- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: guerler: Charts: Add zoomable heatmaps, add chart type definition to charts model
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cab2ae91c6a9/ Changeset: cab2ae91c6a9 User: guerler Date: 2014-06-05 00:57:27 Summary: Charts: Add zoomable heatmaps, add chart type definition to charts model Affected #: 19 files diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js @@ -15,7 +15,6 @@ { // finalize configuration chart.settings.set('plotoptions_series_stacking', 'normal'); - chart.settings.set('x_axis_categories', []) // draw chart var hc = new Highcharts(this.app, this.options); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js @@ -15,7 +15,6 @@ { // finalize configuration chart.settings.set('plotoptions_series_stacking', 'normal'); - chart.settings.set('x_axis_categories', []) // draw chart var hc = new Highcharts(this.app, this.options); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js @@ -11,7 +11,7 @@ }, // render - draw : function(process_id, chart, request_dictionary) + draw : function(process_id, chart, request_dictionary, callback) { // configure request var index = 0; @@ -29,7 +29,7 @@ chart.settings.set('legend_enabled', 'false') // create configuration - this.hc_config = configmaker(chart, chart.settings); + this.hc_config = configmaker(chart, callback); // request data var self = this; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js @@ -1,10 +1,14 @@ // dependencies define([], function() { -// widget -return function(chart, settings) { - // highcharts configuration - return { +// highcharts configuration +return function(chart) { + + // get chart settings + var settings = chart.settings; + + // initialize config object + var hc_config = { chart: { type : '', zoomType : 'xy' @@ -23,7 +27,6 @@ }, xAxis: { - categories : settings.get('x_axis_categories'), title: { text : settings.get('x_axis_label') }, @@ -60,7 +63,6 @@ enabled : !(settings.get('y_axis_type') == 'hide') } }, - plotOptions: { series: { animation : false, @@ -89,44 +91,10 @@ }, series: [] - }/*, + } - // highcharts stacking - hc_stacklabels: { - enabled: true, - style: { - fontWeight: 'bold', - color: (Highcharts.theme && Highcharts.theme.textColor) || 'gray' - } - }, - - // initialize - initialize: function(settings) { - // stacking - if (settings.get('x_stacked')) { - this.hc_config.xAxis.stackLabels = this.hc_stacklabels; - this.hc_config.plotOptions.column = { - stacking : 'normal', - dataLabels : { - enabled : true, - color: (Highcharts.theme && Highcharts.theme.dataLabelsColor) || 'white', - style: { - textShadow: '0 0 3px black, 0 0 3px black' - } - } - } - } - - // stacking - if (settings.get('y_stacked')) { - this.hc_config.yAxis.stackLabels = this.hc_stacklabels; - this.hc_config.plotOptions.column = { - stacking : 'normal' - } - } - - console.log(this.hc_config); - }*/ + // callback + return hc_config; }; }); \ No newline at end of file diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js @@ -22,15 +22,13 @@ // render draw : function(process_id, hc_type, chart, request_dictionary, callback) { - // create configuration - this.hc_config = configmaker(chart, chart.settings); - // request data var self = this; this.app.datasets.request(request_dictionary, function() { + // check if this chart has multiple panels if (self.options.canvas.length == 1) { // groups - if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0])) { + if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0], callback)) { // set chart state chart.state('ok', 'Chart drawn.'); } @@ -40,9 +38,9 @@ for (var group_index in request_dictionary.groups) { // get group var group = request_dictionary.groups[group_index]; - + // draw group - if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index])) { + if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index], callback)) { valid = false; break; } @@ -60,9 +58,17 @@ }, // draw all data into a single canvas - _drawGroups: function(hc_type, chart, groups, canvas) { + _drawGroups: function(hc_type, chart, groups, canvas, callback) { + // create configuration + var hc_config = configmaker(chart); + + // make custom wrapper callback + if (callback) { + callback(hc_config); + } + // reset - this.hc_config.series = []; + hc_config.series = []; // loop through data groups for (var key in groups) { @@ -92,12 +98,12 @@ }; // append series - this.hc_config.series.push(hc_series); + hc_config.series.push(hc_series); } // draw plot try { - canvas.highcharts(this.hc_config); + canvas.highcharts(hc_config); return true; } catch (err) { var regex = /\www\.highcharts\.com([^&]+)/; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js @@ -3,18 +3,21 @@ return $.extend(true, {}, config, { title : 'Heatmap', category : 'Data processing (requires \'charts\' tool from Toolshed)', - execute : 'heatmap', + //execute : 'heatmap', use_panels : true, + keywords : 'default highcharts', columns: { - row_label: { + y: { title : 'Row labels', - is_label : true + is_label : true, + is_numeric : true }, - col_label: { + x: { title : 'Column labels', - is_label : true + is_label : true, + is_numeric : true }, - value: { + z: { title : 'Observations', is_numeric : true } diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js @@ -1,5 +1,5 @@ // dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { +define(['plugin/charts/highcharts/common/wrapper'], function(HighchartsWrapper) { // widget return Backbone.View.extend( @@ -13,13 +13,14 @@ // render draw : function(process_id, chart, request_dictionary) { - // finalize configuration - chart.settings.set('plotoptions_series_stacking', 'normal'); - chart.settings.set('x_axis_categories', []) - // draw chart - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'heatmap', chart, request_dictionary); + var hc = new HighchartsWrapper(this.app, this.options); + hc.draw(process_id, 'heatmap', chart, request_dictionary, function(model) { + model.colorAxis = { + minColor : '#00FF99', + maxColor : '#000066' + } + }); } }); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/nvd3/common/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js @@ -198,7 +198,7 @@ show_legend : { title : 'Show legend', info : 'Would you like to add a legend?', - type : 'select', + type : 'radiobutton', init : 'true', data : [ { diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png has changed diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/library/jobs.js --- a/config/plugins/visualizations/charts/static/library/jobs.js +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -60,7 +60,7 @@ var chart_type = chart.get('type'); // get chart settings - var chart_settings = this.app.types.get(chart_type); + var chart_definition = chart.definition; // configure tool data = { @@ -70,7 +70,7 @@ 'id' : chart.get('dataset_id'), 'src' : 'hda' }, - 'module' : chart_settings.execute, + 'module' : chart_definition.execute, 'columns' : columns_string, 'settings' : settings_string } diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/library/storage.js --- a/config/plugins/visualizations/charts/static/library/storage.js +++ b/config/plugins/visualizations/charts/static/library/storage.js @@ -114,6 +114,9 @@ // initiating chart console.debug('Storage::load() - Loading chart type ' + chart_type + '.'); + // parse chart definition + this.chart.definition = chart_definition; + // main this.chart.set(chart_dict.attributes); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/plugins/heatmap/heatmap.css --- a/config/plugins/visualizations/charts/static/plugins/heatmap/heatmap.css +++ /dev/null @@ -1,76 +0,0 @@ -<style> - /* disable text selection */ - svg *::selection { - background : transparent; - } - - svg *::-moz-selection { - background:transparent; - } - - svg *::-webkit-selection { - background:transparent; - } - rect.selection { - stroke : #333; - stroke-dasharray: 4px; - stroke-opacity : 0.5; - fill : transparent; - } - - rect.cell-border { - stroke: #eee; - stroke-width:0.3px; - } - - rect.cell-selected { - stroke: rgb(51,102,153); - stroke-width:0.5px; - } - - rect.cell-hover { - stroke: #F00; - stroke-width:0.3px; - } - - text.mono { - font-size: 9pt; - font-family: Consolas, courier; - fill: #aaa; - } - - text.text-selected { - fill: #000; - } - - text.text-highlight { - fill: #c00; - } - text.text-hover { - fill: #00C; - } - #heatmap-tooltip { - position: absolute; - width: 200px; - height: auto; - padding: 10px; - background-color: white; - -webkit-border-radius: 10px; - -moz-border-radius: 10px; - border-radius: 10px; - -webkit-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4); - -moz-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4); - box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4); - pointer-events: none; - } - - #heatmap-tooltip.hidden { - display: none; - } - - #heatmap-tooltip p { - margin: 0; - font-family: sans-serif; - font-size: 12px; - line-height: 20px; - } \ No newline at end of file diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/plugins/highcharts/heatmap.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/plugins/highcharts/heatmap.js @@ -0,0 +1,21 @@ +/* + Highcharts JS v4.0.1 (2014-04-24) + + (c) 2011-2014 Torstein Honsi + + License: www.highcharts.com/license +*/ +(function(g){var j=g.Axis,x=g.Chart,o=g.Color,y=g.Legend,s=g.LegendSymbolMixin,t=g.Series,u=g.getOptions(),k=g.each,p=g.extend,z=g.extendClass,l=g.merge,q=g.pick,v=g.numberFormat,m=g.seriesTypes,w=g.wrap,n=function(){},r=g.ColorAxis=function(){this.isColorAxis=!0;this.init.apply(this,arguments)};p(r.prototype,j.prototype);p(r.prototype,{defaultColorAxisOptions:{lineWidth:0,gridLineWidth:1,tickPixelInterval:72,startOnTick:!0,endOnTick:!0,offset:0,marker:{animation:{duration:50},color:"gray",width:0.01}, +labels:{overflow:"justify"},minColor:"#EFEFFF",maxColor:"#003875",tickLength:5},init:function(b,a){var d=b.options.legend.layout!=="vertical",c;c=l(this.defaultColorAxisOptions,{side:d?2:1,reversed:!d},a,{isX:d,opposite:!d,showEmpty:!1,title:null,isColor:!0});j.prototype.init.call(this,b,c);a.dataClasses&&this.initDataClasses(a);this.initStops(a);this.isXAxis=!0;this.horiz=d;this.zoomEnabled=!1},tweenColors:function(b,a,d){var c=a.rgba[3]!==1||b.rgba[3]!==1;return(c?"rgba(":"rgb(")+Math.round(a.rgba[0]+ +(b.rgba[0]-a.rgba[0])*(1-d))+","+Math.round(a.rgba[1]+(b.rgba[1]-a.rgba[1])*(1-d))+","+Math.round(a.rgba[2]+(b.rgba[2]-a.rgba[2])*(1-d))+(c?","+(a.rgba[3]+(b.rgba[3]-a.rgba[3])*(1-d)):"")+")"},initDataClasses:function(b){var a=this,d=this.chart,c,e=0,h=this.options;this.dataClasses=c=[];k(b.dataClasses,function(f,i){var g,f=l(f);c.push(f);if(!f.color)h.dataClassColor==="category"?(g=d.options.colors,f.color=g[e++],e===g.length&&(e=0)):f.color=a.tweenColors(o(h.minColor),o(h.maxColor),i/(b.dataClasses.length- +1))})},initStops:function(b){this.stops=b.stops||[[0,this.options.minColor],[1,this.options.maxColor]];k(this.stops,function(a){a.color=o(a[1])})},setOptions:function(b){j.prototype.setOptions.call(this,b);this.options.crosshair=this.options.marker;this.coll="colorAxis"},setAxisSize:function(){var b=this.legendSymbol,a=this.chart,d,c,e;if(b)this.left=d=b.attr("x"),this.top=c=b.attr("y"),this.width=e=b.attr("width"),this.height=b=b.attr("height"),this.right=a.chartWidth-d-e,this.bottom=a.chartHeight- +c-b,this.len=this.horiz?e:b,this.pos=this.horiz?d:c},toColor:function(b,a){var d,c=this.stops,e,h=this.dataClasses,f,i;if(h)for(i=h.length;i--;){if(f=h[i],e=f.from,c=f.to,(e===void 0||b>=e)&&(c===void 0||b<=c)){d=f.color;if(a)a.dataClass=i;break}}else{this.isLog&&(b=this.val2lin(b));d=1-(this.max-b)/(this.max-this.min);for(i=c.length;i--;)if(d>c[i][0])break;e=c[i]||c[i+1];c=c[i+1]||e;d=1-(c[0]-d)/(c[0]-e[0]||1);d=this.tweenColors(e.color,c.color,d)}return d},getOffset:function(){var b=this.legendGroup; +if(b&&(j.prototype.getOffset.call(this),!this.axisGroup.parentGroup))this.axisGroup.add(b),this.gridGroup.add(b),this.labelGroup.add(b),this.added=!0},setLegendColor:function(){var b,a=this.options;b=this.horiz?[0,0,1,0]:[0,0,0,1];this.legendColor={linearGradient:{x1:b[0],y1:b[1],x2:b[2],y2:b[3]},stops:a.stops||[[0,a.minColor],[1,a.maxColor]]}},drawLegendSymbol:function(b,a){var d=b.padding,c=b.options,e=this.horiz,h=q(c.symbolWidth,e?200:12),f=q(c.symbolHeight,e?12:200),c=q(c.labelPadding,e?10:30); +this.setLegendColor();a.legendSymbol=this.chart.renderer.rect(0,b.baseline-11,h,f).attr({zIndex:1}).add(a.legendGroup);a.legendSymbol.getBBox();this.legendItemWidth=h+d+(e?0:c);this.legendItemHeight=f+d+(e?c:0)},setState:n,visible:!0,setVisible:n,getSeriesExtremes:function(){var b;if(this.series.length)b=this.series[0],this.dataMin=b.valueMin,this.dataMax=b.valueMax},drawCrosshair:function(b,a){var d=!this.cross,c=a&&a.plotX,e=a&&a.plotY,h,f=this.pos,i=this.len;if(a)h=this.toPixels(a.value),h<f?h= +f-2:h>f+i&&(h=f+i+2),a.plotX=h,a.plotY=this.len-h,j.prototype.drawCrosshair.call(this,b,a),a.plotX=c,a.plotY=e,!d&&this.cross&&this.cross.attr({fill:this.crosshair.color}).add(this.labelGroup)},getPlotLinePath:function(b,a,d,c,e){return e?this.horiz?["M",e-4,this.top-6,"L",e+4,this.top-6,e,this.top,"Z"]:["M",this.left,e,"L",this.left-6,e+6,this.left-6,e-6,"Z"]:j.prototype.getPlotLinePath.call(this,b,a,d,c)},update:function(b,a){k(this.series,function(a){a.isDirtyData=!0});j.prototype.update.call(this, +b,a);this.legendItem&&(this.setLegendColor(),this.chart.legend.colorizeItem(this,!0))},getDataClassLegendSymbols:function(){var b=this,a=this.chart,d=[],c=a.options.legend,e=c.valueDecimals,h=c.valueSuffix||"",f;k(this.dataClasses,function(c,g){var j=!0,l=c.from,m=c.to;f="";l===void 0?f="< ":m===void 0&&(f="> ");l!==void 0&&(f+=v(l,e)+h);l!==void 0&&m!==void 0&&(f+=" - ");m!==void 0&&(f+=v(m,e)+h);d.push(p({chart:a,name:f,options:{},drawLegendSymbol:s.drawRectangle,visible:!0,setState:n,setVisible:function(){j= +this.visible=!j;k(b.series,function(a){k(a.points,function(a){a.dataClass===g&&a.setVisible(j)})});a.legend.colorizeItem(this,j)}},c))});return d},name:""});w(x.prototype,"getAxes",function(b){var a=this.options.colorAxis;b.call(this);this.colorAxis=[];a&&new r(this,a)});w(y.prototype,"getAllItems",function(b){var a=[],d=this.chart.colorAxis[0];d&&(d.options.dataClasses?a=a.concat(d.getDataClassLegendSymbols()):a.push(d),k(d.series,function(a){a.options.showInLegend=!1}));return a.concat(b.call(this))}); +g={pointAttrToOptions:{stroke:"borderColor","stroke-width":"borderWidth",fill:"color",dashstyle:"dashStyle"},pointArrayMap:["value"],axisTypes:["xAxis","yAxis","colorAxis"],optionalAxis:"colorAxis",trackerGroups:["group","markerGroup","dataLabelsGroup"],getSymbol:n,parallelArrays:["x","y","value"],translateColors:function(){var b=this,a=this.options.nullColor,d=this.colorAxis;k(this.data,function(c){var e=c.value;if(e=e===null?a:d?d.toColor(e,c):c.color||b.color)c.color=e})}};u.plotOptions.heatmap= +l(u.plotOptions.scatter,{animation:!1,borderWidth:0,nullColor:"#F8F8F8",dataLabels:{format:"{point.value}",verticalAlign:"middle",crop:!1,overflow:!1,style:{color:"white",fontWeight:"bold",textShadow:"0 0 5px black"}},marker:null,tooltip:{pointFormat:"{point.x}, {point.y}: {point.value}<br/>"},states:{normal:{animation:!0},hover:{brightness:0.2}}});m.heatmap=z(m.scatter,l(g,{type:"heatmap",pointArrayMap:["y","value"],hasPointSpecificOptions:!0,supportsDrilldown:!0,getExtremesFromAll:!0,init:function(){m.scatter.prototype.init.apply(this, +arguments);this.pointRange=this.options.colsize||1;this.yAxis.axisPointRange=this.options.rowsize||1},translate:function(){var b=this.options,a=this.xAxis,d=this.yAxis;this.generatePoints();k(this.points,function(c){var e=(b.colsize||1)/2,h=(b.rowsize||1)/2,f=Math.round(a.len-a.translate(c.x-e,0,1,0,1)),e=Math.round(a.len-a.translate(c.x+e,0,1,0,1)),g=Math.round(d.translate(c.y-h,0,1,0,1)),h=Math.round(d.translate(c.y+h,0,1,0,1));c.plotX=(f+e)/2;c.plotY=(g+h)/2;c.shapeType="rect";c.shapeArgs={x:Math.min(f, +e),y:Math.min(g,h),width:Math.abs(e-f),height:Math.abs(h-g)}});this.translateColors()},drawPoints:m.column.prototype.drawPoints,animate:n,getBox:n,drawLegendSymbol:s.drawRectangle,getExtremes:function(){t.prototype.getExtremes.call(this,this.valueData);this.valueMin=this.dataMin;this.valueMax=this.dataMax;t.prototype.getExtremes.call(this)}}))})(Highcharts); \ No newline at end of file diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -47,7 +47,7 @@ 'back' : new Ui.ButtonIcon({ icon : 'fa-caret-left', tooltip : 'Return to Viewer', - title : 'Return', + title : 'Cancel', onclick : function() { // show viewport self.app.go('viewer'); @@ -63,15 +63,27 @@ // grid with chart types // this.types = new TypesView(app, { - onchange : function(type) { + onchange : function(chart_type) { + // get chart definition + var chart_definition = self.app.types.get(chart_type); + if (!chart_definition) { + console.debug('FAILED - Editor::onchange() - Chart type not supported.'); + } + + // parse chart definition + self.chart.definition = chart_definition; + // reset type relevant chart content self.chart.settings.clear(); // update chart type - self.chart.set({type: type}); + self.chart.set({type: chart_type}); // set modified flag self.chart.set('modified', true); + + // log + console.debug('Editor::onchange() - Switched chart type.'); }, ondblclick : function(chart_id) { self._saveChart(); @@ -230,6 +242,9 @@ // update titles this._refreshGroupKey(); + + // reset + this.chart.set('modified', true); }, // remove group @@ -252,7 +267,7 @@ _resetChart: function() { // reset chart details this.chart.set('id', Utils.uuid()); - this.chart.set('type', 'nvd3_bar'); + this.chart.set('type', 'highcharts_bar'); this.chart.set('dataset_id', this.app.options.config.dataset_id); this.chart.set('title', 'New Chart'); @@ -262,18 +277,30 @@ // create chart _saveChart: function() { - // ensure that data group is available + // update chart data + this.chart.set({ + type : this.types.value(), + title : this.title.value(), + date : Utils.time() + }); + + // make sure that at least one data group is available if (this.chart.groups.length == 0) { + this.message.update({message: 'Please select data columns before drawing the chart.'