commit/galaxy-central: carlfeberhard: UI: add pagination jquery plugin able to handle known/unknown data totals; Scatterplot: use that plugin for pagination, add class for highlighted data points
by commits-noreply＠bitbucket.org 14 Feb '14
by commits-noreply＠bitbucket.org 14 Feb '14
14 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/955e973c5b33/
Changeset: 955e973c5b33
User: carlfeberhard
Date: 2014-02-14 16:17:56
Summary: UI: add pagination jquery plugin able to handle known/unknown data totals; Scatterplot: use that plugin for pagination, add class for highlighted data points
Affected #: 9 files
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js
--- a/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js
@@ -5,7 +5,7 @@
Better separation of AJAX in scatterplot.js (maybe pass in function?)
Labels should auto fill in chart control when dataset has column_names
Allow column selection/config using the peek output as a base for UI
- Allow setting perPage in config
+ Allow setting perPage in chart controls
Allow option to auto set width/height based on screen real estate avail.
Handle large number of pages better (Known genes hg19)
Use d3.nest to allow grouping, pagination/filtration by group (e.g. chromCol)
@@ -243,7 +243,7 @@
alert( 'Error loading data:\n' + xhr.responseText );
})
.then( function(){
- editor.render();
+ editor.display.render();
});
},
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 config/plugins/visualizations/scatterplot/src/scatterplot-display.js
--- a/config/plugins/visualizations/scatterplot/src/scatterplot-display.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot-display.js
@@ -11,25 +11,15 @@
initialize : function( attributes ){
this.data = null,
this.dataset = attributes.dataset;
- this.calcNumPages();
- },
-
- calcNumPages : function(){
- var config = this.model.get( 'config' );
- this.lineCount = this.dataset.metadata_data_lines,
- this.numPages = ( this.lineCount )?( Math.ceil( this.lineCount / config.pagination.perPage ) ):( undefined );
- if( !this.lineCount || this.numPages === undefined ){
- console.warn( 'no data total found' );
- }
+ this.lineCount = this.dataset.metadata_data_lines || null;
},
fetchData : function(){
-//TODO: doesn't work bc it's rendered in render()...
- this.showLoadingIndicator( 'getting data' );
+ this.showLoadingIndicator();
//console.debug( 'currPage', this.config.pagination.currPage );
var view = this,
config = this.model.get( 'config' ),
-//TODO: very tied to datasets - should be generalized eventually
+ //TODO: very tied to datasets - should be generalized eventually
xhr = jQuery.getJSON( '/api/datasets/' + this.dataset.id, {
data_type : 'raw_data',
provider : 'dataset-column',
@@ -37,6 +27,7 @@
offset : ( config.pagination.currPage * config.pagination.perPage )
});
xhr.done( function( data ){
+ // no need to hide loading indicator, line info will write over that
view.data = data.data;
view.trigger( 'data:fetched', view );
view.renderData();
@@ -63,6 +54,7 @@
var html = [
'<div class="controls clear">',
'<div class="left">',
+ '<div class="page-control"></div>',
'</div>',
'<div class="right">',
'<p class="scatterplot-data-info"></p>',
@@ -92,11 +84,24 @@
},
renderLeftControls : function(){
- if( this.lineCount ){
- this.$el.find( '.controls .left' ).empty().append( this.renderPagination() );
- } else {
- this.$el.find( '.controls .left' ).empty().append( this.renderPrevNext() );
- }
+ var display = this,
+ config = this.model.get( 'config' );
+
+ this.$el.find( '.controls .left .page-control' ).pagination({
+ startingPage : config.pagination.currPage,
+ perPage : config.pagination.perPage,
+ totalDataSize: this.lineCount,
+ currDataSize : this.data.length
+
+ //TODO: move to named function and remove only named
+ }).off().on( 'pagination.page-change', function( event, page ){
+ //console.debug( 'pagination:page-change', page );
+ config.pagination.currPage = page;
+ display.model.set( 'config', { pagination: config.pagination });
+ //console.debug( pagination, display.model.get( 'config' ).pagination );
+ display.resetZoom();
+ display.fetchData();
+ });
return this;
},
@@ -155,83 +160,6 @@
return this;
},
- // ------------------------------------------------------------------------ data pagination
