galaxy-commits May 2014

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commit/galaxy-central: guerler: Charts: Heatmaps revised plugin code, now modularized and enabled for variable data
by commits-noreply＠bitbucket.org 01 May '14

01 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f6561aae5484/ Changeset: f6561aae5484 User: guerler Date: 2014-05-01 21:25:06 Summary: Charts: Heatmaps revised plugin code, now modularized and enabled for variable data Affected #: 3 files diff -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 config/plugins/visualizations/charts/static/charts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js @@ -4,6 +4,7 @@ title : 'Heatmap', library : '', tag : 'div', + use_panels : true, columns : { col_label : { title : 'Columns', diff -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -20,313 +20,215 @@ cellSize: 0, // color buckets - colorBuckets: 0, + nColors: 0, // default settings optionsDefault: { - margin : { + pace : 1000, + margin : { top : 50, right : 10, bottom : 50, left : 100 }, - colors : ['#005824','#1A693B','#347B53','#4F8D6B','#699F83','#83B09B','#9EC2B3','#B8D4CB','#D2E6E3','#EDF8FB','#FFFFFF','#F1EEF6','#E6D3E1','#DBB9CD','#D19EB9','#C684A4','#BB6990','#B14F7C','#A63467','#9B1A53','#91003F'] + colors : ['#005824','#1A693B','#347B53','#4F8D6B','#699F83','#83B09B','#9EC2B3','#B8D4CB','#D2E6E3','#EDF8FB','#FFFFFF','#F1EEF6','#E6D3E1','#DBB9CD','#D19EB9','#C684A4','#BB6990','#B14F7C','#A63467','#9B1A53','#91003F'] }, // initialize initialize: function(options) { + // link this + var self = this; + // load options this.options = Utils.merge(options, this.optionsDefault) - // add ui elements - this.options.div.append(this._templateTooltip()); - this.options.div.append(this._templateSelect()); + // check requirements + if (!this.options.data || !this.options.div) { + console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data) missing.'); + return; + } - // access data - var data = this.options.data; + // link data + this.data = this.options.data; - // identify unique labels - var col_hash = {}; - var row_hash = {}; + // set element + this.setElement(this.options.div); - // create label indices - this.colNumber = 0; - this.rowNumber = 0; - for (var i in data) { - var cell = data[i]; + // + // data indexing + // + + // labels in alphabetical order + this.rowLabel = []; + this.colLabel = []; + + // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting) + this.colRank = {}; + this.rowRank = {}; + + // identify unqiue labels + for (var i in this.data) { + var cell = this.data[i]; // add label to index list var col_label = cell.col_label; - if (col_hash[col_label] === undefined) { - col_hash[col_label] = ++this.colNumber; + if (this.colRank[col_label] === undefined) { + this.colRank[col_label] = true; + this.colLabel.push(col_label); } var row_label = cell.row_label; - if (row_hash[row_label] === undefined) { - row_hash[row_label] = ++this.rowNumber; + if (this.rowRank[row_label] === undefined) { + this.rowRank[row_label] = true; + this.rowLabel.push(row_label); } } - // add indices to data - for (var i in data) { - var cell = data[i]; - cell.col = col_hash[cell.col_label]; - cell.row = row_hash[cell.row_label]; + // set sizes + this.rowNumber = this.rowLabel.length + this.colNumber = this.colLabel.length + + // sort labels alphabetical + this.rowLabel.sort(); + this.colLabel.sort(); + + // generate sorted key list for rows + this.rowIndex = [] + for (var i in this.rowLabel) { + var row_label = this.rowLabel[i]; + var row_index = parseInt(i); + this.rowRank[row_label] = row_index; + + // should contain clustering + this.rowIndex.push(row_index); } - // add row labels - this.rowIndex = [] - for (var key in row_hash) { - this.rowLabel.push(key); - this.rowIndex.push(row_hash[key]); + // generate sorted key list for columns + this.colIndex = [] + for (var i in this.colLabel) { + var col_label = this.colLabel[i]; + var col_index = parseInt(i); + this.colRank[col_label] = col_index; + + // should contain clustering + this.colIndex.push(col_index); } - // add col labels - this.colIndex = [] - for (var key in col_hash) { - this.colLabel.push(key); - this.colIndex.push(col_hash[key]); + // + // parse indexing to cells, identify data range + // + + // min/max + this.max = undefined; + this.min = undefined + + // add indices to data + for (var i in this.data) { + // get cell data + var cell = this.data[i]; + + // add rank + cell.col_rank = this.colRank[cell.col_label]; + cell.row_rank = this.rowRank[cell.row_label]; + + // identify max/min values + if (this.min == undefined || this.min > cell.value) { + this.min = cell.value; + } + if (this.max == undefined || this.max < cell.value) { + this.max = cell.value; + } } - console.log(this.rowIndex); - console.log(this.colIndex); + // middle + this.mid = (this.max + this.min) / 2; + + // + // set colors + // // identify buckets - this.colorBuckets = this.options.colors.length; + this.nColors = this.options.colors.length; + // color scale + this.colorScale = d3.scale.quantile() + .domain([this.min, this.mid, this.max]) + .range(this.options.colors); + + // + // add ui elements + // + // create ui elements + this.$tooltip = $(this._templateTooltip()); + this.$select = $(this._templateSelect()); + + // append + this.$el.append(this.$tooltip); + this.