + buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <b>Tags:</b>\n "; + buffer += "\n "; + buffer += "\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + stack1 = depth0.annotation; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n </div>\n </div>\n</div>\n"; + return buffer;} +function program25(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.annotation; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n "; + return buffer;} + +function program27(depth0,data) { + + + return "\n <em>Describe or add notes to history</em>\n ";} + +function program29(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div id=\"message-container\">\n <div class=\""; + foundHelper = helpers.status; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "message\">\n "; + foundHelper = helpers.message; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; + return buffer;} + +function program31(depth0,data) { + + + return "\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n ";} + +function program33(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\">\n "; + buffer += "\n</div>\n\n"; + return buffer;} + +function program35(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\">\n"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n"; + return buffer;} +function program36(depth0,data) { + + + return "Your history is empty. Click 'Get Data' on the left pane to start";} + + buffer += "<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; + foundHelper = helpers.baseURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.baseURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n "; + stack1 = depth0.userRoles; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n<div class=\"clear\"></div>\n\n"; + buffer += "\n"; + stack1 = depth0.showDeleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.showHidden; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; + stack1 = depth0.userRoles; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(18, program18, data),fn:self.program(16, program16, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n"; + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + buffer += "\n"; + buffer += "\n"; + stack1 = depth0.userRoles; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.message; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n<div id=\"quota-message-container\">\n "; + stack1 = depth0.over_quota; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n\n"; + stack1 = depth0.itemsLength; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(35, program35, data),fn:self.program(33, program33, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + return buffer;}); +})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -64,7 +64,7 @@ <a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a></div> {{else}} -<a href="" title="Download" class="icon-button disk tooltip"></a> +<a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a> {{/if}} </script> @@ -96,3 +96,112 @@ <br /> {{/each}} </script> + + +<script type="text/template" class="template-history" id="template-history-historyPanel"> +<div id="top-links" class="historyLinks"> + <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{baseURL}}"></a> + <a title='{{#local}}collapse all{{/local}}' class='icon-button toggle tooltip' href='#' style="display: none"></a> + {{#if userRoles}} + <div style="width: 40px; float: right; white-space: nowrap;"> + <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" + class="icon-button tags tooltip" target="galaxy_main" href="{{tagURL}}"></a> + <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" + class="icon-button annotate tooltip" target="galaxy_main" href="{{annotateURL}}"></a> + </div> + {{/if}} +</div> +<div class="clear"></div> + +{{! TODO: move to js with no reload - use each with historyLinks }} +{{#if showDeleted}} +<div class="historyLinks"> + <a href="{{hideDeletedURL}}">{{#local}}hide deleted{{/local}}</a> +</div> +{{/if}} + +{{#if showHidden}} +<div class="historyLinks"> + <a href="{{hideHiddenURL}}">{{#local}}hide hidden{{/local}}</a> +</div> +{{/if}} + +{{! history name (if any) }} +<div id="history-name-area" class="historyLinks"> + <div id="history-name-container" style="position: relative;"> + {{#if userRoles}} + {{! TODO: factor out conditional css }} + <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{diskSize}}</div> + <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">{{name}}</div> + + {{else}} + <div id="history-size">{{diskSize}}</div> + {{/if}} + </div> +</div> +<div