-//TODO: to pagination control
- goToPage : function( page ){
- var pagination = this.model.get( 'config' ).pagination;
- //console.debug( 'goToPage', page, pagination, this.numPages );
- if( page <= 0 ){ page = 0; }
- if( this.numPages && page >= this.numPages ){ page = this.numPages - 1; }
- if( page === pagination.currPage ){ return this; }
-
- //console.debug( '\t going to page ' + page )
- pagination.currPage = page;
- this.model.set( 'config', { pagination: pagination });
- this.resetZoom();
- this.fetchData();
- return this;
- },
-
- nextPage : function(){
- var currPage = this.model.get( 'config' ).pagination.currPage;
- return this.goToPage( currPage + 1 );
- },
-
- prevPage : function(){
- var currPage = this.model.get( 'config' ).pagination.currPage;
- return this.goToPage( currPage - 1 );
- },
-
- /** render previous and next pagination buttons */
- renderPrevNext : function(){
- var config = this.model.get( 'config' );
- // if there's no data or there's less than one page of data - return null
- if( !this.data ){ return null; }
- if( config.pagination.currPage === 0 && this.data.length < config.pagination.perPage ){ return null; }
-
- var view = this,
- $prev = $( '<li><a href="javascript:void(0);">Prev</a></li>' )
- .click( function(){ view.prevPage(); }),
- $next = $( '<li><a href="javascript:void(0);">Next</a></li>' )
- .click( function(){ view.nextPage(); });
-
- // disable if it either end
- if( config.pagination.currPage === 0 ){
- $prev.addClass( 'disabled' );
- }
- if( this.numPages && config.pagination.currPage === ( this.numPages - 1 ) ){
- $next.addClass( 'disabled' );
- }
- return $( '<ul/>' ).addClass( 'pagination data-prev-next' ).append([ $prev, $next ]);
- },
-
- /** render page links for each possible page (if we can) */
- renderPagination : function(){
- var config = this.model.get( 'config' );
- // if there's no data, no page count, or there's less than one page of data - return null
- if( !this.data ){ return null; }
- if( !this.numPages ){ return null; }
- if( config.pagination.currPage === 0 && this.data.length < config.pagination.perPage ){ return null; }
-
- var view = this,
- $pagesList = $( '<ul/>' ).addClass( 'pagination data-pages' );
- pageNumClick = function( ev ){
- view.goToPage( $( this ).data( 'page' ) );
- };
-
- for( var i=0; i<this.numPages; i+=1 ){
- // add html5 data tag 'page' for later click event handler use
- var $pageLi = $([ '<li><a href="javascript:void(0);">', i + 1, '</a></li>' ].join( '' ))
- .attr( 'data-page', i ).click( pageNumClick );
- // highlight the current page
- if( i === config.pagination.currPage ){
- $pageLi.addClass( 'active' );
- }
- $pagesList.append( $pageLi );
- }
- return $pagesList;
- },
-
// ------------------------------------------------------------------------ statistics display
/** create a webworker to calc stats for data given */
getStats : function(){
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 config/plugins/visualizations/scatterplot/src/scatterplot.js
--- a/config/plugins/visualizations/scatterplot/src/scatterplot.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot.js
@@ -237,6 +237,7 @@
datapoints.on( 'mouseover', function( d, i ){
var datapoint = d3.select( this );
datapoint
+ .classed( 'highlight', true )
.style( 'fill', 'red' )
.style( 'fill-opacity', 1 );
@@ -273,6 +274,7 @@
datapoints.on( 'mouseout', function(){
// return the point to normal, remove hoverlines and info box
d3.select( this )
+ .classed( 'highlight', false )
.style( 'fill', 'black' )
.style( 'fill-opacity', 0.2 );
content.selectAll( '.hoverline' ).remove();
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
--- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
+++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
@@ -1,1 +1,1 @@