}); var group = this._addGroupModel(); this.tabs.show(group.id); return; } - // very selected group columns + // make sure that all necessary columns are assigned var self = this; var valid = true; + var chart_def = this.chart.definition; this.chart.groups.each(function(group) { - for (var key in group.attributes) { + if (!valid) { + return; + } + for (var key in chart_def.columns) { if (group.attributes[key] == 'null') { self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); self.tabs.show(group.id); @@ -290,13 +317,6 @@ // show viewport this.app.go('viewer'); - - // update chart data - this.chart.set({ - type : this.types.value(), - title : this.title.value(), - date : Utils.time() - }); // wait until chart is ready var self = this; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -74,16 +74,16 @@ var self = this; // configure chart type - var chart_settings = this.app.types.get(chart_type); - + var chart_definition = this.chart.definition; + // reset table this.table.delAll(); // load list for select fields var select_list = {}; - for (var id in chart_settings.columns) { + for (var id in chart_definition.columns) { // get definition - var data_def = chart_settings.columns[id]; + var data_def = chart_definition.columns[id]; if (!data_def) { console.debug('Group::_refreshTable() - Skipping column definition.'); continue; @@ -114,7 +114,7 @@ this.app.datasets.request({id : dataset_id}, function(dataset) { // update select fields for (var id in select_list) { - self._addRow(id, dataset, select_list, chart_settings.columns[id]) + self._addRow(id, dataset, select_list, chart_definition.columns[id]) } // loading @@ -126,15 +126,15 @@ }, // add row - _addRow: function(id, dataset, select_list, chart_setting) { + _addRow: function(id, dataset, select_list, column_definition) { // link this var self = this; // is a numeric number required - var is_label = chart_setting.is_label; - var is_auto = chart_setting.is_auto; - var is_numeric = chart_setting.is_numeric; - var is_unique = chart_setting.is_unique; + var is_label = column_definition.is_label; + var is_auto = column_definition.is_auto; + var is_numeric = column_definition.is_numeric; + var is_unique = column_definition.is_unique; // configure columns var columns = []; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/settings.js --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -33,17 +33,14 @@ // update dataset _refresh: function() { - // identify datasets - var chart_type = this.chart.get('type'); + // get settings + var chart_definition = this.chart.definition; // check if dataset is available - if (!chart_type) { + if (!chart_definition) { return; } - // get settings - var chart_definition = this.app.types.get(chart_type); - // set title this.form.title(chart_definition.category + ' - ' + chart_definition.title + ':'); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/types.js --- a/config/plugins/visualizations/charts/static/views/types.js +++ b/config/plugins/visualizations/charts/static/views/types.js @@ -32,13 +32,13 @@ // construct chart type subset selection buttons this.library = new Ui.RadioButton({ data : [ { label: 'Default', value: 'default' }, - { label: 'NVD3 (only)', value: 'nvd3' }, - { label: 'Highcharts (only)', value: 'highcharts' }], + { label: 'Classic', value: 'nvd3' }, + { label: 'Zoomable', value: 'highcharts' }], onchange: function(value) { self._filter(value); } }); - $el.append(Utils.wrap(this.library.$el).css('text-align', 'center')); + $el.append(Utils.wrap(this.library.$el)); // set element this.setElement($el); @@ -86,7 +86,7 @@ var type = types[id]; var $el = this.$el.find('#' + id); var keywords = type.keywords || ''; - if (keywords.indexOf(value) == -1) { + if (keywords.indexOf(value) == -1 && value != 'all') { $el.hide(); } else { $el.show(); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -136,10 +136,10 @@ var chart_type = chart.get('type'); // load chart settings - this.chart_settings = this.app.types.get(chart_type); + this.chart_definition = chart.definition; // read settings - var use_panels = this.chart_settings.use_panels; + var use_panels = this.chart_definition.use_panels; // determine number of svg/div-elements to create var n_panels = 1; @@ -148,14 +148,14 @@ } // create canvas element and add to canvas list - this._createContainer(this.chart_settings.tag, n_panels); + this._createContainer(this.chart_definition.tag, n_panels); // set chart state chart.state('wait', 'Please wait...'); // clean up data if there is any from previous jobs - if (!this.chart_settings.execute || - (this.chart_settings.execute && chart.get('modified'))) { + if (!this.chart_definition.execute || + (this.chart_definition.execute && chart.get('modified'))) { // reset jobs this.app.jobs.cleanup(chart); @@ -171,7 +171,7 @@ var view = new ChartView(self.app, {canvas : self.canvas_list}); // request data - if (self.chart_settings.execute) { + if (self.chart_definition.execute) { self.app.jobs.request(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { view.draw(process_id, chart, self._defaultRequestDictionary(chart)); @@ -203,7 +203,7 @@ group_index++; // add selected columns to column string - for (var key in self.chart_settings.columns) { + for (var key in self.chart_definition.columns) { request_string += key + '_' + group_index + ':' + (parseInt(group.get(key)) + 1) + ', '; } }); @@ -236,7 +236,7 @@ }; // update request dataset id - if (this.chart_settings.execute) { + if (this.chart_definition.execute) { request_dictionary.id = chart.get('dataset_id_job'); } else { request_dictionary.id = chart.get('dataset_id'); @@ -249,9 +249,9 @@ // add columns var columns = {}; - for (var column_key in self.chart_settings.columns) { + for (var column_key in self.chart_definition.columns) { // get settings for column - var column_settings = self.chart_settings.columns[column_key]; + var column_settings = self.chart_definition.columns[column_key]; // add to columns columns[column_key] = { diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -28,10 +28,8 @@ ## install highcharts module ${h.javascript_link( app_root + "plugins/highcharts/highcharts.js" )} ${h.javascript_link( app_root + "plugins/highcharts/highcharts-more.js" )} + ${h.javascript_link( app_root + "plugins/highcharts/heatmap.js" )} - ## install heat map module - ${h.stylesheet_link( app_root + "plugins/heatmap/heatmap.css" )} - ## install boxplot module ##${h.javascript_link( app_root + "plugins/box.js" )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Merge bugfix from stable.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f70167e188f9/ Changeset: f70167e188f9 User: davebgx Date: 2014-06-04 21:15:23 Summary: Merge bugfix from stable. Affected #: 2 files diff -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1694,6 +1694,8 @@ def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" + invalid_file_tups = [] + metadata_dict = {} repository = suc.get_installed_tool_shed_repository( trans, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) 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: davebgx: Fix resetting all metadata based on issue found by Nicola Soranzo.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fb68af9a775a/ Changeset: fb68af9a775a Branch: stable User: davebgx Date: 2014-06-04 21:04:33 Summary: Fix resetting all metadata based on issue found by Nicola Soranzo. Affected #: 1 file diff -r 18777feed30bc0a41e2f46b49e561cd23eb3b564 -r fb68af9a775a956fcc397b22d16f2119401d926d lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1712,6 +1712,8 @@ def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" + invalid_file_tups = [] + metadata_dict = {} repository = suc.get_installed_tool_shed_repository( trans, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) 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: jmchilton: Update LWR client throught LWR changeset 860ba9c.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72bb9c96a5ba/ Changeset: 72bb9c96a5ba User: jmchilton Date: 2014-06-04 19:16:38 Summary: Update LWR client throught LWR changeset 860ba9c. Allows asynchornous submission of LWR jobs to remote servers without a remote LWR service running. LWR still needs to be configured there and job updates are should be configured to be sent back to Galaxy through AMQP. A long running process will be executed on the remote server to monitor the job - while this will always be needed in some cases - for others it would be great to be able to embedded the update steps into the job to be submitted to the DRM itself so that this long running process can be just a submission. This is one more potential step down the road toward allowing remote execution of Galaxy jobs with ever fewer remote constraints. Extensions to this would include allowing Galaxy job updates via the jobs API (along with staging) so MQ becomes optional, allowing auto-configuration of remote LWR application if unavailable or unconfigured, more transfer options (scp), more CLI shell options (fabric, ansible, etc...). Affected #: 7 files diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -402,7 +402,10 @@ def __job_state( self, job, job_wrapper ): job_state = AsynchronousJobState() - job_state.job_id = str( job.get_job_runner_external_id() ) + # TODO: Determine why this is set when using normal message queue updates + # but not CLI submitted MQ updates... + raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id + job_state.job_id = str( raw_job_id ) job_state.runner_url = job_wrapper.get_job_runner_url() job_state.job_destination = job_wrapper.job_destination job_state.job_wrapper = job_wrapper diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -8,6 +8,8 @@ from .decorators import retry from .util import copy from .util import ensure_directory +from .util import to_base64_json + import logging log = logging.getLogger(__name__) @@ -285,16 +287,25 @@ self._raw_execute("download_output", output_params, output_path=output_path) -class MessageJobClient(BaseJobClient): +class BaseMessageJobClient(BaseJobClient): def __init__(self, destination_params, job_id, client_manager): - super(MessageJobClient, self).__init__(destination_params, job_id) + super(BaseMessageJobClient, self).__init__(destination_params, job_id) if not self.job_directory: error_message = "Message-queue based LWR client requires destination define a remote job_directory to stage files into." raise Exception(error_message) self.client_manager = client_manager - def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): + def clean(self): + del self.client_manager.status_cache[self.job_id] + + def full_status(self): + full_status = self.client_manager.status_cache.get(self.job_id, None) + if full_status is None: + raise Exception("full_status() called before a final status was properly cached with cilent manager.") + return full_status + + def _build_setup_message(self, command_line, dependencies_description, env, remote_staging, job_config): """ """ launch_params = dict(command_line=command_line, job_id=self.job_id) @@ -313,21 +324,54 @@ # before queueing. setup_params = _setup_params_from_job_config(job_config) launch_params["setup_params"] = setup_params + return launch_params + + +class MessageJobClient(BaseMessageJobClient): + + def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): + """ + """ + launch_params = self._build_setup_message( + command_line, + dependencies_description=dependencies_description, + env=env, + remote_staging=remote_staging, + job_config=job_config + ) response = self.client_manager.exchange.publish("setup", launch_params) log.info("Job published to setup message queue.") return response - def clean(self): - del self.client_manager.status_cache[self.job_id] + def kill(self): + self.client_manager.exchange.publish("kill", dict(job_id=self.job_id)) - def full_status(self): - full_status = self.client_manager.status_cache.get(self.job_id, None) - if full_status is None: - raise Exception("full_status() called before a final status was properly cached with cilent manager.") - return full_status + +class MessageCLIJobClient(BaseMessageJobClient): + + def __init__(self, destination_params, job_id, client_manager, shell): + super(MessageCLIJobClient, self).__init__(destination_params, job_id, client_manager) + self.remote_lwr_path = destination_params["remote_lwr_path"] + self.shell = shell + + def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): + """ + """ + launch_params = self._build_setup_message( + command_line, + dependencies_description=dependencies_description, + env=env, + remote_staging=remote_staging, + job_config=job_config + ) + base64_message = to_base64_json(launch_params) + submit_command = os.path.join(self.remote_lwr_path, "scripts", "submit.bash") + # TODO: Allow configuration of manager, app, and ini path... + self.shell.execute("nohup %s --base64 %s &" % (submit_command, base64_message)) def kill(self): - self.client_manager.exchange.publish("kill", dict(job_id=self.job_id)) + # TODO + pass class InputCachingJobClient(JobClient): diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/interface.py --- a/lib/galaxy/jobs/runners/lwr_client/interface.py +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -78,8 +78,8 @@ def execute(self, command, args={}, data=None, input_path=None, output_path=None): # If data set, should be unicode (on Python 2) or str (on Python 3). - from lwr import routes - from lwr.framework import build_func_args + from lwr.web import routes + from lwr.web.framework import build_func_args controller = getattr(routes, command) action = controller.func body_args = dict(body=self.