$el.append(this.$select); + + // add event to select field + this.$select.on('change', function(){ + self._order(this.value); + }); + + // // draw - this._draw(this.options.div, this.options.data); + // + this._draw(); }, - _draw: function(container, data) { + _draw: function() { + // link this + var self = this; + + // container + var container_width = this.$el.width(); + var container_height = this.$el.height(); + // get height - this.width = parseInt(container.width()) - this.options.margin.left; - this.height = parseInt(container.height()) - 2*this.options.margin.top; + this.width = this.$el.width() - this.options.margin.left - this.options.margin.right; + this.height = this.$el.height() - this.options.margin.top - this.options.margin.bottom; // calculate cell size - this.cellSize = Math.min( this.height / (this.rowNumber), - this.width / (this.colNumber)); + this.cellSize = Math.min(parseInt(this.height / this.rowNumber), + parseInt(this.width / this.colNumber)); // set width/height for plugin - this.width = this.options.cellSize * this.colNumber; - this.height = this.options.cellSize * this.rowNumber; + this.width = this.cellSize * this.colNumber; + this.height = this.cellSize * this.rowNumber; - // set legend width - this.legendElementWidth = this.options.cellSize * 2.5; - - // configure - var margin = this.options.margin; - var cellSize = this.cellSize; - var colNumber = this.colNumber; - var rowNumber = this.rowNumber; - var colorBuckets = this.colorBuckets; - var colors = this.options.colors; - var rowIndex = this.rowIndex; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - var rowLabel = this.rowLabel; - var width = this.width; - var height = this.height; - var legendElementWidth = this.legendElementWidth; + // get dimensions + var margin = this.options.margin; + var width = this.width; + var height = this.height; - // color scale - var colorScale = d3.scale.quantile() - .domain([ -10, 0, 10]) - .range(colors); - - // add graph - var svg = d3.select(container[0]).append('svg') + // add main group and translate + this.svg = d3.select(this.$el[0]).append('svg') .attr("width", width + margin.left + margin.right) .attr("height", height + margin.top + margin.bottom) .append("g") - .attr("transform", "translate(" + margin.left + "," + margin.top + ")") + .attr("transform", "translate(" + (container_width - width) / 2 + "," + (container_height - height) / 2 + ")") - // row labels - var rowSortOrder=false; - var colSortOrder=false; - var rowLabels = svg.append("g") - .selectAll(".rowLabelg") - .data(rowLabel) - .enter() - .append("text") - .text(function (d) { return d; }) - .attr("x", 0) - .attr("y", function (d, i) { return rowIndex.indexOf(i+1) * cellSize; }) - .style("font-size", cellSize + "px") - .style("text-anchor", "end") - .attr("transform", "translate(-10," + cellSize / 1.5 + ")") - .attr("class", function (d,i) { return "rowLabel mono r"+i;} ) - .on("mouseover", function(d) { - d3.select(this).classed("text-hover",true); - d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); - }) - .on("mouseout" , function(d) { - d3.select(this).classed("text-hover",false); - d3.select(this).style("font-size", parseInt(cellSize) + "px"); - }) - .on("click", function(d,i) {rowSortOrder=!rowSortOrder; sortbylabel("r",i,rowSortOrder);d3.select("#order").property("selectedIndex", 4).node().focus();;}); + // reset sorting + this.rowSortOrder = false; + this.colSortOrder = false; - // column labels - var colLabels = svg.append("g") - .selectAll(".colLabelg") - .data(colLabel) - .enter() - .append("text") - .text(function (d) { return d; }) - .attr("x", 0) - .attr("y", function (d, i) { return colIndex.indexOf(i+1) * cellSize; }) - .style("font-size", cellSize + "px") - .style("text-anchor", "left") - .attr("transform", "translate("+cellSize/2 + ",-17) rotate (-90)") - .attr("class", function (d,i) { return "colLabel mono c"+i;} ) - .on("mouseover", function(d) { - d3.select(this).classed("text-hover",true); - d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); - }) - .on("mouseout" , function(d) { - d3.select(this).classed("text-hover",false); - d3.select(this).style("font-size", parseInt(cellSize) + "px"); - }) - .on("click", function(d,i) {colSortOrder=!colSortOrder; sortbylabel("c",i,colSortOrder);d3.select("#order").property("selectedIndex", 4).node().focus();;}); - - // heat map - var heatMap = svg.append("g").attr("class","g3") - .selectAll(".cellg") - .data(data,function(d){return d.row+":"+d.col;}) - .enter() - .append("rect") - .attr("x", function(d) { return colIndex.indexOf(d.col) * cellSize; }) - .attr("y", function(d) { return rowIndex.indexOf(d.row) * cellSize; }) - .attr("class", function(d){return "cell cell-border cr"+(d.row-1)+" cc"+(d.col-1);}) - .attr("width", cellSize) - .attr("height", cellSize) - .style("fill", function(d) { return colorScale(d.value); }) - // .on("click", function(d) { - // var rowtext=d3.select(".r"+(d.row-1)); - // if(rowtext.classed("text-selected")==false){ - // rowtext.classed("text-selected",true); - // }else{ - // rowtext.classed("text-selected",false); - // } - //}) - .on("mouseover", function(d){ - //highlight text - d3.select(this).classed("cell-hover",true); - d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row-1);}); - d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col-1);}); - //d3.selectAll(".colLabel").style("font-size", parseInt(cellSize * 1.3) + "px"); - //d3.selectAll(".rowLabel").style("font-size", parseInt(cellSize * 1.3) + "px"); - - //Update the tooltip position and value - d3.select("#heatmap-tooltip") - .style("left", (d3.event.pageX+10) + "px") - .style("top", (d3.event.pageY-10) + "px") - .select("#value") - .text("lables:"+rowLabel[d.row-1]+","+colLabel[d.col-1]+"\ndata:"+d.value+"\nrow-col-idx:"+d.col+","+d.row+"\ncell-xy "+this.x.baseVal.value+", "+this.y.baseVal.value); - //Show the tooltip - d3.select("#heatmap-tooltip").classed("hidden", false); - }) - .on("mouseout", function(){ - d3.select(this).classed("cell-hover",false); - d3.selectAll(".rowLabel").classed("text-highlight",false); - d3.selectAll(".colLabel").classed("text-highlight",false); - //d3.selectAll(".colLabel").style("font-size", parseInt(cellSize) + "px"); - //d3.selectAll(".rowLabel").style("font-size", parseInt(cellSize) + "px"); - d3.select("#heatmap-tooltip").classed("hidden", true); - }); - - var legend = svg.selectAll(".legend") - .data([-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,8,9,10]) - .enter().append("g") - .attr("class", "legend"); - - legend.append("rect") - .attr("x", function(d, i) { return legendElementWidth * i; }) - .attr("y", height+(cellSize*2)) - .attr("width", legendElementWidth) - .attr("height", cellSize) - .style("fill", function(d, i) { return colors[i]; }); - - legend.append("text") - .attr("class", "mono") - .text(function(d) { return d; }) - .attr("width", legendElementWidth) - .attr("x", function(d, i) { return legendElementWidth * i; }) - .attr("y", height + (cellSize*4)) - .style("font-size", cellSize + "px"); - - // change ordering of cells - function sortbylabel(rORc,i,sortOrder) { - var t = svg.transition().duration(3000); - var values=[]; - var sorted; // sorted is zero-based index - d3.selectAll(".c"+rORc+i) - .filter(function(ce){ - values.push(ce.value); - }); - if(rORc=="r"){ // sort valuesatio of a gene - sorted=d3.range(colNumber).sort(function(a,b){ if(sortOrder){ return values[b]-values[a];}else{ return values[a]-values[b];}}); - t.selectAll(".cell") - .attr("x", function(d) { return sorted.indexOf(d.col-1) * cellSize; }); - t.selectAll(".colLabel") - .attr("y", function (d, i) { return sorted.indexOf(i) * cellSize; }); - } else { // sort valuesatio of a contrast - sorted=d3.range(rowNumber).sort(function(a,b){if(sortOrder){ return values[b]-values[a];}else{ return values[a]-values[b];}}); - t.selectAll(".cell") - .attr("y", function(d) { return sorted.indexOf(d.row-1) * cellSize; }); - t.selectAll(".rowLabel") - .attr("y", function (d, i) { return sorted.indexOf(i) * cellSize; }); - } - } - - d3.select("#order").on("change",function(){ - order(this.value); - }); - - function order(value) { - if(value=="hclust"){ - var t = svg.transition().duration(3000); - t.selectAll(".cell") - .attr("x", function(d) { return colIndex.indexOf(d.col) * cellSize; }) - .attr("y", function(d) { return rowIndex.indexOf(d.row) * cellSize; }); - - t.selectAll(".rowLabel") - .attr("y", function (d, i) { return rowIndex.indexOf(i+1) * cellSize; }); - - t.selectAll(".colLabel") - .attr("y", function (d, i) { return colIndex.indexOf(i+1) * cellSize; }); - - } else if (value=="probecontrast") { - var t = svg.transition().duration(3000); - t.selectAll(".cell") - .attr("x", function(d) { return (d.col - 1) * cellSize; }) - .attr("y", function(d) { return (d.row - 1) * cellSize; }); - - t.selectAll(".rowLabel") - .attr("y", function (d, i) { return i * cellSize; }); - - t.selectAll(".colLabel") - .attr("y", function (d, i) { return i * cellSize; }); - } else if (value=="probe") { - var t = svg.transition().duration(3000); - t.selectAll(".cell") - .attr("y", function(d) { return (d.row - 1) * cellSize; }); - - t.selectAll(".rowLabel") - .attr("y", function (d, i) { return i * cellSize; }); - } else if (value=="contrast"){ - var t = svg.transition().duration(3000); - t.selectAll(".cell") - .attr("x", function(d) { return (d.col - 1) * cellSize; }); - t.selectAll(".colLabel") - .attr("y", function (d, i) { return i * cellSize; }); - } - } - + // build + this.rowLabels = this._buildRowLabels(); + this.colLabels = this._buildColLabels(); + this.heatMap = this._buildHeatMap(); + this.legend = this._buildLegend(); + }, + + // selection of cells + _addSelectionTool: function() { + // + // selection + // var sa=d3.select(".g3") .on("mousedown", function() { if( !d3.event.altKey) { - d3.selectAll(".cell-selected").classed("cell-selected",false); - d3.selectAll(".rowLabel").classed("text-selected",false); - d3.selectAll(".colLabel").classed("text-selected",false); + d3.selectAll(".cell-selected").classed("cell-selected", false); + d3.selectAll(".rowLabel").classed("text-selected", false); + d3.selectAll(".colLabel").classed("text-selected", false); } var p = d3.mouse(this); sa.append("rect") @@ -374,8 +276,7 @@ // deselect all temporary selected state objects d3.selectAll(".cell-selection.cell-selected").classed("cell-selected", false); d3.selectAll(".text-selection.text-selected").classed("text-selected",false); - - d3.selectAll('.cell').filter(function(cell_d, i) { + d3.selectAll(".cell").filter(function(cell_d, i) { if(!d3.select(this).classed("cell-selected") && // inner circle inside selection