-function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+i((f=b.x,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+i((f=b.y,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n <option value="',(d=c.index)?d=d.call(a,{hash:{},data:b}):(d=a.index,d=typeof d===j?d.apply(a):d),e+=k(d)+'">',(d=c.name)?d=d.call(a,{hash:{},data:b}):(d=a.name,d=typeof d===j?d.apply(a):d),e+=k(d)+"</option>\n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='<p class="help-text">\n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n\n<div class="column-select">\n <label>Data column for X: </label>\n <select name="xColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n<div class="column-select">\n <label>Data column for Y: </label>\n <select name="yColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n</div>\n<div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="idColumn">\n ',h=c.each.call(b,b.allColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="first-line-header" style="display: none;">\n <p>Possible headers: ',(h=c.possibleHeaders)?h=h.call(b,{hash:{},data:e}):(h=b.possibleHeaders,h=typeof h===j?h.apply(b):h),i+=k(h)+'\n </p>\n <label for="first-line-header-checkbox">Use the above as column headers?</label>\n <input type="checkbox" name="include-id" id="first-line-header-checkbox"\n ',h=c["if"].call(b,b.usePossibleHeaders,{hash:{},inverse:l.noop,fn:l.program(3,g,e),data:e}),(h||0===h)&&(i+=h),i+='/>\n <p class="help-text-small">\n It looks like Galaxy couldn\'t get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n<!-- <button class="copy-btn btn btn-default"\n title="Save this as a new visualization">Save to new</button>-->\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.dataset,d=c.metadata_column_names||[],e=this.model.get("config"),f=[],g=_.map(c.metadata_column_types,function(a,b){var c={index:b,type:a,name:d[b]||"column "+(b+1)};return("int"===c.type||"float"===c.type)&&f.push(c),c});f.length<2&&(f=g);var h=a.find(".tab-pane#data-control");h.html(ScatterplotConfigEditor.templates.dataControl({allColumns:g,numericColumns:f}));var i={xColumn:_.isFinite(e.xColumn)?e.xColumn:f[0].index,yColumn:_.isFinite(e.yColumn)?e.yColumn:f[1].index,idColumn:g[0].index};if(_.isFinite(e.idColumn))i.idColumn=e.idColumn;else if(g.length>2){var j=_.find(g,function(a,b){return b!==i.xColumn&&b!==i.yColumn});i.idColumn=j.index}return e=this.model.set("config",i,{silent:!0}).get("config"),h.find('[name="xColumn"]').val(e.xColumn).on("change",function(){b.model.set("config",{xColumn:Number($(this).val())})}),h.find('[name="yColumn"]').val(e.yColumn).on("change",function(){b.model.set("config",{yColumn:Number($(this).val())})}),h.find('select[name="idColumn"]').val(e.idColumn).on("change",function(){b.model.set("config",{idColumn:Number($(this).val())})}),void 0!==e.idColumn&&h.find("#include-id-checkbox").prop("checked",!0).trigger("change"),h.find("[title]").tooltip(),h},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.calcNumPages()},calcNumPages:function(){var a=this.model.get("config");this.lineCount=this.dataset.metadata_data_lines,this.numPages=this.lineCount?Math.ceil(this.lineCount/a.pagination.perPage):void 0,this.lineCount&&void 0!==this.numPages||console.warn("no data total found")},fetchData:function(){this.showLoadingIndicator("getting data");var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="left">',"</div>",'<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){return this.lineCount?this.$el.find(".controls .left").empty().append(this.renderPagination()):this.$el.find(".controls .left").empty().append(this.renderPrevNext()),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},goToPage:function(a){var b=this.model.get("config").pagination;return 0>=a&&(a=0),this.numPages&&a>=this.numPages&&(a=this.numPages-1),a===b.currPage?this:(b.currPage=a,this.model.set("config",{pagination:b}),this.resetZoom(),this.fetchData(),this)},nextPage:function(){var a=this.model.get("config").pagination.currPage;return this.goToPage(a+1)},prevPage:function(){var a=this.model.get("config").pagination.currPage;return this.goToPage(a-1)},renderPrevNext:function(){var a=this.model.get("config");if(!this.data)return null;if(0===a.pagination.currPage&&this.data.length<a.pagination.perPage)return null;var b=this,c=$('<li><a href="javascript:void(0);">Prev</a></li>').click(function(){b.prevPage()}),d=$('<li><a href="javascript:void(0);">Next</a></li>').click(function(){b.nextPage()});return 0===a.pagination.currPage&&c.addClass("disabled"),this.numPages&&a.pagination.currPage===this.numPages-1&&d.addClass("disabled"),$("<ul/>").addClass("pagination data-prev-next").append([c,d])},renderPagination:function(){var