__build_body(data, input_path)) diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -8,6 +8,7 @@ from .client import JobClient from .client import InputCachingJobClient from .client import MessageJobClient +from .client import MessageCLIJobClient from .interface import HttpLwrInterface from .interface import LocalLwrInterface from .object_client import ObjectStoreClient @@ -71,6 +72,12 @@ pass +try: + from galaxy.jobs.runners.util.cli import factory as cli_factory +except ImportError: + from lwr.managers.util.cli import factory as cli_factory + + class MessageQueueClientManager(object): def __init__(self, **kwds): @@ -90,7 +97,8 @@ def callback_wrapper(body, message): try: if "job_id" in body: - self.status_cache[body["job_id"]] = body + job_id = body["job_id"] + self.status_cache[job_id] = body log.debug("Handling asynchronous status update from remote LWR.") callback(body) except Exception: @@ -116,9 +124,15 @@ return self.active def get_client(self, destination_params, job_id, **kwargs): + if job_id is None: + raise Exception("Cannot generate LWR client for empty job_id.") destination_params = _parse_destination_params(destination_params) destination_params.update(**kwargs) - return MessageJobClient(destination_params, job_id, self) + if 'shell_plugin' in destination_params: + shell = cli_factory.get_shell(destination_params) + return MessageCLIJobClient(destination_params, job_id, self, shell) + else: + return MessageJobClient(destination_params, job_id, self) class ObjectStoreClientManager(object): diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -7,6 +7,8 @@ import os.path import hashlib import shutil +import json +import base64 def unique_path_prefix(path): @@ -70,6 +72,20 @@ if key.startswith(prefix)]) +def to_base64_json(data): + """ + + >>> x = from_base64_json(to_base64_json(dict(a=5))) + >>> x["a"] + 5 + """ + return base64.b64encode(json.dumps(data)) + + +def from_base64_json(data): + return json.loads(base64.b64decode(data)) + + class PathHelper(object): ''' diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/util/cli/__init__.py --- a/lib/galaxy/jobs/runners/util/cli/__init__.py +++ b/lib/galaxy/jobs/runners/util/cli/__init__.py @@ -43,11 +43,19 @@ Return shell and job interface defined by and configured via specified params. """ + shell = self.get_shell_plugin(shell_params) + job_interface = self.get_job_interface(job_params) + return shell, job_interface + + def get_shell_plugin(self, shell_params): shell_plugin = shell_params.get('plugin', DEFAULT_SHELL_PLUGIN) + shell = self.cli_shells[shell_plugin](**shell_params) + return shell + + def get_job_interface(self, job_params): job_plugin = job_params['plugin'] - shell = self.cli_shells[shell_plugin](**shell_params) job_interface = self.cli_job_interfaces[job_plugin](**job_params) - return shell, job_interface + return job_interface def split_params(params): diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/util/cli/factory.py --- /dev/null +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -0,0 +1,18 @@ +try: + from galaxy.jobs.runners.util.cli import ( + CliInterface, + split_params + ) + code_dir = 'lib' +except ImportError: + from lwr.managers.util.cli import ( + CliInterface, + split_params + ) + code_dir = '.' + + +def get_shell(params): + cli_interface = CliInterface(code_dir=code_dir) + shell_params, _ = split_params(params) + return cli_interface.get_shell_plugin(shell_params) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18777feed30b/ Changeset: 18777feed30b Branch: stable User: dan Date: 2014-06-04 17:05:36 Summary: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided. Affected #: 1 file diff -r c68aa8a8e769437473bd23586d1b55fc66cc8c47 -r 18777feed30bc0a41e2f46b49e561cd23eb3b564 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -448,6 +448,8 @@ # Handle secure / insecure Tool Shed URL protocol changes and port changes. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' ) + # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided + url = urllib2.urlopen( urllib2.Request( url ) ).geturl() request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) ) response = urllib2.urlopen( request ).read() if response: 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: dan: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d6b71244ff9/ Changeset: 3d6b71244ff9 User: dan Date: 2014-06-04 17:05:36 Summary: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided. Affected #: 1 file diff -r 819818c880b543d9ef32aa61a099235c20937dae -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -447,6 +447,8 @@ # Handle secure / insecure Tool Shed URL protocol changes and port changes. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' ) + # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided + url = urllib2.urlopen( urllib2.Request( url ) ).geturl() request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) ) response = urllib2.urlopen( request ).read() if response: 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: Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/819818c880b5/ Changeset: 819818c880b5 User: greg Date: 2014-06-04 15:21:18 Summary: Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string. Affected #: 1 file diff -r 0cb88fa06c32e13c8881ed90af02b239aa574313 -r 819818c880b543d9ef32aa61a099235c20937dae lib/tool_shed/scripts/api/common.py --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -197,7 +197,7 @@ print e.read( 1024 ) sys.exit( 1 ) else: - return 'Error. '+ str( e.read( 1024 ) ) + return dict( status='error', message=str( e.read( 1024 ) ) ) if not return_formatted: return r print 'Response' 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: dan: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c68aa8a8e769/ Changeset: c68aa8a8e769 Branch: stable User: dan Date: 2014-06-03 23:03:17 Summary: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm Affected #: 1 file diff -r f9c050410d6a56d7f6fe503b4f22f286bd5a40e2 -r c68aa8a8e769437473bd23586d1b55fc66cc8c47 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -738,6 +738,8 @@ return rval elif app_action == None: #redirect user to url generated by display link + #Fix for Safari caching display links, which can change if the underlying dataset has an attribute change, e.g. name, metadata, etc + trans.response.headers[ 'Cache-Control' ] = [ 'no-cache', 'max-age=0', 'no-store', 'must-revalidate' ] return trans.response.send_redirect( display_link.display_url() ) else: msg.append( ( 'Invalid action provided: %s' % app_action, 'error' ) ) 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: guerler: Charts: Improve notifications and error handling
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0cb88fa06c32/ Changeset: 0cb88fa06c32 User: guerler Date: 2014-06-04 09:54:54 Summary: Charts: Improve notifications and error handling Affected #: 4 files diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js @@ -30,22 +30,28 @@ this.app.datasets.request(request_dictionary, function() { if (self.options.canvas.length == 1) { // groups - self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0]); - - // set chart state - chart.state('ok', 'Chart drawn.'); + if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0])) { + // set chart state + chart.state('ok', 'Chart drawn.'); + } } else { // loop through data groups + var valid = true; for (var group_index in request_dictionary.groups) { // get group var group = request_dictionary.groups[group_index]; // draw group - self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index]); + if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index])) { + valid = false; + break; + } } // set chart state - chart.state('ok', 'Multi-panel chart drawn.'); + if (valid) { + chart.state('ok', 'Multi-panel chart drawn.'); + } } // unregister process @@ -90,7 +96,19 @@ } // draw plot - canvas.highcharts(this.hc_config); + try { + canvas.highcharts(this.hc_config); + return true; + } catch (err) { + var regex = /\www\.highcharts\.com([^&]+)/; + var match = err.match(regex); + if (match.length > 0) { + chart.state('failed', 'Highcharts error: <a target="_blank" href="http://' + match[0] + '">' + match[0] + '</a>'); + } else { + chart.state('failed', err); + } + return false; + } } }); diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -28,6 +28,9 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); + // message element + this.message = new Ui.Message(); + // create portlet this.portlet = new Portlet.View({ icon : 'fa-bar-chart-o', @@ -38,10 +41,6 @@ tooltip : 'Draw Chart', title : 'Draw', onclick : function() { - // show viewport - self.app.go('viewer'); - - // save chart self._saveChart(); } }), @@ -75,10 +74,6 @@ self.chart.set('modified', true); }, ondblclick : function(chart_id) { - // show viewport - self.app.go('viewer'); - - // save chart self._saveChart(); } }); @@ -135,6 +130,7 @@ }); // append tabs + this.portlet.append(this.message.$el); this.portlet.append(this.tabs.$el); // elements @@ -266,6 +262,35 @@ // create chart _saveChart: function() { + // ensure that data group is available + if (this.chart.groups.length == 0) { + var group = this._addGroupModel(); + this.tabs.show(group.id); + return; + } + + // very selected group columns + var self = this; + var valid = true; + this.chart.groups.each(function(group) { + for (var key in group.attributes) { + if (group.attributes[key] == 'null') { + self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); + self.tabs.show(group.id); + valid = false; + return; + } + } + }); + + // validate if columns have been selected + if (!valid) { + return; + } + + // show viewport + this.app.go('viewer'); + // update chart data this.chart.set({ type : this.types.value(), @@ -273,11 +298,6 @@ date : Utils.time() }); - // ensure that data group is available - if (this.chart.groups.length == 0) { - this._addGroupModel(); - } - // wait until chart is ready var self = this; this.chart.deferred.execute(function() { diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -21,6 +21,9 @@ // link this var self = this; + // message element + this.message = new Ui.Message(); + // create portlet this.portlet = new Portlet.View({ icon : 'fa-bar-chart-o', @@ -53,6 +56,7 @@ }); // append portlet + this.portlet.append(this.message.$el); this.portlet.append(this.viewport_view.$el); // set element @@ -91,22 +95,7 @@ if (chart.deferred.ready()) { callback(); } else { - // show modal - var self = this; - this.app.modal.show({ - title : 'Please wait!', - body : 'Your chart is currently being processed. Please wait and try again.', - buttons : { - 'Close' : function() {self.app.modal.hide();}, - 'Retry' : function() { - // hide modal - self.app.modal.hide(); - - // retry - setTimeout(function() { self._wait(chart, callback); }, self.app.config.get('query_timeout')); - } - } - }); + this.message.update({message: 'Your chart is currently being processed. Please wait and try again.'}); } } }); diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -39,7 +39,7 @@ this.chart.on('set:state', function() { // get info element var $info = self.$el.find('#info'); - var $container = self.$el.find('container'); + var $container = self.$el.find('.charts-viewport-container'); // get icon var $icon = $info.find('#icon'); @@ -51,21 +51,20 @@ $info.show(); $info.find('#text').html(self.chart.get('state_info')); - // hide containers - $container.hide(); - // check status var state = self.chart.get('state'); switch (state) { case 'ok': $info.hide(); - $container.show() + $container.show(); break; case 'failed': $icon.addClass('icon fa fa-warning'); + $container.hide(); break; default: $icon.addClass('icon fa fa-spinner fa-spin'); + $container.show(); } }); }, @@ -182,7 +181,6 @@ } ); } else { - // load data into view view.draw(process_id, chart, self._defaultRequestDictionary(chart)); } }); 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: guerler: Charts: Extend boxplot options
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c1a51c9f85f/ Changeset: 9c1a51c9f85f User: guerler Date: 2014-06-04 08:10:32 Summary: Charts: Extend boxplot options Affected #: 3 files diff -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb -r 9c1a51c9f85f52d4570dede166155700130d8234 config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js @@ -1,6 +1,6 @@ -define([], function() { +define(['plugin/charts/highcharts/common/config'], function(config) { -return $.extend(true, {}, { +return $.extend(true, {}, config, { title : 'Box plot', category : 'Data processing (requires \'charts\' tool from Toolshed)', library : 'Highcharts', diff -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb -r 9c1a51c9f85f52d4570dede166155700130d8234 config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js @@ -29,7 +29,7 @@ chart.settings.set('legend_enabled', 'false') // create configuration - this.hc_config = configmaker(chart.settings); + this.hc_config = configmaker(chart, chart.settings); // request data var self = this; diff -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb -r 9c1a51c9f85f52d4570dede166155700130d8234 config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js @@ -36,6 +36,8 @@ }, labels: { formatter : function() { + if (settings.get('x_axis_type') == 'auto') + return this.value; var format = d3.format(settings.get('x_axis_tick') + settings.get('x_axis_type')); return format(this.value); }, @@ -50,6 +52,8 @@ }, labels: { formatter : function() { + if (settings.get('y_axis_type') == 'auto') + return this.value; var format = d3.format(settings.get('y_axis_tick') + settings.get('y_axis_type')); return format(this.value); }, 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: guerler: Charts: Remove helper function
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c93e85d8ac0d/ Changeset: c93e85d8ac0d User: guerler Date: 2014-06-04 07:52:58 Summary: Charts: Remove helper function Affected #: 1 file diff -r 2df424fc0536831e49b09d4d2ffa3a111fba1282 -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js @@ -3,15 +3,6 @@ // widget return function(chart, settings) { - // helper label enabled - var labelEnabled = function(axis) { - if (settings.get(axis + '_type') == 'hide') { - return false; - } else { - return true; - } - }; - // highcharts configuration return { chart: { @@ -48,7 +39,7 @@ var format = d3.format(settings.get('x_axis_tick') + settings.get('x_axis_type')); return format(this.value); }, - enabled : labelEnabled('x_axis') + enabled : !(settings.get('x_axis_type') == 'hide') }, tickPixelInterval : 100 }, @@ -62,7 +53,7 @@ var format = d3.format(settings.get('y_axis_tick') + settings.get('y_axis_type')); return format(this.value); }, - enabled : labelEnabled('y_axis') + enabled : !(settings.get('y_axis_type') == 'hide') } }, 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: guerler: Charts: Adding chart subset selection filter, setting zoomable charts as default
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

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commit/galaxy-central: dannon: Pack scripts.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1be07de86c2a/ Changeset: 1be07de86c2a User: dannon Date: 2014-06-03 23:42:17 Summary: Pack scripts. Affected #: 1 file diff -r e33a715ee045acac64b9e8e4ac14bcdc31ef6ca7 -r 1be07de86c2a606518a7cfc2913230c29a7210f8 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false;s.hide()}})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false}s.hide()})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file 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: dannon: Stop loading indicator at the end of get_next_chunk regardless of result.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e33a715ee045/ Changeset: e33a715ee045 User: dannon Date: 2014-06-03 23:40:00 Summary: Stop loading indicator at the end of get_next_chunk regardless of result. Affected #: 1 file diff -r 58a057a02b896ae6d32571f7141f46ccb9006e54 -r e33a715ee045acac64b9e8e4ac14bcdc31ef6ca7 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -180,8 +180,8 @@ if (result) { self._renderChunk(result); loading_chunk = false; - loading_indicator.hide(); } + loading_indicator.hide(); }); } }); 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: davebgx: Merge fix from stable.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/58a057a02b89/ Changeset: 58a057a02b89 User: davebgx Date: 2014-06-03 23:04:13 Summary: Merge fix from stable. Affected #: 1 file diff -r d1d3a8f09b2bcaf23962310f5d535758823e13d7 -r 58a057a02b896ae6d32571f7141f46ccb9006e54 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -623,11 +623,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', install_dir ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) basic_util.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -881,11 +881,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( trans.app ) ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) 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: dan: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1d3a8f09b2b/ Changeset: d1d3a8f09b2b User: dan Date: 2014-06-03 23:03:17 Summary: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm Affected #: 1 file diff -r 72dea09e14ab6e87e7537b23f8c9af2cd6f50c6b -r d1d3a8f09b2bcaf23962310f5d535758823e13d7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -738,6 +738,8 @@ return rval elif app_action == None: #redirect user to url generated by display link + #Fix for Safari caching display links, which can change if the underlying dataset has an attribute change, e.g. name, metadata, etc + trans.response.headers[ 'Cache-Control' ] = [ 'no-cache', 'max-age=0', 'no-store', 'must-revalidate' ] return trans.response.send_redirect( display_link.display_url() ) else: msg.append( ( 'Invalid action provided: %s' % app_action, 'error' ) ) 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: davebgx: Add change that was lost when resolving a merge conflict.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f9c050410d6a/ Changeset: f9c050410d6a Branch: stable User: davebgx Date: 2014-06-03 22:52:18 Summary: Add change that was lost when resolving a merge conflict. Affected #: 1 file diff -r 96fdb9168f28b2ffa463195d084c9278efb2465a -r f9c050410d6a56d7f6fe503b4f22f286bd5a40e2 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -622,11 +622,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -880,11 +880,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( trans.app ) ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) 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: Fix import in the Tool Shed's common_install_util module.