style="clear: both;"></div> + +{{#if deleted}} +{{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} +{{/if}} + +{{! tags and annotations }} +{{! TODO: wire these to js events }} +{{#if userRoles}} +{{! TODO: move inline styles out }} +<div style="margin: 0px 5px 10px 5px"> + + <div id="history-tag-area" style="display: none"> + <b>Tags:</b> + {{! load via js render_individual_tagging_element }} + {{! render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") }} + </div> + + <div id="history-annotation-area" style="display: none"> + <strong>Annotation / Notes:</strong> + <div id="history-annotation-container"> + <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> + {{#if annotation}} + {{annotation}} + {{else}} + <em>Describe or add notes to history</em> + {{/if}} + </div> + </div> + </div> +</div> +{{/if}} + +{{#if message}} +<div id="message-container"> + <div class="{{status}}message"> + {{message}} + </div><br /> +</div> +{{/if}} + +<div id="quota-message-container"> + {{#if over_quota}} + <div id="quota-message" class="errormessage"> + You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + </div> + <br/> + {{/if}} +</div> + +{{#if itemsLength}} +<div id="{{id}}-datasets" class="history-datasets-list"> + {{! NOTE: HistoryItemViews will be appended here }} +</div> + +{{else}}{{! no history items }} +<div class="infomessagesmall" id="emptyHistoryMessage"> +{{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} +</div> +{{/if}} +</script> + + + diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -97,15 +97,16 @@ # edit attr button if for_editing: if not( hda.deleted or hda.purged ): - edit_url = h.url_for( controller='dataset', action='edit', dataset_id=encoded_data_id ) + edit_url = h.url_for( controller='dataset', action='edit', + dataset_id=encoded_data_id ) add_to_data( edit_url=edit_url ) # delete button if for_editing and not ( deleted or dataset_purged or purged ): - add_to_data( delete_url=h.url_for( controller='dataset', action='delete', dataset_id=encoded_data_id, - ##TODO: loose end - show_deleted_on_refresh=show_deleted - )) + delete_url = h.url_for( controller='dataset', action='delete', + dataset_id=encoded_data_id, + show_deleted_on_refresh=show_deleted ) + add_to_data( delete_url=delete_url ) # ................................................................ primary actions (error, info, download) # download links (hda and associated meta files) @@ -127,7 +128,21 @@ # error report if for_editing: #NOTE: no state == 'error' check - add_to_data( report_error_url=h.url_for( h.url_for( controller='dataset', action='errors', id=encoded_data_id ) ) ) + ##TODO: has to have an _UN_ encoded id + #report_error_url = h.url_for( controller='dataset', action='errors', id=encoded_data_id ) + report_error_url = h.url_for( controller='dataset', action='errors', id=hda.id ) + add_to_data( report_error_url=report_error_url ) + + # info/params + show_params_url = h.url_for( controller='dataset', action='show_params', dataset_id=encoded_data_id ) + add_to_data( show_params_url=show_params_url ) + + # rerun + if for_editing: + ##TODO: has to have an _UN_ encoded id + #rerun_url = h.url_for( controller='tool_runner', action='rerun', id=encoded_data_id ) + rerun_url = h.url_for( controller='tool_runner', action='rerun', id=hda.id ) + add_to_data( rerun_url=rerun_url ) # visualizations if hda.ext in app.datatypes_registry.get_available_tracks(): @@ -265,39 +280,61 @@ %></%def> - +##TODO: remove after filling tags.js +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /><%def name="context_to_js()"><% ##print 'context', context, dir( context ) ##print 'context.kwargs', context.kwargs ##print 'history:', history - user_is_admin = trans.user_is_admin() - user_roles = trans.get_current_user_roles() - prepped_hdas = [ - prep_hda( hda, True ) for hda in datasets ] + ##TODO: move to API + for_editing = True context_dict = { 'history' : { - 'id' : trans.security.encode_id( history.id ), - 'name' : history.name + 'id' : trans.security.encode_id( history.id ), + 'name' : history.name, + + 'status' : status, + 'showDeleted' : show_deleted, + 'showHidden' : show_hidden, + 'quotaMsg' : over_quota, + 'message' : message, ##'go outside' + + 'deleted' : history.deleted, + 'diskSize' : history.get_disk_size( nice_size=True ), + + ## maybe security issues... + 'userIsAdmin' : trans.user_is_admin(), + 'userRoles' : [ role.get_api_value() for role in trans.get_current_user_roles() ], + + ##tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), + ## tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") + 