a=this.model.get("config");if(!this.data)return null;if(!this.numPages)return null;if(0===a.pagination.currPage&&this.data.length<a.pagination.perPage)return null;var b=this,c=$("<ul/>").addClass("pagination data-pages");pageNumClick=function(){b.goToPage($(this).data("page"))};for(var d=0;d<this.numPages;d+=1){var e=$(['<li><a href="javascript:void(0);">',d+1,"</a></li>"].join("")).attr("data-page",d).click(pageNumClick);d===a.pagination.currPage&&e.addClass("active"),c.append(e)}return c},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.x.label,e=b.y.label,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}});
\ No newline at end of file
+function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+i((f=b.x,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+i((f=b.y,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n <option value="',(d=c.index)?d=d.call(a,{hash:{},data:b}):(d=a.index,d=typeof d===j?d.apply(a):d),e+=k(d)+'">',(d=c.name)?d=d.call(a,{hash:{},data:b}):(d=a.name,d=typeof d===j?d.apply(a):d),e+=k(d)+"</option>\n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='<p class="help-text">\n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n\n<div class="column-select">\n <label>Data column for X: </label>\n <select name="xColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n<div class="column-select">\n <label>Data column for Y: </label>\n <select name="yColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n</div>\n<div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="idColumn">\n ',h=c.each.call(b,b.allColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="first-line-header" style="display: none;">\n <p>Possible headers: ',(h=c.possibleHeaders)?h=h.call(b,{hash:{},data:e}):(h=b.possibleHeaders,h=typeof h===j?h.apply(b):h),i+=k(h)+'\n </p>\n <label for="first-line-header-checkbox">Use the above as column headers?</label>\n <input type="checkbox" name="include-id" id="first-line-header-checkbox"\n ',h=c["if"].call(b,b.usePossibleHeaders,{hash:{},inverse:l.noop,fn:l.program(3,g,e),data:e}),(h||0===h)&&(i+=h),i+='/>\n <p class="help-text-small">\n It looks like Galaxy couldn\'t get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n<!-- <button class="copy-btn btn btn-default"\n title="Save this as a new visualization">Save to new</button>-->\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.dataset,d=c.metadata_column_names||[],e=this.model.get("config"),f=[],g=_.map(c.metadata_column_types,function(a,b){var c={index:b,type:a,name:d[b]||"column "+(b+1)};return("int"===c.type||"float"===c.type)&&f.push(c),c});f.length<2&&(f=g);var h=a.find(".tab-pane#data-control");h.html(ScatterplotConfigEditor.templates.dataControl({allColumns:g,numericColumns:f}));var i={xColumn:_.isFinite(e.xColumn)?e.xColumn:f[0].index,yColumn:_.isFinite(e.yColumn)?e.yColumn:f[1].index,idColumn:g[0].index};if(_.isFinite(e.idColumn))i.idColumn=e.idColumn;else if(g.length>2){var j=_.find(g,function(a,b){return b!==i.xColumn&&b!==i.yColumn});i.idColumn=j.index}return e=this.model.set("config",i,{silent:!0}).get("config"),h.find('[name="xColumn"]').val(e.xColumn).on("change",function(){b.model.set("config",{xColumn:Number($(this).val())})}),h.find('[name="yColumn"]').val(e.yColumn).on("change",function(){b.model.set("config",{yColumn:Number($(this).val())})}),h.find('select[name="idColumn"]').val(e.idColumn).on("change",function(){b.model.set("config",{idColumn:Number($(this).val())})}),void 0!==e.idColumn&&h.find("#include-id-checkbox").prop("checked",!0).trigger("change"),h.find("[title]").tooltip(),h},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.calcNumPages()},calcNumPages:function(){var a=this.model.get("config");this.lineCount=this.dataset.metadata_data_lines,this.numPages=this.lineCount?Math.ceil(this.lineCount/a.pagination.perPage):void 0,this.lineCount&&void 0!==this.numPages||console.warn("no data total found")},fetchData:function(){this.showLoadingIndicator("getting data");var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="left">','<div class="page-control"></div>',"</div>",'<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount||null,currDataSize:this.data.length,maxWidth:540}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.x.label,e=b.y.label,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}});