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72dea09e14ab/ Changeset: 72dea09e14ab User: greg Date: 2014-06-03 22:34:59 Summary: Fix import in the Tool Shed's common_install_util module. Affected #: 1 file diff -r 465b390ffeeda37663b92de91c1fa50a46743292 -r 72dea09e14ab6e87e7537b23f8c9af2cd6f50c6b lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -18,7 +18,6 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager log = logging.getLogger( __name__ ) 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: davebgx: Merge in set_environment bugfix from stable.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/465b390ffeed/ Changeset: 465b390ffeed User: davebgx Date: 2014-06-03 22:09:03 Summary: Merge in set_environment bugfix from stable. Affected #: 6 files diff -r beef22110c25635ed18a3c24f9d94442a4a4cc9c -r 465b390ffeeda37663b92de91c1fa50a46743292 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 @@ -465,11 +465,11 @@ tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) diff -r beef22110c25635ed18a3c24f9d94442a4a4cc9c -r 465b390ffeeda37663b92de91c1fa50a46743292 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -187,7 +187,6 @@ a partial or full list of ToolDependency records associated with the tool_shed_repository. """ tag_manager = TagManager() - sa_session = app.install_model.context # The value of package_name should match the value of the "package" type in the tool config's # <requirements> tag set, but it's not required. package_name = elem.get( 'name', None ) diff -r beef22110c25635ed18a3c24f9d94442a4a4cc9c -r 465b390ffeeda37663b92de91c1fa50a46743292 lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -97,7 +97,8 @@ return tool_dependency, proceed_with_install, action_elem_tuples def load_tag_handlers( self ): - tag_handlers = dict( install=tag_handler.Install(), + tag_handlers = dict( environment_variable=tag_handler.SetEnvironment(), + install=tag_handler.Install(), package=tag_handler.Package(), readme=tag_handler.ReadMe(), repository=tag_handler.Repository(), diff -r beef22110c25635ed18a3c24f9d94442a4a4cc9c -r 465b390ffeeda37663b92de91c1fa50a46743292 lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -446,9 +446,12 @@ def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): + # We need to handle two tag sets for package_elem here, this: # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> # </set_environment> + # or this: + # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> action_elem_tuples = [] proceed_with_install = False if tool_dependency_db_records is None: @@ -479,6 +482,9 @@ <set_environment version="1.0"><environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable></set_environment> + + This method must also handle the sub-element tag:: + <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> """ # TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like # the following. See the implementation of support for this in the tool dependency package type's method above. @@ -495,11 +501,19 @@ tool_dependencies = [] env_var_version = elem.get( 'version', '1.0' ) tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( app ) ) - for env_var_elem in elem: - # Althoug we're in a loop here, this method will always return only a single ToolDependency or None. + if elem.tag == 'environment_variable': + # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + elems = [ elem ] + else: + # <set_environment version="1.0"> + # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + # </set_environment> + elems = [ env_var_elem for env_var_elem in elem ] + for env_var_elem in elems: env_var_name = env_var_elem.get( 'name', None ) - # The value of env_var_name must match the text value of at least 1 <requirement> tag in the tool config's <requirements> tag set whose - # "type" attribute is "set_environment" (e.g., <requirement type="set_environment">R_SCRIPT_PATH</requirement>). + # The value of env_var_name must match the text value of at least 1 <requirement> tag in the + # tool config's <requirements> tag set whose "type" attribute is "set_environment" (e.g., + # <requirement type="set_environment">R_SCRIPT_PATH</requirement>). env_var_action = env_var_elem.get( 'action', None ) if env_var_name and env_var_action: # Tool dependencies of type "set_environmnet" always have the version attribute set to None. diff -r beef22110c25635ed18a3c24f9d94442a4a4cc9c -r 465b390ffeeda37663b92de91c1fa50a46743292 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -447,11 +447,11 @@ # Get the tool_dependencies.xml file from disk. tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=self.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=True ) + common_install_util.install_specified_tool_dependencies( app=self.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=True ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' diff -r beef22110c25635ed18a3c24f9d94442a4a4cc9c -r 465b390ffeeda37663b92de91c1fa50a46743292 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -18,6 +18,7 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install.install_manager import InstallManager +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager log = logging.getLogger( __name__ ) @@ -483,7 +484,8 @@ all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict -def install_specified_packages( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_tool_migration_manager=False ): +def install_specified_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, + from_tool_migration_manager=False ): """ Follow the recipe in the received tool_dependencies_config to install specified packages for repository tools. The received list of tool_dependencies are the database records for those @@ -502,28 +504,46 @@ log.debug( "The received tool_dependencies.xml file is likely invalid: %s" % str( error_message ) ) return installed_packages root = tree.getroot() + elems = [] for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - attr_tup = ( package_name, package_version, 'package' ) + if elem.tag == 'set_environment': + version = elem.get( 'version', '1.0' ) + if version != '1.0': + raise Exception( 'The <set_environment> tag must have a version attribute with value 1.0' ) + for sub_elem in elem: + elems.append( sub_elem ) + else: + elems.append( elem ) + for elem in elems: + name = elem.get( 'name', None ) + version = elem.get( 'version', None ) + type = elem.get( 'type', None ) + if type is None: + if elem.tag in [ 'environment_variable', 'set_environment' ]: + type = 'set_environment' + else: + type = 'package' + if ( name and type == 'set_environment' ) or ( name and version ): + # elem is a package set_environment tag set. + attr_tup = ( name, version, type ) try: index = attr_tups_of_dependencies_for_install.index( attr_tup ) except Exception, e: index = None if index is not None: tool_dependency = tool_dependencies[ index ] + # If the tool_dependency.type is 'set_environment', then the call to process_tag_set() will + # handle everything - no additional installation is necessary. tool_dependency, proceed_with_install, action_elem_tuples = \ tag_manager.process_tag_set( app, tool_shed_repository, tool_dependency, elem, - package_name, - package_version, + name, + version, from_tool_migration_manager=from_tool_migration_manager, tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: + if ( tool_dependency.type == 'package' and proceed_with_install ): try: tool_dependency = install_manager.install_package( app, elem, @@ -531,8 +551,8 @@ tool_dependencies=tool_dependencies, from_tool_migration_manager=from_tool_migration_manager ) except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) + error_message = "Error installing tool dependency %s version %s: %s" % \ + ( str( name ), str( version ), str( e ) ) log.exception( error_message ) if tool_dependency: # Since there was an installation error, update the tool dependency status to Error. The 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: Fix for installing tool dependencies with type set_environment.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96fdb9168f28/ Changeset: 96fdb9168f28 Branch: stable User: greg Date: 2014-06-03 21:34:53 Summary: Fix for installing tool dependencies with type set_environment. Affected #: 6 files diff -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 -r 96fdb9168f28b2ffa463195d084c9278efb2465a 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 @@ -471,11 +471,11 @@ tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) diff -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 -r 96fdb9168f28b2ffa463195d084c9278efb2465a lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -182,7 +182,6 @@ a partial or full list of ToolDependency records associated with the tool_shed_repository. """ tag_manager = TagManager() - sa_session = app.install_model.context # The value of package_name should match the value of the "package" type in the tool config's # <requirements> tag set, but it's not required. package_name = elem.get( 'name', None ) diff -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 -r 96fdb9168f28b2ffa463195d084c9278efb2465a lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -97,7 +97,8 @@ return tool_dependency, proceed_with_install, action_elem_tuples def load_tag_handlers( self ): - tag_handlers = dict( install=tag_handler.Install(), + tag_handlers = dict( environment_variable=tag_handler.SetEnvironment(), + install=tag_handler.Install(), package=tag_handler.Package(), readme=tag_handler.ReadMe(), repository=tag_handler.Repository(), diff -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 -r 96fdb9168f28b2ffa463195d084c9278efb2465a lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -437,9 +437,12 @@ def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): + # We need to handle two tag sets for package_elem here, this: # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> # </set_environment> + # or this: + # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> action_elem_tuples = [] proceed_with_install = False if tool_dependency_db_records is None: @@ -470,6 +473,9 @@ <set_environment version="1.0"><environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable></set_environment> + + This method must also handle the sub-element tag:: + <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> """ # TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like # the following. See the implementation of support for this in the tool dependency package type's method above. @@ -485,11 +491,19 @@ tool_dependencies = [] env_var_version = elem.get( 'version', '1.0' ) tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( app ) ) - for env_var_elem in elem: - # Althoug we're in a loop here, this method will always return only a single ToolDependency or None. + if elem.tag == 'environment_variable': + # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + elems = [ elem ] + else: + # <set_environment version="1.0"> + # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + # </set_environment> + elems = [ env_var_elem for env_var_elem in elem ] + for env_var_elem in elems: env_var_name = env_var_elem.get( 'name', None ) - # The value of env_var_name must match the text value of at least 1 <requirement> tag in the tool config's <requirements> tag set whose - # "type" attribute is "set_environment" (e.g., <requirement type="set_environment">R_SCRIPT_PATH</requirement>). + # The value of env_var_name must match the text value of at least 1 <requirement> tag in the + # tool config's <requirements> tag set whose "type" attribute is "set_environment" (e.g., + # <requirement type="set_environment">R_SCRIPT_PATH</requirement>). env_var_action = env_var_elem.get( 'action', None ) if env_var_name and env_var_action: # Tool dependencies of type "set_environmnet" always have the version attribute set to None. diff -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 -r 96fdb9168f28b2ffa463195d084c9278efb2465a lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -446,11 +446,11 @@ # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=self.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=True ) + common_install_util.install_specified_tool_dependencies( app=self.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=True ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' diff -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 -r 96fdb9168f28b2ffa463195d084c9278efb2465a lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -18,6 +18,7 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install.install_manager import InstallManager +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager log = logging.getLogger( __name__ ) @@ -483,7 +484,8 @@ all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict -def install_specified_packages( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_tool_migration_manager=False ): +def install_specified_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, + from_tool_migration_manager=False ): """ Follow the recipe in the received tool_dependencies_config to install specified packages for repository tools. The received list of tool_dependencies are the database records for those @@ -502,28 +504,46 @@ log.debug( "The received tool_dependencies.xml file is likely invalid: %s" % str( error_message ) ) return installed_packages root = tree.getroot() + elems = [] for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - attr_tup = ( package_name, package_version, 'package' ) + if elem.tag == 'set_environment': + version = elem.get( 'version', '1.0' ) + if version != '1.0': + raise Exception( 'The <set_environment> tag must have a version attribute with value 1.0' ) + for sub_elem in elem: + elems.append( sub_elem ) + else: + elems.append( elem ) + for elem in elems: + name = elem.get( 'name', None ) + version = elem.get( 'version', None ) + type = elem.get( 'type', None ) + if type is None: + if elem.tag in [ 'environment_variable', 'set_environment' ]: + type = 'set_environment' + else: + type = 'package' + if ( name and type == 'set_environment' ) or ( name and version ): + # elem is a package set_environment tag set. + attr_tup = ( name, version, type ) try: index = attr_tups_of_dependencies_for_install.index( attr_tup ) except Exception, e: index = None if index is not None: tool_dependency = tool_dependencies[ index ] + # If the tool_dependency.type is 'set_environment', then the call to process_tag_set() will + # handle everything - no additional installation is necessary. tool_dependency, proceed_with_install, action_elem_tuples = \ tag_manager.process_tag_set( app, tool_shed_repository, tool_dependency, elem, - package_name, - package_version, + name, + version, from_tool_migration_manager=from_tool_migration_manager, tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: + if ( tool_dependency.type == 'package' and proceed_with_install ): try: tool_dependency = install_manager.install_package( app, elem, @@ -531,8 +551,8 @@ tool_dependencies=tool_dependencies, from_tool_migration_manager=from_tool_migration_manager ) except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) + error_message = "Error installing tool dependency %s version %s: %s" % \ + ( str( name ), str( version ), str( e ) ) log.exception( error_message ) if tool_dependency: # Since there was an installation error, update the tool dependency status to Error. The 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: Pes-8 fixes for the Tool Shed's repository_registry module.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/beef22110c25/ Changeset: beef22110c25 User: greg Date: 2014-06-03 21:19:54 Summary: Pes-8 fixes for the Tool Shed's repository_registry module. Affected #: 1 file diff -r da344cf4304429522fd5a214e3fc91697ca682b3 -r beef22110c25635ed18a3c24f9d94442a4a4cc9c lib/tool_shed/repository_registry.py --- a/lib/tool_shed/repository_registry.py +++ b/lib/tool_shed/repository_registry.py @@ -55,7 +55,7 @@ self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 0 if category_name not in self.certified_level_one_viewable_suites_by_category: self.certified_level_one_viewable_suites_by_category[ category_name ] = 0 - + def add_entry( self, repository ): try: if repository: @@ -156,7 +156,7 @@ model.RepositoryMetadata.table.c.changeset_revision, latest_installable_changeset_revision ) ) return clause_list - + def get_certified_level_one_tuple( self, repository ): """ Return True if the latest installable changeset_revision of the received repository is level one certified. @@ -333,7 +333,7 @@ del self.certified_level_one_viewable_repositories_and_suites_by_category[ catgeory_name ] if catgeory_name in self.certified_level_one_viewable_suites_by_category: del self.certified_level_one_viewable_suites_by_category[ catgeory_name ] - + def remove_entry( self, repository ): try: if repository: 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: Fix debug typo in the Tool Shed's step handler.