frame (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && @@ -385,11 +286,11 @@ .classed("cell-selection", true) .classed("cell-selected", true); - d3.select(".r"+(cell_d.row-1)) + d3.select(".r"+(cell_d.row_rank)) .classed("text-selection",true) .classed("text-selected",true); - d3.select(".c"+(cell_d.col-1)) + d3.select(".c"+(cell_d.col_rank)) .classed("text-selection",true) .classed("text-selected",true); } @@ -417,14 +318,353 @@ }); }, + // build legend + _buildLegend: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var height = this.height; + var legendCellWidth = this.width / this.nColors; + + // create range labels + var dataRange = []; + for(var i = 0; i < this.nColors; i++) { + dataRange.push(''); + } + + // prepare indices + var dataRangeMin = 0; + var dataRangeMid = parseInt((dataRange.length - 1) / 2); + var dataRangeMax = dataRange.length - 1; + + // add labels + dataRange[dataRangeMin] = this.min; + dataRange[dataRangeMid] = this.mid; + dataRange[dataRangeMax] = this.max; + + // create legend + var legend = this.svg.selectAll(".legend") + .data(dataRange) + .enter().append("g") + .attr("class", "legend"); + + // add boxes + legend.append("rect") + .attr("x", function(d, i) { + return legendCellWidth * i; + }) + .attr("y", height + cellSize) + .attr("width", legendCellWidth) + .attr("height", cellSize) + .style("fill", function(d, i) { + return self.options.colors[i]; + }); + + // add text + legend.append("text") + .attr("class", "mono") + .text(function(d) { + return d; + }) + .attr("width", legendCellWidth) + .attr("x", function(d, i) { + return legendCellWidth * i; + }) + .attr("y", height + cellSize) + .style("font-size", cellSize + "px"); + }, + + // build column labels + _buildColLabels: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // column labels + var colLabels = this.svg.append("g") + .selectAll(".colLabelg") + .data(colLabel) + .enter() + .append("text") + .text(function (d) { + return d; + }) + .attr("x", 0) + .attr("y", function (d, i) { + return colIndex.indexOf(i) * cellSize; + }) + .style("font-size", cellSize + "px") + .style("text-anchor", "left") + .attr("transform", "translate(" + cellSize / 2 + ", -17) rotate (-90)") + .attr("class", function (d, i) { + return "colLabel mono c" + i; + }) + .on("mouseover", function(d) { + d3.select(this).classed("text-hover",true); + d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); + }) + .on("mouseout" , function(d) { + d3.select(this).classed("text-hover",false); + d3.select(this).style("font-size", parseInt(cellSize) + "px"); + }) + .on("click", function(d, i) { + self.colSortOrder=!self.colSortOrder; + self._sortByLabel("c", i, self.colSortOrder); + d3.select("#order").property("selectedIndex", 4).node().focus(); + }); + }, + + // build row labels + _buildRowLabels: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + + // draw labels + var rowLabels = this.svg.append("g") + .selectAll(".rowLabelg") + .data(rowLabel) + .enter() + .append("text") + .text(function (d) { + return d; + }) + .attr("x", 0) + .attr("y", function (d, i) { + return rowIndex.indexOf(i) * cellSize; + }) + .style("font-size", cellSize + "px") + .style("text-anchor", "end") + .attr("transform", "translate(-10," + cellSize / 1.5 + ")") + .attr("class", function (d, i) { + return "rowLabel mono r" + i; + } ) + .on("mouseover", function(d) { + d3.select(this).classed("text-hover",true); + d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); + }) + .on("mouseout" , function(d) { + d3.select(this).classed("text-hover",false); + d3.select(this).style("font-size", parseInt(cellSize) + "px"); + }) + .on("click", function(d, i) { + self.rowSortOrder=!self.rowSortOrder; + self._sortByLabel("r", i, self.rowSortOrder); + d3.select("#order").property("selectedIndex", 4).node().focus(); + }); + }, + + // build heat map + _buildHeatMap: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // heat map + var heatMap = this.svg.append("g").attr("class","g3") + .selectAll(".cellg") + .data(self.data, function(d) { + return d.row_rank + ":" + d.col_rank; + }) + .enter() + .append("rect") + .attr("x", function(d) { + return colIndex.indexOf(d.col_rank) * cellSize; + }) + .attr("y", function(d) { + return rowIndex.indexOf(d.row_rank) * cellSize; + }) + .attr("class", function(d){ + return "cell cell-border cr" + d.row_rank + " cc" + d.col_rank; + }) + .attr("width", cellSize) + .attr("height", cellSize) + .style("fill", function(d) { + return self.colorScale(d.value); + }) + .on("mouseover", function(d){ + // highlight text + d3.select(this).classed("cell-hover",true); + d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row_rank);}); + d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col_rank);}); + + // update the tooltip position and value + d3.select("#heatmap-tooltip") + .style("left", (d3.event.pageX+10) + "px") + .style("top", (d3.event.pageY-10) + "px") + .select("#value") + .text("Label: " + rowLabel[d.row_rank] + " | " + colLabel[d.col_rank] + ", Value: " + d.value); + // show the tooltip + d3.select("#heatmap-tooltip").classed("hidden", false); + }) + .on("mouseout", function(){ + d3.select(this).classed("cell-hover",false); + d3.selectAll(".rowLabel").classed("text-highlight",false); + d3.selectAll(".colLabel").classed("text-highlight",false); + d3.select("#heatmap-tooltip").classed("hidden", true); + }); + }, + + // change