\ No newline at end of file
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 config/plugins/visualizations/scatterplot/static/scatterplot.css
--- a/config/plugins/visualizations/scatterplot/static/scatterplot.css
+++ b/config/plugins/visualizations/scatterplot/static/scatterplot.css
@@ -125,13 +125,9 @@
margin: 0px;
}
-.scatterplot-display .controls .left {
- float: left;
-}
-
-.scatterplot-display .controls .pagination {
- display: inline-block;
- margin: 0px;
+.scatterplot-display .pagination-scroll-container {
+ /* float left makes this not collapse very well */
+ max-width: 540px;
}
.scatterplot-display .controls .data-prev-next {
@@ -139,22 +135,16 @@
margin: 0px 4px 0px 0px;
}
-.scatterplot-display .controls .pagination-container {
- display: inline-block;
- overflow: auto;
- max-width: 256px;
- /*very tweaky*/
- margin: 0px 8px 0px 0px;
- height: 27px;
- padding-top: 5px;
+.scatterplot-display .controls {
}
-.scatterplot-display .controls .pagination-container a {
- display: inline;
- /* WTH, bootstrap? */
- position: static;
- float: none;
- /* up from 4px -> 5px */
- padding: 5px 10px 5px 10px;
+
+.scatterplot-display .controls .left,
+.scatterplot-display .controls .right {
+ position: relative;
+}
+
+.scatterplot-display .controls .left {
+ float: left;
}
.scatterplot-display .controls .right {
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 config/plugins/visualizations/scatterplot/templates/scatterplot.mako
--- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
+++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
@@ -32,6 +32,7 @@
<script type="text/javascript" src="/static/scripts/libs/d3.js"></script><script type="text/javascript" src="/static/scripts/mvc/base-mvc.js"></script>
+<script type="text/javascript" src="/static/scripts/mvc/ui.js"></script><script type="text/javascript" src="/static/scripts/mvc/visualization/visualization-model.js"></script><script type="text/javascript" src="/plugins/visualizations/scatterplot/static/scatterplot-edit.js"></script>
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 static/scripts/mvc/ui.js
--- a/static/scripts/mvc/ui.js
+++ b/static/scripts/mvc/ui.js
@@ -517,6 +517,90 @@
//==============================================================================
+function LoadingIndicator( $where, options ){
+//TODO: move out of global
+//TODO: too specific to history panel
+
+ var self = this;
+ // defaults
+ options = jQuery.extend({
+ cover : false
+ }, options || {} );
+
+ function render(){
+ var html = [
+ '<div class="loading-indicator">',
+ '<div class="loading-indicator-text">',
+ '<span class="fa fa-spinner fa-spin fa-lg"></span>',
+ '<span class="loading-indicator-message">loading...</span>',
+ '</div>',
+ '</div>'
+ ].join( '\n' );
+
+ var $indicator = $( html ).hide().css( options.css || {
+ position : 'fixed'
+ }),
+ $text = $indicator.children( '.loading-indicator-text' );
+
+ if( options.cover ){
+ $indicator.css({
+ 'z-index' : 2,
+ top : $where.css( 'top' ),
+ bottom : $where.css( 'bottom' ),
+ left : $where.css( 'left' ),
+ right : $where.css( 'right' ),
+ opacity : 0.5,
+ 'background-color': 'white',
+ 'text-align': 'center'
+ });
+ $text = $indicator.children( '.loading-indicator-text' ).css({
+ 'margin-top' : '20px'
+ });
+
+ } else {
+ $text = $indicator.children( '.loading-indicator-text' ).css({
+ margin : '12px 0px 0px 10px',
+ opacity : '0.85',
+ color : 'grey'
+ });
+ $text.children( '.loading-indicator-message' ).css({
+ margin : '0px 8px 0px 0px',
+ 'font-style' : 'italic'
+ });
+ }
+ return $indicator;
+ }
+
+ self.show = function( msg, speed, callback ){
+ msg = msg || 'loading...';
+ speed = speed || 'fast';
+ // since position is fixed - we insert as sibling
+ self.$indicator = render().insertBefore( $where );
+ self.message( msg );
+ self.$indicator.fadeIn( speed, callback );
+ return self;
+ };
+
+ self.message = function( msg ){
+ self.$indicator.find( 'i' ).text( msg );
+ };
+
+ self.hide = function( speed, callback ){
+ speed = speed || 'fast';
+ if( self.$indicator && self.$indicator.size() ){
+ self.$indicator.fadeOut( speed, function(){