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da344cf43044/ Changeset: da344cf43044 User: greg Date: 2014-06-03 19:56:51 Summary: Fix debug typo in the Tool Shed's step handler. Affected #: 1 file diff -r d80f43f448db62f5444726220b74d1814f6804a7 -r da344cf4304429522fd5a214e3fc91697ca682b3 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1040,7 +1040,7 @@ filtered_actions = actions[ 1: ] env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) if env_shell_file_paths is None: - log.debug( 'Missing Rerl environment, make sure your specified Rerl installation exists.' ) + log.debug( 'Missing Perl environment, make sure your specified Rerl installation exists.' ) if initial_download: return tool_dependency, filtered_actions, dir return tool_dependency, None, None 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: Fix documentation in the Tool Shed API users controller.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d80f43f448db/ Changeset: d80f43f448db User: greg Date: 2014-06-03 19:53:12 Summary: Fix documentation in the Tool Shed API users controller. Affected #: 1 file diff -r 13ab3f66d332126c72b23290f7d458223795ffce -r d80f43f448db62f5444726220b74d1814f6804a7 lib/galaxy/webapps/tool_shed/api/users.py --- a/lib/galaxy/webapps/tool_shed/api/users.py +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -24,6 +24,8 @@ : param key: the current Galaxy admin user's API key The following parameters are included in the payload. + :param email (required): the email address of the user + :param password (required): the password of the user :param username (required): the public username of the user """ user_dict = dict( message = '', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31b2924315d0/ Changeset: 31b2924315d0 User: jmchilton Date: 2014-06-03 19:48:18 Summary: Mechanism to define site-specific parameters to aid defining job destinations. This is based on work by Hector del Risco at the University of Florida. Various tool-style parameters can be defined in job_resource_params_conf.xml (see sample) and these define the pool of all possible resource parameters that can be injected into a tool. These can be groupped together and assigned to tools in job_conf.xml (see documented changes to job_conf.xml.sample_advanced). A conditional is then injected into each tool that gives the end-user the ability to select these parameters. The values of these parameters (as a dict) can then be obtained by dynamic job destination that define a 'resource_params' argument. Lots here still needs to be tested/verified - can workflows exported from Galaxies without resource parameters (or different ones, be reused in Galaxies with resource parameters) (I think yes?)? can workflows exported with resource parameters be used in other Galaxies (I think yes?), how best to present UI while running workflows? (maybe nothing needs to be changed), should exported job parameter data be swept clean (say when exporting a workflow for instance). A great extension to this would be to support conditional when defining parameters. Finally, the Galaxy team will make a reasonable effort to support this syntax for job_conf.xml, job_resource_params_conf.xml, and internal interface for job parameters for sometime once this changeset has reached -stable but until these interfaces may change. Affected #: 8 files diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -240,6 +240,15 @@ <param id="request_cpus">8</param></destination></destinations> + <resources default="default"> +  + <group id="default"></group> + <group id="memoryonly">memory</group> + <group id="all">processors,memory,time,project</group> + </resources><tools> + <tool id="longbar" destination="dynamic" resources="all" /><tool id="baz" handler="special_handlers" destination="bigmem"/></tools><limits> diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 job_resource_params_conf.xml.sample --- /dev/null +++ b/job_resource_params_conf.xml.sample @@ -0,0 +1,6 @@ +<parameters> + <param label="Processors" name="processors" type="integer" size="2" min="1" max="64" value="" help="Number of processing cores, 'ppn' value (1-64). Leave blank to use default value." /> + <param label="Memory" name="memory" type="integer" size="3" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." /> + <param label="Time" name="time" type="integer" size="3" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." /> + <param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." /> +</parameters> diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -152,6 +152,7 @@ self.dependency_resolvers_config_file = resolve_path( kwargs.get( 'dependency_resolvers_config_file', 'dependency_resolvers_conf.xml' ), self.root ) self.job_metrics_config_file = resolve_path( kwargs.get( 'job_metrics_config_file', 'job_metrics_conf.xml' ), self.root ) self.job_config_file = resolve_path( kwargs.get( 'job_config_file', 'job_conf.xml' ), self.root ) + self.job_resource_params_file = resolve_path( kwargs.get( 'job_resource_params_file', 'job_resource_params_conf.xml' ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) ) self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -79,6 +79,9 @@ self['params'] = dict() super(JobToolConfiguration, self).__init__(**kwds) + def get_resource_group( self ): + return self.get( "resources", None ) + class JobConfiguration( object ): """A parser and interface to advanced job management features. @@ -99,8 +102,12 @@ self.destination_tags = {} self.default_destination_id = None self.tools = {} + self.resource_groups = {} + self.default_resource_group = None + self.resource_parameters = {} self.limits = Bunch() + self.__parse_resource_parameters() # Initialize the config try: tree = util.parse_xml(self.app.config.job_config_file) @@ -190,6 +197,16 @@ # Determine the default destination self.default_destination_id = self.__get_default(destinations, self.destinations.keys()) + # Parse resources... + resources = root.find('resources') + if resources is not None: + self.default_resource_group = resources.get( "default", None ) + for group in self.__findall_with_required(resources, 'group'): + id = group.get('id') + fields_str = group.get('fields', None) or group.text or '' + fields = [ f for f in fields_str.split(",") if f ] + self.resource_groups[ id ] = fields + # Parse tool mappings tools = root.find('tools') if tools is not None: @@ -297,6 +314,49 @@ log.debug('Done loading job configuration') + def get_tool_resource_parameters( self, tool_id ): + """ Given a tool id, return XML elements describing parameters to + insert into job resources. + + :tool id: A tool ID (a string) + + :returns: List of parameter elements. + """ + fields = [] + + if not tool_id: + return fields + + # TODO: Only works with exact matches, should handle different kinds of ids + # the way destination lookup does. + resource_group = None + if tool_id in self.tools: + resource_group = self.tools[ tool_id ][ 0 ].get_resource_group() + resource_group = resource_group or self.default_resource_group + + if resource_group and resource_group in self.resource_groups: + fields_names = self.resource_groups[ resource_group ] + fields = [ self.resource_parameters[ n ] for n in fields_names ] + + return fields + + def __parse_resource_parameters( self ): + if not os.path.exists( self.app.config.job_resource_params_file ): + return + + resource_definitions = util.parse_xml( self.app.config.job_resource_params_file ) + resource_definitions_root = resource_definitions.getroot() + # TODO: Also handling conditionals would be awesome! + for parameter_elem in resource_definitions_root.findall( "param" ): + name = parameter_elem.get( "name" ) + # Considered prepending __job_resource_param__ here and then + # stripping it off when making it available to dynamic job + # destination. Not needed because resource parameters are wrapped + # in a conditional. + ## expanded_name = "__job_resource_param__%s" % name + ## parameter_elem.set( "name", expanded_name ) + self.resource_parameters[ name ] = parameter_elem + def __get_default(self, parent, names): """Returns the default attribute set in a parent tag like <handlers> or <destinations>, or return the ID of the child, if there is no explicit default and only one child. diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -71,7 +71,7 @@ actual_args[ possible_arg_name ] = possible_args[ possible_arg_name ] # Don't hit the DB to load the job object if not needed - if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names: + if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names or "resource_params" in function_arg_names: job = self.job_wrapper.get_job() history = job.history user = history and history.user @@ -86,6 +86,24 @@ if "user_email" in function_arg_names: actual_args[ "user_email" ] = user_email + if "resource_params" in function_arg_names: + # Find the dymically inserted resource parameters and give them + # to rule. + app = self.job_wrapper.app + param_values = job.get_param_values( app, ignore_errors=True ) + resource_params = {} + try: + resource_params_raw = param_values[ "__job_resource" ] + if resource_params_raw[ "__job_resource__select" ].lower() in [ "1", "yes", "true" ]: + for key, value in resource_params_raw.iteritems(): + #if key.startswith( "__job_resource_param__" ): + # resource_key = key[ len( "__job_resource_param__" ): ] + # resource_params[ resource_key ] = value + resource_params[ key ] = value + except KeyError: + pass + actual_args[ "resource_params" ] = resource_params + return expand_function( **actual_args ) def __convert_url_to_destination( self, url ): diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -86,6 +86,16 @@ WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) +JOB_RESOURCE_CONDITIONAL_XML = """<conditional name="__job_resource"> + <param name="__job_resource__select" type="select" label="Job Resource Parameters"> + <option value="no">Use default job resource parameters</option> + <option value="yes">Specify job resource parameters</option> + </param> + <when value="no"></when> + <when value="yes"> + </when> +</conditional>""" + class ToolNotFoundException( Exception ): pass @@ -678,6 +688,24 @@ elif root.get( 'tool_type', None ) is not None: ToolClass = tool_types.get( root.get( 'tool_type' ) ) else: + # Normal tool - only insert dynamic resource parameters for these + # tools. + if hasattr( self.app, "job_config" ): # toolshed may not have job_config? + tool_id = root.get( 'id' ) if root else None + parameters = self.app.job_config.get_tool_resource_parameters( tool_id ) + if parameters: + inputs = root.find('inputs') + # If tool has not inputs, create some so we can insert conditional + if not inputs: + inputs = ElementTree.fromstring( "<inputs></inputs>") + root.append( inputs ) + # Insert a conditional allowing user to specify resource parameters. + conditional_element = ElementTree.fromstring( JOB_RESOURCE_CONDITIONAL_XML ) + when_yes_elem = conditional_element.findall( "when" )[ 1 ] + for parameter in parameters: + when_yes_elem.append( parameter ) + inputs.append( conditional_element ) + ToolClass = Tool return ToolClass( config_file, root, self.app, guid=guid, repository_id=repository_id, **kwds ) diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 test/unit/jobs/test_job_configuration.py --- a/test/unit/jobs/test_job_configuration.py +++ b/test/unit/jobs/test_job_configuration.py @@ -20,6 +20,7 @@ self.config = bunch.Bunch( job_config_file=os.path.join( self.temp_directory, "job_conf.xml" ), use_tasked_jobs=False, + job_resource_params_file="/tmp/fake_absent_path", ) self.__write_config_from( SIMPLE_JOB_CONF ) self.app = bunch.Bunch( config=self.config, job_metrics=MockJobMetrics() ) diff -r 1d1d881508b121df607d9096386effdbe072427e -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -807,6 +807,12 @@ # individually. This only affects cluster jobs, not local jobs. #environment_setup_file = None + +# Optional file containing job resource data entry fields definition. +# These fields will be presented to users in the tool forms and allow them to +# overwrite default job resources such as number of processors, memory, and walltime. +#job_resource_params_file = job_resource_params_conf.xml + # If using job concurrency limits (configured in job_config_file), several # extra database queries must be performed to determine the number of jobs a # user has dispatched to a given destination. By default, these queries will https://bitbucket.org/galaxy/galaxy-central/commits/13ab3f66d332/ Changeset: 13ab3f66d332 User: jmchilton Date: 2014-06-03 19:48:18 Summary: Fix unit tests for 46a487e. Affected #: 1 file diff -r 31b2924315d0b48fa7648ab4bfd04ef754829f71 -r 13ab3f66d332126c72b23290f7d458223795ffce test/unit/jobs/test_job_configuration.py --- a/test/unit/jobs/test_job_configuration.py +++ b/test/unit/jobs/test_job_configuration.py @@ -100,16 +100,17 @@ assert limits.walltime is None assert limits.walltime_delta is None assert limits.output_size is None - assert limits.concurrent_jobs == {} + assert limits.destination_user_concurrent_jobs == {} + assert limits.destination_total_concurrent_jobs == {} def test_limit_overrides( self ): self.__with_advanced_config() limits = self.job_config.limits assert limits.registered_user_concurrent_jobs == 2 assert limits.anonymous_user_concurrent_jobs == 1 - assert limits.concurrent_jobs[ "local" ] == 1 - assert limits.concurrent_jobs[ "mycluster" ] == 2 - assert limits.concurrent_jobs[ "longjobs" ] == 1 + assert limits.destination_user_concurrent_jobs[ "local" ] == 1 + assert limits.destination_user_concurrent_jobs[ "mycluster" ] == 2 + assert limits.destination_user_concurrent_jobs[ "longjobs" ] == 1 assert limits.walltime_delta == datetime.timedelta( 0, 0, 0, 0, 0, 24 ) def test_env_parsing( self ): 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: History panel: allow multi-select with shift key to select range of datasets