ordering of cells + _sortByLabel: function(rORc, i, sortOrder) { + // get cell size + var cellSize = this.cellSize; + + // define transition / prepare element + var t = this.svg.transition().duration(this.options.pace); + + // collect cells + var cells=[]; + t.selectAll(".c" + rORc + i) + .filter(function(ce){ + cells.push(ce); + }); + + // sort cells + cells.sort(function(a, b) { + if (sortOrder) { + return b.value - a.value; + } else { + return a.value - b.value; + } + }); + + // rows or columns + if(rORc == "r") { + // get sorted key list + var sorted = []; + for (var i in cells) { + sorted.push(cells[i].col_rank); + } + + // sort cells + t.selectAll(".cell") + .attr("x", function(d) { + return sorted.indexOf(d.col_rank) * cellSize; + }); + + // sort labels + t.selectAll(".colLabel") + .attr("y", function (d, i) { + return sorted.indexOf(i) * cellSize; + }); + } else { + // get sorted key list + sorted = []; + for (var i in cells) { + sorted.push(cells[i].row_rank); + } + + // sort cells + t.selectAll(".cell") + .attr("y", function(d) { + return sorted.indexOf(d.row_rank) * cellSize; + }); + + // sort labels + t.selectAll(".rowLabel") + .attr("y", function (d, i) { + return sorted.indexOf(i) * cellSize; + }); + } + }, + + // sort function + _order: function (value) { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // set duration / select element + var t = this.svg.transition().duration(this.options.pace); + if(value=="hclust"){ + t.selectAll(".cell") + .attr("x", function(d) { + return colIndex.indexOf(d.col_rank) * cellSize; + }) + .attr("y", function(d) { + return rowIndex.indexOf(d.row_rank) * cellSize; + }); + + t.selectAll(".rowLabel") + .attr("y", function(d, i) { + return rowIndex.indexOf(i) * cellSize; + }); + + t.selectAll(".colLabel") + .attr("y", function(d, i) { + return colIndex.indexOf(i) * cellSize; + }); + + } else if (value=="byboth") { + t.selectAll(".cell") + .attr("x", function(d) { + return d.col_rank * cellSize; + }) + .attr("y", function(d) { + return d.row_rank * cellSize; + }); + + t.selectAll(".rowLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + + t.selectAll(".colLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + } else if (value=="byrow") { + t.selectAll(".cell") + .attr("y", function(d) { + return d.row_rank * cellSize; + }); + + t.selectAll(".rowLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + } else if (value=="bycol"){ + t.selectAll(".cell") + .attr("x", function(d) { + return d.col_rank * cellSize; + }); + t.selectAll(".colLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + } + }, + // template _templateSelect: function() { return '<select id="order">' + - '<option value="hclust">by cluster</option>' + - '<option value="probecontrast">by probe name and contrast name</option>' + - '<option value="probe">by probe name</option>' + - '<option value="contrast">by contrast name</option>' + - '<option value="custom">by log2 ratio</option>' + + '<option value="hclust">Cluster</option>' + + '<option value="byboth">Sort by row and column</option>' + + '<option value="byrow">Sort by row label</option>' + + '<option value="bycol">Sort by column label</option>' + '</select>'; }, diff -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js @@ -1,5 +1,5 @@ // dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, Plugin) { +define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { // widget return Backbone.View.extend( @@ -17,13 +17,17 @@ var self = this; this.app.datasets.request(request_dictionary, function() { - console.log(request_dictionary.groups); + // loop through data groups + for (var group_index in request_dictionary.groups) { + // get group + var group = request_dictionary.groups[group_index]; - // draw plot - new Plugin({ - 'data' : request_dictionary.groups[0].values, - 'div' : self.options.canvas[0] - }); + // draw plot + var heatmap = new HeatmapPlugin({ + 'data' : group.values, + 'div' : self.options.canvas[group_index] + }); + } // set chart state chart.state('ok', 'Heat map drawn.'); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History: remove unused server templates history_common, history_item, and history_annotation_table; Pages: remove unused dialog for annotated histories
by commits-noreply＠bitbucket.org 01 May '14

01 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f89fecb2f07/ Changeset: 5f89fecb2f07 User: carlfeberhard Date: 2014-05-01 15:17:19 Summary: History: remove unused server templates history_common, history_item, and history_annotation_table; Pages: remove unused dialog for annotated histories Affected #: 6 files diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -697,16 +697,6 @@ return self._datasets_selection_grid( trans, **kwargs ) @web.expose - @web.require_login("get annotation table for history") - def get_history_annotation_table( self, trans, id ): - """ Returns HTML for an annotation table for a history. """ - history = self.get_history( trans, id, False, True ) - - if history: - datasets = self.get_history_datasets( trans, history ) - return trans.fill_template( "page/history_annotation_table.mako", history=history, datasets=datasets, show_deleted=False ) - - @web.expose def get_editor_iframe( self, trans ): """ Returns the document for the page editor's iframe. """ return trans.fill_template( "page/wymiframe.mako" ) diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -20,10 +20,7 @@ DIALOG_EMBED_DATASET : "embed_dataset", DIALOG_EMBED_WORKFLOW : "embed_workflow", DIALOG_EMBED_PAGE : "embed_page", - DIALOG_EMBED_VISUALIZATION : "embed_visualization", - - // Annotation dialogs. - DIALOG_HISTORY_ANNOTATE : "history_annotate", + DIALOG_EMBED_VISUALIZATION : "embed_visualization" }; // Initialize Galaxy elements. @@ -464,25 +461,8 @@ "</div>" ].join( '' ); // Insert embedded item into document. - //wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. wym.insert(item_embed_html); - // TODO: can we fix this? - // Due to oddities of wym.insert() [likely due to inserting a <div> and/or a complete paragraph], an - // empty paragraph (or two!) may be included either before an embedded item. Remove these paragraphs. - //$("#" + item_elt_id, wym._doc.body).each( function() { - // // Remove previous empty paragraphs. - // var removing = true; - // while (removing) - // { - // var prev_elt = $(this).prev(); - // if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" ) - // prev_elt.remove(); - // else - // removing = false; - // } - //}); - }); hide_modal(); }, @@ -495,55 +475,6 @@ } }); } - - // ANNOTATE HISTORY DIALOG - if ( dialogType == Galaxy.DIALOG_ANNOTATE_HISTORY ) { - $.ajax( - { - url: list_histories_for_selection_url, - data: {}, - error: function() { alert( "Grid refresh failed" ) }, - success: function(table_html) - { - show_modal( - "Insert Link to History", - table_html, - { - "Annotate": function() - { - // Insert links to history for each checked item. - var item_ids = new Array(); - $('input[name=id]:checked').each(function() { - var item_id = $(this).val(); - - // Get annotation table for history. - $.ajax( - { - url: get_history_annotation_table_url, - data: { id : item_id }, - error: function() { alert( "Grid refresh failed" ) }, - success: function(result) - { - // Insert into document. - wym.insert(result); - - init_galaxy_elts(wym); - - } - }); - }); - - hide_modal(); - }, - "Cancel": function() - { - hide_modal(); - } - } - ); - } - }); - } }; $(function(){ diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -19,7 +19,6 @@ set_accessible_url = "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}", get_name_and_link_url = "${h.url_for( controller='ITEM_CONTROLLER', action='get_name_and_link_async' )}?id=", list_histories_for_selection_url = "${h.url_for(controller='page', action='list_histories_for_selection' )}", - get_history_annotation_table_url = "${h.url_for(controller='page', action='get_history_annotation_table' )}", editor_base_path = "${h.url_for('/static/wymeditor')}/", iframe_base_path = "${h.url_for('/static/wymeditor/iframe/galaxy')}/", save_url = "${h.url_for(controller='page', action='save' )}"; diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/page/history_annotation_table.mako --- a/templates/webapps/galaxy/page/history_annotation_table.mako +++ /dev/null @@ -1,61 +0,0 @@ -<%namespace file="../tagging_common.mako" import="render_tagging_element_html" /> -<%namespace file="../root/history_common.mako" import="render_dataset" /> - -<div class="annotated_item"> - <table> - ## Table header. - <tr> - <th colspan='2'>History '${history.get_display_name()}'</th> - </tr> - <tr> - ## Status messages and tags. - <td colspan='2'> - %if history.deleted: - <div class="warningmessagesmall"> - ${_('This is a deleted history.')} - </div> - %endif - ## Tags come for free with community tagging, so not sure if this is necessary. - ##%if trans.get_user() is not None: - ## Tags: ${render_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} - ##%endif - </td> - </tr> - <tr> - <td colspan="2" class="annotation" item_class="History" item_id="${trans.security.encode_id( history.id )}">Description of History: - <ol> - <li>What was the motivation for this history? - <li>What is the outcome of this history? - <li>What are unresolved questions from this history? - <li>What new questions arise from this history? - </ol> - </td> - </tr> - - ## Table body. For each dataset, there is an area to annotate the dataset. - %if not datasets: - <tr> - <td> - <div class="infomessagesmall" id="emptyHistoryMessage"> - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </td> - </tr> - %else: - ## Render requested datasets. - %for data in datasets: - %if data.visible: - <tr> - <td valign="top" class="annotation" item_class="HistoryDatasetAssociation" item_id="${trans.security.encode_id( data.id )}">Describe this step: why was it done? what data did it produce?</td> - ##<td valign="top" class="annotation">Describe this step: why was it done? what data does it produce?