'tags' : [], + ##TODO: broken - of course + ##TODO: remove after filling tags.js + ##'tagHTML' : render_individual_tagging_element( + ## user=trans.get_user(), + ## tagged_item=history, + ## elt_context="history.mako", + ## use_toggle_link=False, + ## input_size="20"), + ##TODO:?? h.to_unicode( annotation ) | h + 'annotation' : h.to_unicode( annotation ), + + ##TODO: broken + 'baseURL' : h.url_for( 'history', show_deleted=show_deleted ), + 'hideDeletedURL' : h.url_for( 'history', show_deleted=False ), + 'hideHiddenURL' : h.url_for( 'history', show_hidden=False ), + 'tagURL' : h.url_for( controller='history', action='tag' ), + 'annotateURL' : h.url_for( controller='history', action='annotate' ) }, - 'annotation' : annotation, - 'hdas' : prepped_hdas, - 'hdaId' : hda_id, - 'showDeleted' : show_deleted, - 'showHidden' : show_hidden, - 'quotaMsg' : over_quota, - 'message' : message, - 'status' : status, + 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], # some of these may be unneeded when all is said and done... - 'forEditing' : True, - - ## maybe security issues... - 'userIsAdmin' : user_is_admin, - 'userRoles' : [ role.get_api_value() for role in user_roles ], - + 'hdaId' : hda_id, + 'forEditing' : for_editing, } %> ${ h.to_json_string( context_dict ) } @@ -307,9 +344,7 @@ ${parent.javascripts()} ${h.js( - "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", - ##"libs/handlebars.full", - "galaxy.autocom_tagging", + "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "mvc/base-mvc", "mvc/ui" )} @@ -324,15 +359,12 @@ "template-history-downloadLinks", "template-history-tagArea", "template-history-annotationArea", - "template-history-displayApps" + "template-history-displayApps", + + "template-history-historyPanel" )} - ## if using in-dom templates they need to go here (before the Backbone classes are defined) - ##NOTE: it's impossible(?) to include _ templates in this way bc they use identical delims as mako - ## (without altering Underscore.templateSettings) - ##<%include file="../../static/scripts/templates/common-templates.html" /> - ##<%include file="../../static/scripts/templates/history-templates.html" /> - + ##TODO: fix: curr hasta be _after_ h.templates - move somehow ${h.js( "mvc/history" ##"mvc/tags", "mvc/annotations" @@ -345,40 +377,34 @@ // Init. on document load. var pageData = ${context_to_js()}; - - //USE_MOCK_DATA = true; - USE_CURR_DATA = true; + if( console && console.debug ){ + window.pageData = pageData; + + ##_.each( pageData.hdas, function( hda ){ + ## console.debug( hda ); + ##}); + } // on ready + USE_CURR_DATA = true; $(function(){ if( console && console.debug ){ console.debug( 'using backbone.js in history panel' ); } - if( window.USE_MOCK_DATA ){ - if( console && console.debug ){ console.debug( '\t using mock data' ); } - createMockHistoryData(); - return; - - //TODO: handle empty history - } else if ( window.USE_CURR_DATA ){ - if( console && console.debug ){ console.debug( '\t using current history data' ); } + if ( window.USE_CURR_DATA ){ + // Navigate to a dataset. + if( pageData.hdaId ){ + self.location = "#" + pageData.hdaId; + } + glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ); glx_history_view = new HistoryView({ model: glx_history }); glx_history_view.render(); return; + + } else { + // sandbox } - - // sandbox here - // testing iconButton - //ibm = new IconButton({ - // icon_class : 'information', - // on_click : function( event ){ console.debug( 'blerg' ); }, - //}); - //mockObj = { one : 1 }; - //ibv = new IconButtonView({ model : ibm }); - //new_click = function( event ){ console.debug( mockObj.one ); } - //$( 'body' ).append( ibv.render().$el ); - }); </script> @@ -387,7 +413,8 @@ <%def name="stylesheets()"> ${parent.stylesheets()} ${h.css("base", "history", "autocomplete_tagging" )} - <style>" + <style> + ## TODO: move to base.less .historyItemBody { display: none; } @@ -425,164 +452,4 @@ ${_('Galaxy History')} </%def> -<body class="historyPage"></body> - -<script type="text/javascript"> -function createMockHistoryData(){ - mockHistory = {}; - mockHistory.data = { - - template : { - id : 'a799d38679e985db', - name : 'template', - data_type : 'fastq', - file_size : 226297533, - genome_build : '?', - metadata_data_lines : 0, - metadata_dbkey : '?', - metadata_sequences : 0, - misc_blurb : '215.8 MB', - misc_info : 'uploaded fastq file (misc_info)', - model_class : 'HistoryDatasetAssociation', - download_url : '', - state : 'ok', - visible : true, - deleted : false, - purged : false, - - hid : 0, - //TODO: move to history - for_editing : true, - //for_editing : false, - - //?? not needed - //can_edit : true, - //can_edit : false, - - accessible : true, - - //TODO: move into model functions (build there (and cache?)) - //!! be careful with adding these accrd. to permissions - //!! IOW, don't send them via template/API if the user doesn't have perms to use - //!! (even if they don't show up) - undelete_url : '', - purge_url : '', - unhide_url : '', - - display_url : 'example.com/display', - edit_url : 'example.com/edit', - delete_url : 'example.com/delete', - - show_params_url : 'example.com/show_params', - rerun_url : 'example.com/rerun', - - retag_url : 'example.com/retag', - annotate_url : 'example.com/annotate', - - peek : [ - '<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>', - '<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>', - '<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>', - '<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>', - '<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>', - '<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>', - '<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>', - '</table>' - ].join( '' ) - } - - }; - _.extend( mockHistory.data, { - - notAccessible : - _.extend( _.clone( mockHistory.data.template ), - { accessible : false }), - - //deleted, purged, visible - deleted : - _.extend( _.clone( mockHistory.data.template ), - { deleted : true, - delete_url : '', - purge_url : 'example.com/purge', - undelete_url : 'example.com/undelete' }), - purgedNotDeleted : - _.extend( _.clone( mockHistory.data.template ), - { purged : true, - delete_url : '' }), - notvisible : - _.extend( _.clone( mockHistory.data.template ), - { visible : false, - unhide_url : 'example.com/unhide' }), - - hasDisplayApps : - _.extend( _.clone( mockHistory.data.template ), - { display_apps : { - 'display in IGB' : { - Web: "/display_application/63cd3858d057a6d1/igb_bam/Web", - Local: "/display_application/63cd3858d057a6d1/igb_bam/Local" - } - } - } - ), - canTrackster : - _.extend( _.clone( mockHistory.data.template ), - { trackster_urls : { - 'data-url' : "example.com/trackster-data", - 'action-url' : "example.com/trackster-action", - 'new-url' : "example.com/trackster-new" - } - } - ), - zeroSize : - _.extend( _.clone( mockHistory.data.template ), - { file_size : 0 }), - - hasMetafiles : - _.extend( _.clone( mockHistory.data.template ), { - download_meta_urls : { - 'bam_index' : "example.com/bam-index" - } - }), - - //states - upload : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.UPLOAD }), - queued : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.QUEUED }), - running : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.RUNNING }), - empty : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.EMPTY }), - error : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.ERROR, - report_error_url: 'example.com/report_err' }), - discarded : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.DISCARDED }), - setting_metadata : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.SETTING_METADATA }), - failed_metadata : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.FAILED_METADATA }) -/* -*/ - }); - - //mockHistory.views.deleted.logger = console; - mockHistory.items = {}; - mockHistory.views = {}; - for( key in mockHistory.data ){ - mockHistory.items[ key ] = new HistoryItem( mockHistory.data[ key ] ); - mockHistory.items[ key ].set( 'name', key ); - mockHistory.views[ key ] = new HistoryItemView({ model : mockHistory.items[ key ] }); - //console.debug( 'view: ', mockHistory.views[ key ] ); - $( 'body' ).append( mockHistory.views[ key ].render() ); - } -} -</script> \ No newline at end of file +<body class="historyPage"></body> \ 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: james_taylor: admin: another import fix
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/78f37cb76a5f/ changeset: 78f37cb76a5f user: james_taylor date: 2012-10-01 22:55:29 summary: admin: another import fix affected #: 1 file diff -r 3c8f65f7e1a4f4217499f2369907a75a8dbcb4e9 -r 78f37cb76a5f981febf36b8119278c59d2319e91 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -4,6 +4,7 @@ from galaxy.model.orm import * from galaxy.util import inflector +from galaxy.web.form_builder import CheckboxField class Admin( object ): # Override these 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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