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d1d881508b1/ Changeset: 1d1d881508b1 User: carlfeberhard Date: 2014-06-03 17:20:15 Summary: History panel: allow multi-select with shift key to select range of datasets Affected #: 10 files diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/mvc/collection/dataset-collection-base.js --- a/static/scripts/mvc/collection/dataset-collection-base.js +++ b/static/scripts/mvc/collection/dataset-collection-base.js @@ -39,41 +39,39 @@ templateSkeleton : function (){ return [ '<div class="dataset hda">', - ' <div class="dataset-warnings">', - '<% if ( deleted ) { %>', - ' <div class="dataset-deleted-msg warningmessagesmall"><strong>', - ' This dataset has been deleted.', // Localize? - ' </div>', - '<% } %>', - '<% if ( ! visible ) { %>', - ' <div class="dataset-hidden-msg warningmessagesmall"><strong>', - ' This dataset has been hidden.', // Localize? - ' </div>', - '<% } %>', - ' </div>', - ' <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', - ' <div class="dataset-primary-actions"></div>', - ' <div class="dataset-title-bar clear" tabindex="0">', - ' <span class="dataset-state-icon state-icon"></span>', - ' <div class="dataset-title">', - ' <span class="hda-hid"><%= hid %></span>', - ' <span class="dataset-name"><%= name %></span>', - ' </div>', - ' </div>', - ' <div class="dataset-body"></div>', - '</div>', + '<div class="dataset-warnings">', + '<% if ( deleted ) { %>', + '<div class="dataset-deleted-msg warningmessagesmall"><strong>', + _l( 'This dataset has been deleted.' ), + '</div>', + '<% } %>', + '<% if ( ! visible ) { %>', + '<div class="dataset-hidden-msg warningmessagesmall"><strong>', + _l( 'This dataset has been hidden.' ), + '</div>', + '<% } %>', + '</div>', + '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', + '<div class="dataset-primary-actions"></div>', + '<div class="dataset-title-bar clear" tabindex="0">', + '<span class="dataset-state-icon state-icon"></span>', + '<div class="dataset-title">', + '<span class="hda-hid"><%= hid %></span> ', + '<span class="dataset-name"><%= name %></span>', + '</div>', + '</div>', + '<div class="dataset-body"></div>', + '</div>' ].join( '' ); }, templateBody : function() { return [ '<div class="dataset-body">', - ' <div class="dataset-summary">', - ' A dataset collection.', - ' </div>', - + '<div class="dataset-summary">', + 'A dataset collection.', + '</div>' ].join( '' ); - }, _buildNewRender : function(){ @@ -170,8 +168,7 @@ */ _render_body_ok : function(){ // most common state renderer and the most complicated - var view = this, - $body = $( _.template(this.templateBody(), this.model.toJSON() ) ) + var $body = $( _.template( this.templateBody(), this.model.toJSON() ) ); // return shortened form if del'd (no display apps or peek?) if( this.model.get( 'deleted' ) ){ @@ -188,4 +185,4 @@ DatasetCollectionBaseView : DatasetCollectionBaseView }; -}); \ No newline at end of file +}); diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/mvc/collection/dataset-collection-edit.js --- a/static/scripts/mvc/collection/dataset-collection-edit.js +++ b/static/scripts/mvc/collection/dataset-collection-edit.js @@ -57,7 +57,7 @@ } deleteBtnData.faIcon = 'fa-times'; return faIconButton( deleteBtnData ); - }, + } }); @@ -66,4 +66,4 @@ DatasetCollectionEditView : DatasetCollectionEditView }; -}); \ No newline at end of file +}); diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -47,7 +47,7 @@ } if( this.draggable ){ this.draggableOn(); } next(); - }); + }); }, /** Show or hide the body/details of history content. @@ -117,7 +117,7 @@ this.$el.find( '.dataset-selector span' ) .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' ); if( !this.selected ){ - this.trigger( 'selected', this ); + this.trigger( 'selected', this, event ); this.selected = true; } return false; @@ -130,7 +130,7 @@ this.$el.find( '.dataset-selector span' ) .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' ); if( this.selected ){ - this.trigger( 'de-selected', this ); + this.trigger( 'de-selected', this, event ); this.selected = false; } return false; @@ -142,7 +142,7 @@ } else { this.select( event ); } - }, + } }); diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -45,6 +45,8 @@ // ---- set up instance vars /** selected hda ids */ this.selectedHdaIds = []; + /** last selected hda */ + this.lastSelectedViewId = null; /** editor for tags - sub-view */ this.tagsEditor = null; @@ -275,7 +277,7 @@ historyContentType = hda.get( 'history_content_type' ), hdaView = null; - if( historyContentType == "dataset" ) { + if( historyContentType === "dataset" ) { hdaView = new this.HDAViewClass({ model : hda, linkTarget : this.linkTarget, @@ -288,7 +290,7 @@ tagsEditorShown : ( this.tagsEditor && !this.tagsEditor.hidden ), annotationEditorShown : ( this.annotationEditor && !this.annotationEditor.hidden ) }); - } else if ( historyContentType == "dataset_collection" ) { + } else if ( historyContentType === "dataset_collection" ) { hdaView = new datasetCollectionEdit.DatasetCollectionEditView({ model : hda, linkTarget : this.linkTarget, @@ -311,12 +313,33 @@ readonlyPanel.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call( this, hdaView ); // maintain a list of hdas that are selected - hdaView.on( 'selected', function( hdaView ){ - var id = hdaView.model.get( 'id' ); - historyView.selectedHdaIds = _.union( historyView.selectedHdaIds, [ id ] ); + hdaView.on( 'selected', function( hdaView, event ){ + if( !event ){ return; } + //console.debug( 'selected', event ); + var selectedIds = []; + //console.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] ); + + // shift will select a range, but not set lastSelectedViewId + if( ( event.shiftKey ) + && ( historyView.lastSelectedViewId && _.has( historyView.hdaViews, historyView.lastSelectedViewId ) ) ){ + var lastSelectedView = historyView.hdaViews[ historyView.lastSelectedViewId ]; + selectedIds = historyView.selectDatasetRange( hdaView, lastSelectedView ) + .map( function( view ){ return view.model.id; }); + + // only + } else { + var id = hdaView.model.get( 'id' ); + historyView.lastSelectedViewId = id; + //console.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId ); + selectedIds = [ id ]; + } + //console.debug( 'selectedIds:', selectedIds ); + historyView.selectedHdaIds = _.union( historyView.selectedHdaIds, selectedIds ); + //TODO: might want to use getSelectedHdaViews instead managing these lists with ops //console.debug( 'selected', historyView.selectedHdaIds ); }); - hdaView.on( 'de-selected', function( hdaView ){ + hdaView.on( 'de-selected', function( hdaView, event ){ + //console.debug( 'de-selected', event ); var id = hdaView.model.get( 'id' ); historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); //console.debug( 'de-selected', historyView.selectedHdaIds ); @@ -386,6 +409,7 @@ view.showSelector(); }); this.selectedHdaIds = []; + this.lastSelectedViewId = null; }, /** hide selectors on all visible hdas and associated controls */ @@ -397,6 +421,7 @@ view.hideSelector(); }); this.selectedHdaIds = []; + this.lastSelectedViewId = null; }, /** show or hide selectors on all visible hdas and associated controls */ @@ -417,11 +442,21 @@ /** deselect all visible hdas */ deselectAllDatasets : function( event ){ + this.lastSelectedViewId = null; _.each( this.hdaViews, function( view ){ view.deselect( event ); }); }, + /** select a range of datasets between A and B */ + selectDatasetRange : function( viewA, viewB ){ + var range = this.hdaViewRange( viewA, viewB ); + _.each( range, function( view ){ + view.select(); + }); + return range; + }, + /** return an array of all currently selected hdas */ getSelectedHdaViews : function(){ return _.filter( this.hdaViews, function( v ){ diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -613,7 +613,7 @@ var hdaId = hda.get( 'id' ), historyContentType = hda.get( "history_content_type" ), hdaView = null; - if( historyContentType == "dataset" ) { + if( historyContentType === "dataset" ){ hdaView = new this.HDAViewClass({ model : hda, linkTarget : this.linkTarget, @@ -717,6 +717,38 @@ // return ( model )?( this.hdaViews[ model.id ] ):( undefined ); //}, + hdaViewRange : function( viewA, viewB ){ + //console.debug( 'a: ', viewA, viewA.model ); + //console.debug( 'b: ', viewB, viewB.model ); + if( viewA === viewB ){ return [ viewA ]; } + //TODO: would probably be better if we cache'd the views as an ordered list (as well as a map) + var panel = this, + withinSet = false, + set = []; + this.model.hdas.getVisible( + this.storage.get( 'show_deleted' ), + this.storage.get( 'show_hidden' ), + this.filters + ).each( function( hda ){ + //console.debug( 'checking: ', hda.get( 'name' ) ); + if( withinSet ){ + //console.debug( '\t\t adding: ', hda.get( 'name' ) ); + set.push( panel.hdaViews[ hda.id ] ); + if( hda === viewA.model || hda === viewB.model ){ + //console.debug( '\t found last: ', hda.get( 'name' ) ); + withinSet = false; + } + } else { + if( hda === viewA.model || hda === viewB.model ){ + //console.debug( 'found first: ', hda.get( 'name' ) ); + withinSet = true; + set.push( panel.hdaViews[ hda.id ] ); + } + } + }); + return set; + }, + // ------------------------------------------------------------------------ panel events /** event map */ events : { diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/packed/mvc/collection/dataset-collection-base.js --- a/static/scripts/packed/mvc/collection/dataset-collection-base.js +++ b/static/scripts/packed/mvc/collection/dataset-collection-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(b,a){var c=a.HistoryContentBaseView.extend({className:"dataset hda history-panel-hda",id:function(){return"hdca-"+this.model.get("id")},initialize:function(d){if(d.logger){this.logger=this.model.logger=d.logger}this.log(this+".initialize:",d);this.selectable=d.selectable||false;this.selected=d.selected||false;this.expanded=d.expanded||false},render:function(e){var d=this._buildNewRender();this._queueNewRender(d,e);return this},templateSkeleton:function(){return['<div class="dataset hda">',' <div class="dataset-warnings">',"<% if ( deleted ) { %>",' <div class="dataset-deleted-msg warningmessagesmall"><strong>'," This dataset has been deleted."," </div>","<% } %>","<% if ( ! visible ) { %>",' <div class="dataset-hidden-msg warningmessagesmall"><strong>'," This dataset has been hidden."," </div>","<% } %>"," </div>",' <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>',' <div class="dataset-primary-actions"></div>',' <div class="dataset-title-bar clear" tabindex="0">',' <span class="dataset-state-icon state-icon"></span>',' <div class="dataset-title">',' <span class="hda-hid"><%= hid %></span>',' <span class="dataset-name"><%= name %></span>'," </div>"," </div>",' <div class="dataset-body"></div>',"</div>",].join("")},templateBody:function(){return['<div class="dataset-body">',' <div class="dataset-summary">'," A dataset collection."," </div>",].join("")},_buildNewRender:function(){var d=$(_.template(this.templateSkeleton(),this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);return d},_render_titleButtons:function(){return[]},_render_body:function(){var e=$('<div>Error: unknown state "'+this.model.get("state")+'".</div>'),d=this["_render_body_"+this.model.get("state")];if(_.isFunction(d)){e=d.call(this)}this._setUpBehaviors(e);if(this.expanded){e.show()}return e},_setUpBehaviors:function(d){d=d||this.$el;make_popup_menus(d);d.find("[title]").tooltip({placement:"bottom"})},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var d=this;function e(){d.$el.children(".dataset-body").replaceWith(d._render_body());d.$el.children(".dataset-body").slideDown(d.fxSpeed,function(){d.expanded=true;d.trigger("body-expanded",d.model.get("id"))})}e()},collapseBody:function(){var d=this;this.$el.children(".dataset-body").slideUp(d.fxSpeed,function(){d.expanded=false;d.trigger("body-collapsed",d.model.get("id"))})},_render_body_ok:function(){var d=this,e=$(_.template(this.templateBody(),this.model.toJSON()));if(this.model.get("deleted")){return e}return e}});return{DatasetCollectionBaseView:c}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(b,a){var c=a.HistoryContentBaseView.extend({className:"dataset hda history-panel-hda",id:function(){return"hdca-"+this.model.get("id")},initialize:function(d){if(d.logger){this.logger=this.model.logger=d.logger}this.log(this+".initialize:",d);this.selectable=d.selectable||false;this.selected=d.selected||false;this.expanded=d.expanded||false},render:function(e){var d=this._buildNewRender();this._queueNewRender(d,e);return this},templateSkeleton:function(){return['<div class="dataset hda">','<div class="dataset-warnings">',"<% if ( deleted ) { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</div>","<% } %>","<% if ( ! visible ) { %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%= hid %></span> ','<span class="dataset-name"><%= name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("")},templateBody:function(){return['<div class="dataset-body">','<div class="dataset-summary">',"A dataset collection.","</div>"].join("")},_buildNewRender:function(){var d=$(_.template(this.templateSkeleton(),this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);return d},_render_titleButtons:function(){return[]},_render_body:function(){var e=$('<div>Error: unknown state "'+this.model.get("state")+'".</div>'),d=this["_render_body_"+this.model.get("state")];if(_.isFunction(d)){e=d.call(this)}this._setUpBehaviors(e);if(this.expanded){e.show()}return e},_setUpBehaviors:function(d){d=d||this.$el;make_popup_menus(d);d.find("[title]").tooltip({placement:"bottom"})},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var d=this;function e(){d.$el.children(".dataset-body").replaceWith(d._render_body());d.$el.children(".dataset-body").slideDown(d.fxSpeed,function(){d.expanded=true;d.trigger("body-expanded",d.model.get("id"))})}e()},collapseBody:function(){var d=this;this.$el.children(".dataset-body").slideUp(d.fxSpeed,function(){d.expanded=false;d.trigger("body-collapsed",d.model.get("id"))})},_render_body_ok:function(){var d=$(_.template(this.templateBody(),this.model.toJSON()));if(this.model.get("deleted")){return d}return d}});return{DatasetCollectionBaseView:c}}); \ No newline at end of file diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/packed/mvc/collection/dataset-collection-edit.js --- a/static/scripts/packed/mvc/collection/dataset-collection-edit.js +++ b/static/scripts/packed/mvc/collection/dataset-collection-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/collection/dataset-collection-base",],function(b,c){var a=c.DatasetCollectionBaseView.extend({initialize:function(d){c.DatasetCollectionBaseView.prototype.initialize.call(this,d)},_render_titleButtons:function(){return c.DatasetCollectionBaseView.prototype._render_titleButtons.call(this).concat([this._render_deleteButton()])},_render_deleteButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var d=this,e={title:_l("Delete"),classes:"dataset-delete",onclick:function(){d.$el.find(".icon-btn.dataset-delete").trigger("mouseout");d.model["delete"]()}};if(this.model.get("deleted")){e={title:_l("Dataset collection is already deleted"),disabled:true}}e.faIcon="fa-times";return faIconButton(e)},});return{DatasetCollectionEditView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/collection/dataset-collection-base",],function(b,c){var a=c.DatasetCollectionBaseView.extend({initialize:function(d){c.DatasetCollectionBaseView.prototype.initialize.call(this,d)},_render_titleButtons:function(){return c.DatasetCollectionBaseView.prototype._render_titleButtons.call(this).concat([this._render_deleteButton()])},_render_deleteButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var d=this,e={title:_l("Delete"),classes:"dataset-delete",onclick:function(){d.$el.find(".icon-btn.dataset-delete").trigger("mouseout");d.model["delete"]()}};if(this.model.get("deleted")){e={title:_l("Dataset collection is already deleted"),disabled:true}}e.faIcon="fa-times";return faIconButton(e)}});return{DatasetCollectionEditView:a}}); \ No newline at end of file diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc","mvc/data","utils/localization"],function(e,b,g,d){var h=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",fxSpeed:"fast",_queueNewRender:function(j,k){k=(k===undefined)?(true):(k);var i=this;if(k){$(i).queue(function(l){this.$el.fadeOut(i.fxSpeed,l)})}$(i).queue(function(l){this.$el.empty().attr("class",i.className).addClass("state-"+i.model.get("state")).append(j.children());if(this.selectable){this.showSelector(0)}l()});if(k){$(i).queue(function(l){this.$el.fadeIn(i.fxSpeed,l)})}$(i).queue(function(l){this.trigger("rendered",i);if(this.model.inReadyState()){this.trigger("rendered:ready",i)}if(this.draggable){this.draggableOn()}l()})},toggleBodyVisibility:function(l,j){var i=32,k=13;if(l&&(l.type==="keydown")&&!(l.keyCode===i||l.keyCode===k)){return true}var m=this.$el.find(".dataset-body");j=(j===undefined)?(!m.is(":visible")):(j);if(j){this.expandBody()}else{this.collapseBody()}return false},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(i){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(i){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(i){if(this.selected){this.deselect(i)}else{this.select(i)}},});var c=h.extend({className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+".initialize:",i);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=i.linkTarget||"_blank";this.selectable=i.selectable||false;this.selected=i.selected||false;this.expanded=i.expanded||false;this.draggable=i.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(j,i){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(j){this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var i=this._buildNewRender();this._queueNewRender(i,j);return this},_buildNewRender:function(){var i=$(c.templates.skeleton(this.model.toJSON()));i.find(".dataset-primary-actions").append(this._render_titleButtons());i.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(i);return i},_setUpBehaviors:function(i){i=i||this.$el;make_popup_menus(i);i.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===e.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===e.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var j={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){j.disabled=true;j.title=d("Cannot display datasets removed from disk")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=d("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=d("This dataset is not yet viewable")}else{j.title=d("View data");j.href=this.urls.display;var i=this;j.onclick=function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+i.model.get("name"),type:"other",content:function(l){var m=new g.TabularDataset({id:i.model.id});$.when(m.fetch()).then(function(){g.createTabularDatasetChunkedView({model:m,parent_elt:l,embedded:true,height:"100%"})})}});k.preventDefault()}}}}}j.faIcon="fa-eye";return faIconButton(j)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var j=this.urls,k=this.model.get("meta_files");if(_.isEmpty(k)){return $(['<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var l="dataset-"+this.model.get("id")+"-popup",i=['<div popupmenu="'+l+'">','<a href="'+j.download+'">',d("Download dataset"),"</a>","<a>"+d("Additional files")+"</a>",_.map(k,function(m){return['<a class="action-button" href="',j.meta_download+m.file_type,'">',d("Download")," ",m.