</td> - <td> - <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )} - </div> - </td> - </tr> - %endif - %endfor - %endif - </table> -</div> \ No newline at end of file diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/root/history_common.mako --- a/templates/webapps/galaxy/root/history_common.mako +++ /dev/null @@ -1,337 +0,0 @@ -<% _=n_ %> - -<%def name="render_download_links( data, dataset_id )"> - <% - from galaxy.datatypes.metadata import FileParameter - %> - %if not data.purged: - ## Check for downloadable metadata files - <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> - %if meta_files: - <div popupmenu="dataset-${dataset_id}-popup"> - <a class="action-button" href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, \ - to_ext=data.ext )}">Download Dataset</a> - <a>Additional Files</a> - %for file_type in meta_files: - <a class="action-button" href="${h.url_for( controller='/dataset', action='get_metadata_file', \ - hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a> - %endfor - </div> - <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> - %endif - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title='${_("Download")}' class="icon-button disk"></a> - %if meta_files: - </div> - %endif - %endif -</%def> - -## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )"> - <% - dataset_id = trans.security.encode_id( data.id ) - - if data.state in ['no state','',None]: - data_state = "queued" - else: - data_state = data.state - current_user_roles = trans.get_current_user_roles() - can_edit = not ( data.deleted or data.purged ) - %> - %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${dataset_id}"> - %else: - <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${dataset_id}"> - %endif - - %if data.deleted or data.purged or data.dataset.purged: - <div class="warningmessagesmall"><strong> - %if data.dataset.purged or data.purged: - This dataset has been deleted and removed from disk. - %else: - This dataset has been deleted. - %if for_editing: - Click <a href="${h.url_for( controller='dataset', action='undelete', dataset_id=dataset_id )}" class="historyItemUndelete" id="historyItemUndeleter-${dataset_id}" target="galaxy_history">here</a> to undelete - %if trans.app.config.allow_user_dataset_purge: - or <a href="${h.url_for( controller='dataset', action='purge', dataset_id=dataset_id )}" class="historyItemPurge" id="historyItemPurger-${dataset_id}" target="galaxy_history">here</a> to immediately remove it from disk. - %else: - it. - %endif - %endif - %endif - </strong></div> - %endif - - %if data.visible is False: - <div class="warningmessagesmall"> - <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', dataset_id=dataset_id )}" class="historyItemUnhide" id="historyItemUnhider-${dataset_id}" target="galaxy_history">here</a> to unhide.</strong> - </div> - %endif - - ## Header row for history items (name, state, action buttons) - <div style="overflow: hidden;" class="historyItemTitleBar"> - <div class="historyItemButtons"> - %if data_state == "upload": - ## TODO: Make these CSS, just adding a "disabled" class to the normal - ## links should be enough. However the number of datasets being uploaded - ## at a time is usually small so the impact of these images is also small. - <span title='${_("Display Data")}' class='icon-button display_disabled'></span> - %if for_editing: - <span title='Edit Attributes' class='icon-button edit_disabled'></span> - %endif - %else: - <% - if for_editing: - display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) - else: - # Get URL for display only. - if data.history.user and data.history.user.username: - display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', - username=data.history.user.username, slug=dataset_id, filename='' ) - else: - # HACK: revert to for_editing display URL when there is no user/username. This should only happen when - # there's no user/username because dataset is being displayed by history/view after error reported. - # There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug - # check user permissions (to the same degree) before displaying. - display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) - %> - %if data.purged: - <span class="icon-button display_disabled" title="Cannot display datasets removed from disk"></span> - %else: - <a class="icon-button display" dataset_id="${dataset_id}" title='${_("View data")}' href="${display_url}" - %if for_editing: - target="galaxy_main" - %endif - ></a> - %endif - - ## edit attr button - %if for_editing: - %if data.deleted and not data.purged: - <span title="Undelete dataset to edit attributes" class="icon-button edit_disabled"></span> - %elif data.purged: - <span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled"></span> - %else: - <a class="icon-button edit" title='${_("Edit attributes")}' href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a> - %endif - %endif - - %endif - - ## delete button - %if for_editing: - %if can_edit: - <a class="icon-button delete" title='${_("Delete")}' href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a> - %else: - <span title="Dataset is already deleted" class="icon-button delete_disabled"></span> - %endif - %endif - </div> - ## Hack, do it in css - %if data_state == "paused": - <span class="fa fa-pause"></span> - %else: - <span class="state-icon"></span> - %endif - <span class="historyItemTitle">${hid}: ${data.display_name()}</span> - </div> - - ## Body for history items, extra info and actions, data "peek" - - <div id="info${data.id}" class="historyItemBody"> - %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - <div>You do not have permission to view this dataset.</div> - %elif data_state == "upload": - <div>Dataset is uploading</div> - %elif data_state == "queued": - <div>${_('Job is waiting to run')}</div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "paused": - <div> - ${_('Job is currently paused:')} <i>${data.display_info().strip().rstrip('.')}.