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+l+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(i)},_render_showParamsButton:function(){return faIconButton({title:d("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var j=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),i=this["_render_body_"+this.model.get("state")];if(_.isFunction(i)){j=i.call(this)}this._setUpBehaviors(j);if(this.expanded){j.show()}return j},_render_stateBodyHelper:function(i,l){l=l||[];var j=this,k=$(c.templates.body(_.extend(this.model.toJSON(),{body:i})));k.find(".dataset-actions .left").append(_.map(l,function(m){return m.call(j)}));return k},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+d("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+d("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+d("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+d("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+d("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+d("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+d("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+d('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var i=['<span class="help-text">',d("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){i="<div>"+this.model.get("misc_blurb")+"</div>"+i}return this._render_stateBodyHelper(i,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+d("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var i=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(d("An error occurred setting the metadata for this dataset"))),j=this._render_body_ok();j.prepend(i);return j},_render_body_ok:function(){var i=this,k=$(c.templates.body(this.model.toJSON())),j=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);k.find(".dataset-actions .left").append(_.map(j,function(l){return l.call(i)}));if(this.model.isDeletedOrPurged()){return k}return k},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var i=this;function j(){i.$el.children(".dataset-body").replaceWith(i._render_body());i.$el.children(".dataset-body").slideDown(i.fxSpeed,function(){i.expanded=true;i.trigger("body-expanded",i.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(k){i.urls=i.model.urls();j()})}else{j()}},collapseBody:function(){var i=this;this.$el.children(".dataset-body").slideUp(i.fxSpeed,function(){i.expanded=false;i.trigger("body-collapsed",i.model.get("id"))})},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var i=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);i.addEventListener("dragstart",this.dragStartHandler,false);i.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var i=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);i.removeEventListener("dragstart",this.dragStartHandler,false);i.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(i){this.trigger("dragstart",this);i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(i){this.trigger("dragend",this);return false},remove:function(j){var i=this;this.$el.fadeOut(i.fxSpeed,function(){i.$el.remove();i.off();if(j){j()}})},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+i+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',d("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',d("This dataset has been deleted and removed from disk")+".","</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',d("This dataset has been deleted")+".","</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',d("This dataset has been hidden")+".","</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var f=_.template(['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',d("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',d("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join(""));c.templates={skeleton:function(i){return a({_l:d,hda:i})},body:function(i){return f({_l:d,hda:i})}};return{HistoryContentBaseView:h,HDABaseView:c}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc","mvc/data","utils/localization"],function(e,b,g,d){var h=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",fxSpeed:"fast",_queueNewRender:function(j,k){k=(k===undefined)?(true):(k);var i=this;if(k){$(i).queue(function(l){this.$el.fadeOut(i.fxSpeed,l)})}$(i).queue(function(l){this.$el.empty().attr("class",i.className).addClass("state-"+i.model.get("state")).append(j.children());if(this.selectable){this.showSelector(0)}l()});if(k){$(i).queue(function(l){this.$el.fadeIn(i.fxSpeed,l)})}$(i).queue(function(l){this.trigger("rendered",i);if(this.model.inReadyState()){this.trigger("rendered:ready",i)}if(this.draggable){this.draggableOn()}l()})},toggleBodyVisibility:function(l,j){var i=32,k=13;if(l&&(l.type==="keydown")&&!(l.keyCode===i||l.keyCode===k)){return true}var m=this.$el.find(".dataset-body");j=(j===undefined)?(!m.is(":visible")):(j);if(j){this.expandBody()}else{this.collapseBody()}return false},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(i){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this,i);this.selected=true}return false},deselect:function(i){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this,i);this.selected=false}return false},toggleSelect:function(i){if(this.selected){this.deselect(i)}else{this.select(i)}}});var c=h.extend({className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+".initialize:",i);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=i.linkTarget||"_blank";this.selectable=i.selectable||false;this.selected=i.selected||false;this.expanded=i.expanded||false;this.draggable=i.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(j,i){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(j){this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var i=this._buildNewRender();this._queueNewRender(i,j);return this},_buildNewRender:function(){var i=$(c.templates.skeleton(this.model.toJSON()));i.find(".dataset-primary-actions").append(this._render_titleButtons());i.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(i);return i},_setUpBehaviors:function(i){i=i||this.$el;make_popup_menus(i);i.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===e.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===e.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var j={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){j.disabled=true;j.title=d("Cannot display datasets removed from disk")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=d("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=d("This dataset is not yet viewable")}else{j.title=d("View data");j.href=this.urls.display;var i=this;j.onclick=function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+i.model.get("name"),type:"other",content:function(l){var m=new g.TabularDataset({id:i.model.id});$.when(m.fetch()).then(function(){g.createTabularDatasetChunkedView({model:m,parent_elt:l,embedded:true,height:"100%"})})}});k.preventDefault()}}}}}j.faIcon="fa-eye";return faIconButton(j)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var j=this.urls,k=this.model.get("meta_files");if(_.isEmpty(k)){return $(['<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var l="dataset-"+this.model.get("id")+"-popup",i=['<div popupmenu="'+l+'">','<a href="'+j.download+'">',d("Download dataset"),"</a>","<a>"+d("Additional files")+"</a>",_.map(k,function(m){return['<a class="action-button" href="',j.meta_download+m.file_type,'">',d("Download")," ",m.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+l+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(i)},_render_showParamsButton:function(){return faIconButton({title:d("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var j=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),i=this["_render_body_"+this.model.get("state")];if(_.isFunction(i)){j=i.call(this)}this._setUpBehaviors(j);if(this.expanded){j.show()}return j},_render_stateBodyHelper:function(i,l){l=l||[];var j=this,k=$(c.templates.body(_.extend(this.model.toJSON(),{body:i})));k.find(".dataset-actions .left").append(_.map(l,function(m){return m.call(j)}));return k},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+d("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+d("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+d("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+d("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+d("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+d("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+d("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+d('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var i=['<span class="help-text">',d("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){i="<div>"+this.model.get("misc_blurb")+"</div>"+i}return this._render_stateBodyHelper(i,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+d("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var i=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(d("An error occurred setting the metadata for this dataset"))),j=this._render_body_ok();j.prepend(i);return j},_render_body_ok:function(){var i=this,k=$(c.templates.body(this.model.toJSON())),j=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);k.find(".dataset-actions .left").append(_.map(j,function(l){return l.call(i)}));if(this.model.isDeletedOrPurged()){return k}return k},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var i=this;function j(){i.$el.children(".dataset-body").replaceWith(i._render_body());i.$el.children(".dataset-body").slideDown(i.fxSpeed,function(){i.expanded=true;i.trigger("body-expanded",i.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(k){i.urls=i.model.urls();j()})}else{j()}},collapseBody:function(){var i=this;this.$el.children(".dataset-body").slideUp(i.fxSpeed,function(){i.expanded=false;i.trigger("body-collapsed",i.model.get("id"))})},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var i=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);i.addEventListener("dragstart",this.dragStartHandler,false);i.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var i=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);i.removeEventListener("dragstart",this.dragStartHandler,false);i.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(i){this.trigger("dragstart",this);i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(i){this.trigger("dragend",this);return false},remove:function(j){var i=this;this.$el.fadeOut(i.fxSpeed,function(){i.$el.remove();i.off();if(j){j()}})},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+i+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',d("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',d("This dataset has been deleted and removed from disk")+".","</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',d("This dataset has been deleted")+".","</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',d("This dataset has been hidden")+".","</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var f=_.template(['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',d("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',d("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join(""));c.templates={skeleton:function(i){return a({_l:d,hda:i})},body:function(i){return f({_l:d,hda:i})}};return{HistoryContentBaseView:h,HDABaseView:c}}); \ No newline at end of file diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.get("id"),l=j.get("history_content_type"),k=null;if(l=="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l=="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(k){var l=k.model.get("id");i.selectedHdaIds=_.union(i.selectedHdaIds,[l])});j.on("de-selected",function(k){var l=k.model.get("id");i.selectedHdaIds=_.without(i.selectedHdaIds,l)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[]},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[]},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.deselect(i)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.get("id"),l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.get("id");i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.get("id");i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file diff -r 46a487e7d5476429cb71885adcbcfb9746ce725a -r 1d1d881508b121df607d9096386effdbe072427e static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/collection/dataset-collection-base","mvc/dataset/hda-base","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(g,k,b,a,f,d){var i=f.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(n){var m="expandedHdas";this.save(m,_.extend(this.get(m),_.object([n],[true])))},removeExpandedHda:function(n){var m="expandedHdas";this.save(m,_.omit(this.get(m),n))},toString:function(){return"HistoryPrefs("+this.id+")"}});i.storageKeyPrefix="history:";i.historyStorageKey=function e(m){if(!m){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+m)}return(i.storageKeyPrefix+m)};i.get=function c(m){return new i({id:i.historyStorageKey(m)})};i.clearAll=function h(n){for(var m in sessionStorage){if(m.indexOf(i.storageKeyPrefix)===0){sessionStorage.removeItem(m)}}};var j=Backbone.View.extend(f.LoggableMixin).extend({HDAViewClass:b.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:d("This history is empty"),noneFoundMsg:d("No matching datasets found"),initialize:function(m){m=m||{};if(m.logger){this.logger=m.logger}this.log(this+".initialize:",m);this.linkTarget=m.linkTarget||"_blank";this.fxSpeed=_.has(m,"fxSpeed")?(m.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=m.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var n=_.pick(m,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,n,false);if(m.onready){m.onready.call(this)}},_setUpListeners:function(){this.on("error",function(n,q,m,p,o){this.errorHandler(n,q,m,p,o)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(m){this.log(this+"",arguments)},this)}return this},errorHandler:function(o,r,n,q,p){console.error(o,r,n,q,p);if(r&&r.status===0&&r.readyState===0){}else{if(r&&r.status===502){}else{var m=this._parseErrorMessage(o,r,n,q,p);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",m.message,m.details)})}else{this.displayMessage("error",m.message,m.details)}}}},_parseErrorMessage:function(p,t,o,s,r){var n=Galaxy.currUser,m={message:this._bePolite(s),details:{user:(n instanceof a.User)?(n.toJSON()):(n+""),source:(p instanceof Backbone.Model)?(p.toJSON()):(p+""),xhr:t,options:(t)?(_.omit(o,"xhr")):(o)}};_.extend(m.details,r||{});if(t&&_.isFunction(t.getAllResponseHeaders)){var q=t.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(u){return u.split(": ")});m.details.xhr.responseHeaders=_.object(q)}return m},_bePolite:function(m){m=m||d("An error occurred while getting updates from the server");return m+". "+d("Please contact a Galaxy administrator if the problem persists")+"."},loadHistoryWithHDADetails:function(o,n,m,q){var p=function(r){return _.keys(i.get(r.id).get("expandedHdas"))};return this.loadHistory(o,n,m,q,p)},loadHistory:function(p,o,n,s,q){var m=this;o=o||{};m.trigger("loading-history",m);var r=g.History.getHistoryData(p,{historyFn:n,hdaFn:s,hdaDetailIds:o.initiallyExpanded||q});return m._loadHistoryFromXHR(r,o).fail(function(v,t,u){m.trigger("error",m,v,o,d("An error was encountered while "+t),{historyId:p,history:u||{}})}).always(function(){m.trigger("loading-done",m)})},_loadHistoryFromXHR:function(o,n){var m=this;o.then(function(p,q){m.JSONToModel(p,q,n)});o.fail(function(q,p){m.render()});return o},JSONToModel:function(p,m,n){this.log("JSONToModel:",p,m,n);n=n||{};var o=new g.History(p,m,n);this.setModel(o);return this},setModel:function(n,m,o){m=m||{};o=(o!==undefined)?(o):(true);this.log("setModel:",n,m,o);this.freeModel();this.selectedHdaIds=[];if(n){this.model=n;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(m.initiallyExpanded,m.show_deleted,m.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(o){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(n,m,o){this.storage=new i({id:i.historyStorageKey(this.model.get("id"))});if(_.isObject(n)){this.storage.set("exandedHdas",n)}if(_.isBoolean(m)){this.storage.set("show_deleted",m)}if(_.isBoolean(o)){this.storage.set("show_hidden",o)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addContentView,this);this.model.on("error error:hdas",function(n,p,m,o){this.errorHandler(n,p,m,o)},this);return this},render:function(o,p){this.log("render:",o,p);o=(o===undefined)?(this.fxSpeed):(o);var m=this,n;if(this.model){n=this.renderModel()}else{n=this.renderWithoutModel()}$(m).queue("fx",[function(q){if(o&&m.$el.is(":visible")){m.$el.fadeOut(o,q)}else{q()}},function(q){m.$el.empty();if(n){m.$el.append(n.children())}q()},function(q){if(o&&!m.$el.is(":visible")){m.$el.fadeIn(o,q)}else{q()}},function(q){if(p){p.call(this)}m.trigger("rendered",this);q()}]);return this},renderWithoutModel:function(){var m=$("<div/>"),n=$("<div/>").addClass("message-container").css({margin:"4px"});return m.append(n)},renderModel:function(){var m=$("<div/>");m.append(j.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(m).text(this.emptyMsg);m.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(m);this.renderHdas(m);return m},_renderEmptyMsg:function(o){var n=this,m=n.$emptyMessage(o);if(!_.isEmpty(n.hdaViews)){m.hide()}else{if(n.searchFor){m.text(n.noneFoundMsg).show()}else{m.text(n.emptyMsg).show()}}return this},_renderSearchButton:function(m){return faIconButton({title:d("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(m){m=m||this.$el;m.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(m.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(m){return(m||this.$el).find(".datasets-list")},$messages:function(m){return(m||this.$el).find(".message-container")},$emptyMessage:function(m){return(m||this.$el).find(".empty-history-message")},renderHdas:function(n){n=n||this.$el;var m=this,p={},o=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(n).empty();if(o.length){o.each(function(r){var q=r.get("id"),s=m._createContentView(r);p[q]=s;if(_.contains(m.selectedHdaIds,q)){s.selected=true}m.attachContentView(s.render(),n)})}this.hdaViews=p;this._renderEmptyMsg(n);return this.hdaViews},_createContentView:function(n){var m=n.get("id"),p=n.get("history_content_type"),o=null;if(p=="dataset"){o=new this.HDAViewClass({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}else{o=new k.DatasetCollectionBaseView({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}this._setUpHdaListeners(o);return o},_setUpHdaListeners:function(n){var m=this;n.on("error",function(p,r,o,q){m.errorHandler(p,r,o,q)});n.on("body-expanded",function(o){m.storage.addExpandedHda(o)});n.on("body-collapsed",function(o){m.storage.removeExpandedHda(o)});return this},attachContentView:function(o,n){n=n||this.$el;var m=this.$datasetsList(n);m.prepend(o.$el);return this},addContentView:function(p){this.log("add."+this,p);var n=this;if(!p.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return n}$({}).queue([function o(r){var q=n.$emptyMessage();if(q.is(":visible")){q.fadeOut(n.fxSpeed,r)}else{r()}},function m(q){var r=n._createContentView(p);n.hdaViews[p.id]=r;r.render().$el.hide();n.scrollToTop();n.attachContentView(r);r.$el.slideDown(n.fxSpeed)}]);return n},refreshContents:function(n,m){if(this.model){return this.model.refresh(n,m)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(m){m.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",m);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",m);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(n){var o=this,p=".history-search-input";function m(q){if(o.model.hdas.haveDetails()){o.searchHdas(q);return}o.$el.find(p).searchInput("toggle-loading");o.model.hdas.fetchAllDetails({silent:true}).always(function(){o.$el.find(p).searchInput("toggle-loading")}).done(function(){o.searchHdas(q)})}n.searchInput({initialVal:o.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:m,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return n},toggleSearchControls:function(o,m){var n=this.$el.find(".history-search-controls"),p=(jQuery.type(o)==="number")?(o):(this.fxSpeed);m=(m!==undefined)?(m):(!n.is(":visible"));if(m){n.slideDown(p,function(){$(this).find("input").focus()})}else{n.slideUp(p)}return m},searchHdas:function(m){var n=this;this.searchFor=m;this.filters=[function(o){return o.matchesAll(n.searchFor)}];this.trigger("search:searching",m,this);this.renderHdas();return this},clearHdaSearch:function(m){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(n,m,o){m=(m!==undefined)?(m):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,o)}else{this.$el.fadeOut(m);this.indicator.show(n,m,o)}},_hideLoadingIndicator:function(m,n){m=(m!==undefined)?(m):(this.fxSpeed);if(this.indicator){this.indicator.hide(m,n)}},displayMessage:function(r,s,q){var o=this;this.scrollToTop();var p=this.$messages(),m=$("<div/>").addClass(r+"message").html(s);if(!_.isEmpty(q)){var n=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(o._messageToModalOptions(r,s,q));return false});m.append(" ",n)}return p.html(m)},_messageToModalOptions:function(q,s,p){var m=this,r=$("<div/>"),o={title:"Details"};function n(t){t=_.omit(t,_.functions(t));return["<table>",_.map(t,function(v,u){v=(_.isObject(v))?(n(v)):(v);return'<tr><td style="vertical-align: top; color: grey">'+u+'</td><td style="padding-left: 8px">'+v+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(p)){o.body=r.append(n(p))}else{o.body=r.html(p)}o.buttons={Ok:function(){Galaxy.modal.hide();m.clearMessages()}};return o},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(m){this.$container().scrollTop(m);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(n){if((!n)||(!this.hdaViews[n])){return this}var m=this.hdaViews[n];this.scrollTo(m.el.offsetTop);return this},scrollToHid:function(m){var n=this.model.hdas.getByHid(m);if(!n){return this}return this.scrollToId(n.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var l=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',d("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',d("You are over your disk quota"),". ",d("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',d("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',d("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',d("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',d("This history is empty"),"</div>"].join("");j.templates={historyPanel:function(m){return _.template(l,m,{variable:"history"})}};return{ReadOnlyHistoryPanel:j}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/collection/dataset-collection-base","mvc/dataset/hda-base","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(g,k,b,a,f,d){var i=f.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(n){var m="expandedHdas";this.save(m,_.extend(this.get(m),_.object([n],[true])))},removeExpandedHda:function(n){var m="expandedHdas";this.save(m,_.omit(this.get(m),n))},toString:function(){return"HistoryPrefs("+this.id+")"}});i.storageKeyPrefix="history:";i.historyStorageKey=function e(m){if(!m){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+m)}return(i.storageKeyPrefix+m)};i.get=function c(m){return new i({id:i.historyStorageKey(m)})};i.clearAll=function h(n){for(var m in sessionStorage){if(m.indexOf(i.storageKeyPrefix)===0){sessionStorage.removeItem(m)}}};var j=Backbone.View.extend(f.LoggableMixin).extend({HDAViewClass:b.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:d("This history is empty"),noneFoundMsg:d("No matching datasets found"),initialize:function(m){m=m||{};if(m.logger){this.logger=m.logger}this.log(this+".initialize:",m);this.linkTarget=m.linkTarget||"_blank";this.fxSpeed=_.has(m,"fxSpeed")?(m.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=m.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var n=_.pick(m,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,n,false);if(m.onready){m.onready.call(this)}},_setUpListeners:function(){this.on("error",function(n,q,m,p,o){this.errorHandler(n,q,m,p,o)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(m){this.log(this+"",arguments)},this)}return this},errorHandler:function(o,r,n,q,p){console.error(o,r,n,q,p);if(r&&r.status===0&&r.readyState===0){}else{if(r&&r.status===502){}else{var m=this._parseErrorMessage(o,r,n,q,p);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",m.message,m.details)})}else{this.displayMessage("error",m.message,m.details)}}}},_parseErrorMessage:function(p,t,o,s,r){var n=Galaxy.currUser,m={message:this._bePolite(s),details:{user:(n instanceof a.User)?(n.toJSON()):(n+""),source:(p instanceof Backbone.Model)?(p.toJSON()):(p+""),xhr:t,options:(t)?(_.omit(o,"xhr")):(o)}};_.extend(m.details,r||{});if(t&&_.isFunction(t.getAllResponseHeaders)){var q=t.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(u){return u.split(": ")});m.details.xhr.responseHeaders=_.object(q)}return m},_bePolite:function(m){m=m||d("An error occurred while getting updates from the server");return m+". "+d("Please contact a Galaxy administrator if the problem persists")+"."},loadHistoryWithHDADetails:function(o,n,m,q){var p=function(r){return _.keys(i.get(r.id).get("expandedHdas"))};return this.loadHistory(o,n,m,q,p)},loadHistory:function(p,o,n,s,q){var m=this;o=o||{};m.trigger("loading-history",m);var r=g.History.getHistoryData(p,{historyFn:n,hdaFn:s,hdaDetailIds:o.initiallyExpanded||q});return m._loadHistoryFromXHR(r,o).fail(function(v,t,u){m.trigger("error",m,v,o,d("An error was encountered while "+t),{historyId:p,history:u||{}})}).always(function(){m.trigger("loading-done",m)})},_loadHistoryFromXHR:function(o,n){var m=this;o.then(function(p,q){m.JSONToModel(p,q,n)});o.fail(function(q,p){m.render()});return o},JSONToModel:function(p,m,n){this.log("JSONToModel:",p,m,n);n=n||{};var o=new g.History(p,m,n);this.setModel(o);return this},setModel:function(n,m,o){m=m||{};o=(o!==undefined)?(o):(true);this.log("setModel:",n,m,o);this.freeModel();this.selectedHdaIds=[];if(n){this.model=n;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(m.initiallyExpanded,m.show_deleted,m.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(o){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(n,m,o){this.storage=new i({id:i.historyStorageKey(this.model.get("id"))});if(_.isObject(n)){this.storage.set("exandedHdas",n)}if(_.isBoolean(m)){this.storage.set("show_deleted",m)}if(_.isBoolean(o)){this.storage.set("show_hidden",o)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addContentView,this);this.model.on("error error:hdas",function(n,p,m,o){this.errorHandler(n,p,m,o)},this);return this},render:function(o,p){this.log("render:",o,p);o=(o===undefined)?(this.fxSpeed):(o);var m=this,n;if(this.model){n=this.renderModel()}else{n=this.renderWithoutModel()}$(m).queue("fx",[function(q){if(o&&m.$el.is(":visible")){m.$el.fadeOut(o,q)}else{q()}},function(q){m.$el.empty();if(n){m.$el.append(n.children())}q()},function(q){if(o&&!m.$el.is(":visible")){m.$el.fadeIn(o,q)}else{q()}},function(q){if(p){p.call(this)}m.trigger("rendered",this);q()}]);return this},renderWithoutModel:function(){var m=$("<div/>"),n=$("<div/>").addClass("message-container").css({margin:"4px"});return m.append(n)},renderModel:function(){var m=$("<div/>");m.append(j.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(m).text(this.emptyMsg);m.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(m);this.renderHdas(m);return m},_renderEmptyMsg:function(o){var n=this,m=n.$emptyMessage(o);if(!_.isEmpty(n.hdaViews)){m.hide()}else{if(n.searchFor){m.text(n.noneFoundMsg).show()}else{m.text(n.emptyMsg).show()}}return this},_renderSearchButton:function(m){return faIconButton({title:d("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(m){m=m||this.$el;m.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(m.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(m){return(m||this.$el).find(".datasets-list")},$messages:function(m){return(m||this.$el).find(".message-container")},$emptyMessage:function(m){return(m||this.$el).find(".empty-history-message")},renderHdas:function(n){n=n||this.$el;var m=this,p={},o=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(n).empty();if(o.length){o.each(function(r){var q=r.get("id"),s=m._createContentView(r);p[q]=s;if(_.contains(m.selectedHdaIds,q)){s.selected=true}m.attachContentView(s.render(),n)})}this.hdaViews=p;this._renderEmptyMsg(n);return this.hdaViews},_createContentView:function(n){var m=n.get("id"),p=n.get("history_content_type"),o=null;if(p==="dataset"){o=new this.HDAViewClass({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}else{o=new k.DatasetCollectionBaseView({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}this._setUpHdaListeners(o);return o},_setUpHdaListeners:function(n){var m=this;n.on("error",function(p,r,o,q){m.errorHandler(p,r,o,q)});n.on("body-expanded",function(o){m.storage.addExpandedHda(o)});n.on("body-collapsed",function(o){m.storage.removeExpandedHda(o)});return this},attachContentView:function(o,n){n=n||this.$el;var m=this.$datasetsList(n);m.prepend(o.$el);return this},addContentView:function(p){this.log("add."+this,p);var n=this;if(!p.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return n}$({}).queue([function o(r){var q=n.$emptyMessage();if(q.is(":visible")){q.fadeOut(n.fxSpeed,r)}else{r()}},function m(q){var r=n._createContentView(p);n.hdaViews[p.id]=r;r.render().$el.hide();n.scrollToTop();n.attachContentView(r);r.$el.slideDown(n.fxSpeed)}]);return n},refreshContents:function(n,m){if(this.model){return this.model.refresh(n,m)}return $.when()},hdaViewRange:function(p,o){if(p===o){return[p]}var m=this,n=false,q=[];this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters).each(function(r){if(n){q.push(m.hdaViews[r.id]);if(r===p.model||r===o.model){n=false}}else{if(r===p.model||r===o.model){n=true;q.push(m.hdaViews[r.id])}}});return q},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(m){m.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",m);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",m);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(n){var o=this,p=".history-search-input";function m(q){if(o.model.hdas.haveDetails()){o.searchHdas(q);return}o.$el.find(p).searchInput("toggle-loading");o.model.hdas.fetchAllDetails({silent:true}).always(function(){o.$el.find(p).searchInput("toggle-loading")}).done(function(){o.searchHdas(q)})}n.searchInput({initialVal:o.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:m,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return n},toggleSearchControls:function(o,m){var n=this.$el.find(".history-search-controls"),p=(jQuery.type(o)==="number")?(o):(this.fxSpeed);m=(m!==undefined)?(m):(!n.is(":visible"));if(m){n.slideDown(p,function(){$(this).find("input").focus()})}else{n.slideUp(p)}return m},searchHdas:function(m){var n=this;this.searchFor=m;this.filters=[function(o){return o.matchesAll(n.searchFor)}];this.trigger("search:searching",m,this);this.renderHdas();return this},clearHdaSearch:function(m){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(n,m,o){m=(m!==undefined)?(m):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,o)}else{this.$el.fadeOut(m);this.indicator.show(n,m,o)}},_hideLoadingIndicator:function(m,n){m=(m!==undefined)?(m):(this.fxSpeed);if(this.indicator){this.indicator.hide(m,n)}},displayMessage:function(r,s,q){var o=this;this.scrollToTop();var p=this.$messages(),m=$("<div/>").addClass(r+"message").html(s);if(!_.isEmpty(q)){var n=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(o._messageToModalOptions(r,s,q));return false});m.append(" ",n)}return p.html(m)},_messageToModalOptions:function(q,s,p){var m=this,r=$("<div/>"),o={title:"Details"};function n(t){t=_.omit(t,_.functions(t));return["<table>",_.map(t,function(v,u){v=(_.isObject(v))?(n(v)):(v);return'<tr><td style="vertical-align: top; color: grey">'+u+'</td><td style="padding-left: 8px">'+v+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(p)){o.body=r.append(n(p))}else{o.body=r.html(p)}o.buttons={Ok:function(){Galaxy.modal.hide();m.clearMessages()}};return o},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(m){this.$container().scrollTop(m);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(n){if((!n)||(!this.hdaViews[n])){return this}var m=this.hdaViews[n];this.scrollTo(m.el.offsetTop);return this},scrollToHid:function(m){var n=this.model.hdas.getByHid(m);if(!n){return this}return this.scrollToId(n.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var l=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',d("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',d("You are over your disk quota"),". ",d("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',d("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',d("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',d("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',d("This history is empty"),"</div>"].join("");j.templates={historyPanel:function(m){return _.template(l,m,{variable:"history"})}};return{ReadOnlyHistoryPanel:j}}); \ 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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