</i> ${_('Use the history menu to resume.')}</div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "running": - <div>${_('Job is currently running')}</div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "error": - %if not data.purged: - <div>${data.get_size( nice_size=True )}</div> - %endif - <div> - An error occurred running this job: <i>${data.display_info().strip()}</i> - </div> - <div> - %if for_editing: - <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main" title="View or report this error" class="icon-button bug"></a> - %endif - %if data.has_data(): - ${render_download_links( data, dataset_id )} - %endif - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "discarded": - <div> - The job creating this dataset was cancelled before completion. - </div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == 'setting_metadata': - <div>${_('Metadata is being Auto-Detected.')}</div> - %elif data_state == "empty": - <div>${_('No data: ')}<i>${data.display_info()}</i></div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state in [ "ok", "failed_metadata" ]: - %if data_state == "failed_metadata": - <div class="warningmessagesmall" style="margin: 4px 0 4px 0"> - An error occurred setting the metadata for this dataset. - %if can_edit: - You may be able to <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">set it manually or retry auto-detection</a>. - %endif - </div> - %endif - <div> - ${data.blurb}<br /> - ${_("format: ")} <span class="${data.ext}">${data.ext}</span>, - ${_("database: ")} - %if data.dbkey == '?' and can_edit: - <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">${_(data.dbkey)}</a> - %else: - <span class="${data.dbkey}">${_(data.dbkey)}</span> - %endif - </div> - %if data.display_info(): - <div class="info">${_('Info: ')}${data.display_info()}</div> - %endif - <div> - %if data.has_data(): - ${render_download_links( data, dataset_id )} - - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed - ## information--URL base, dataset id, dbkey, visualizations--in anchor. - <% - visualizations = data.get_visualizations() - %> - %if visualizations: - <a href="${h.url_for( controller='visualization' )}" - class="icon-button chart_curve visualize-icon" - title="Visualize" - dataset_id="${dataset_id}" - %if data.dbkey != '?': - dbkey="${data.dbkey}" - %endif - visualizations="${','.join(visualizations)}"></a> - %endif - %if trans.user: - %if not display_structured: - <div style="float: right"> - <a href="${h.url_for( controller='tag', action='retag', item_class=data.__class__.__name__, item_id=dataset_id )}" target="galaxy_main" title="Edit dataset tags" class="icon-button tags"></a> - <a href="${h.url_for( controller='dataset', action='annotate', id=dataset_id )}" target="galaxy_main" title="Edit dataset annotation" class="icon-button annotate"></a> - </div> - %endif - <div style="clear: both"></div> - <div class="tag-area" style="display: none"> - <strong>Tags:</strong> - <div class="tag-elt"></div> - </div> - <div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none"> - <strong>Annotation:</strong> - <div id="${dataset_id}-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt editable-text" title="Edit dataset annotation"></div> - </div> - - %endif - %else: - ## When displaying datasets for viewing, this is often needed to prevent peek from overlapping - ## icons. - <div style="clear: both"></div> - %endif - <div style="clear: both"></div> - %for display_app in data.datatype.get_display_types(): - <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> - %if len( display_links ) > 0: - ${data.datatype.get_display_label(display_app)} - %for display_name, display_link in display_links: - <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> - %endfor - <br /> - %endif - %endfor - %for display_app in data.get_display_applications( trans ).itervalues(): - ${display_app.name} - %for link_app in display_app.links.itervalues(): - <a target="${link_app.url.get( 'target_frame', '_blank' )}" href="${link_app.get_display_url( data, trans )}">${_(link_app.name)}</a> - %endfor - <br /> - %endfor - %elif for_editing: - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - - </div> - %if data.peek != "no peek": - <div><pre id="peek${data.id}" class="peek">${_(h.to_unicode(data.display_peek()))}</pre></div> - %endif - %else: - <div>${_('Error: unknown dataset state "%s".') % data_state}</div> - %endif - - ## Recurse for child datasets - - %if len( data.children ) > 0: - ## FIXME: This should not be in the template, there should - ## be a 'visible_children' method on dataset. - <% - children = [] - for child in data.children: - if child.visible: - children.append( child ) - %> - %if len( children ) > 0: - <div> - There are ${len( children )} secondary datasets. - %for idx, child in enumerate(children): - ${render_dataset( child, idx + 1, show_deleted_on_refresh = show_deleted_on_refresh )} - %endfor - </div> - %endif - %endif - - <div style="clear: both;"></div> - - </div> - - - </div> - -</%def> diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/root/history_item.mako --- a/templates/webapps/galaxy/root/history_item.mako +++ /dev/null @@ -1,3 +0,0 @@ -<%namespace file="history_common.mako" import="render_dataset" /> - -${render_dataset( data, hid )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits May 2014