+ self.$indicator.remove();
+ if( callback ){ callback(); }
+ });
+ } else {
+ if( callback ){ callback(); }
+ }
+ return self;
+ };
+ return self;
+}
+
+//==============================================================================
(function(){
/** searchInput: (jQuery plugin)
* Creates a search input, a clear button, and loading indicator
@@ -614,7 +698,7 @@
clearSearchInput.call( this, event );
});
}
-
+
// .................................................................... loadingIndicator rendering
// a button for clearing the search bar, placed on the right hand side
function $loadingIndicator(){
@@ -803,91 +887,6 @@
//==============================================================================
-function LoadingIndicator( $where, options ){
-//TODO: move out of global
-//TODO: too specific to history panel
-
- var self = this;
- // defaults
- options = jQuery.extend({
- cover : false
- }, options || {} );
-
- function render(){
- var html = [
- '<div class="loading-indicator">',
- '<div class="loading-indicator-text">',
- '<span class="fa fa-spinner fa-spin fa-lg"></span>',
- '<span class="loading-indicator-message">loading...</span>',
- '</div>',
- '</div>'
- ].join( '\n' );
-
- var $indicator = $( html ).hide().css( options.css || {
- position : 'fixed'
- }),
- $text = $indicator.children( '.loading-indicator-text' );
-
- if( options.cover ){
- $indicator.css({
- 'z-index' : 2,
- top : $where.css( 'top' ),
- bottom : $where.css( 'bottom' ),
- left : $where.css( 'left' ),
- right : $where.css( 'right' ),
- opacity : 0.5,
- 'background-color': 'white',
- 'text-align': 'center'
- });
- $text = $indicator.children( '.loading-indicator-text' ).css({
- 'margin-top' : '20px'
- });
-
- } else {
- $text = $indicator.children( '.loading-indicator-text' ).css({
- margin : '12px 0px 0px 10px',
- opacity : '0.85',
- color : 'grey'
- });
- $text.children( '.loading-indicator-message' ).css({
- margin : '0px 8px 0px 0px',
- 'font-style' : 'italic'
- });
- }
- return $indicator;
- }
-
- self.show = function( msg, speed, callback ){
- msg = msg || 'loading...';
- speed = speed || 'fast';
- // since position is fixed - we insert as sibling
- self.$indicator = render().insertBefore( $where );
- self.message( msg );
- self.$indicator.fadeIn( speed, callback );
- return self;
- };
-
- self.message = function( msg ){
- self.$indicator.find( 'i' ).text( msg );
- };
-
- self.hide = function( speed, callback ){
- speed = speed || 'fast';
- if( self.$indicator && self.$indicator.size() ){
- self.$indicator.fadeOut( speed, function(){
- self.$indicator.remove();
- if( callback ){ callback(); }
- });
- } else {
- if( callback ){ callback(); }
- }
- return self;
- };
- return self;
-}
-
-
-//==============================================================================
/**
* Template function that produces a bootstrap dropdown to replace the
* vanilla HTML select input. Pass in an array of options and an initial selection:
@@ -1082,3 +1081,221 @@
}
});
}());
+
+
+//==============================================================================
+(function(){
+ /** Builds (twitter bootstrap styled) pagination controls.
+ * If the totalDataSize is not null, a horizontal list of page buttons is displayed.
+ * If totalDataSize is null, two links ('Prev' and 'Next) are displayed.
+ * When pages are changed, a 'pagination.page-change' event is fired
+ * sending the event and the (0-based) page requested.
+ */
+ function Pagination( element, options ){
+ /** the total number of pages */
+ this.numPages = null;
+ /** the current, active page */
+ this.currPage = 0;
+ return this.init( element, options );
+ }
+
+ /** data key under which this object will be stored in the element */
+ Pagination.prototype.DATA_KEY = 'pagination';
+ /** default options */
+ Pagination.prototype.defaults = {
+ /** which page to begin at */
+ startingPage : 0,
+ /** number of data per page */
+ perPage : 20,
+ /** the total number of data (null == unknown) */
+ totalDataSize : null,
+ /** size of current data on current page */
+ currDataSize : null
+ };
+
+ /** init the control, calc numPages if possible, and render
+ * @param {jQuery} the element that will contain the pagination control
+ * @param {Object} options a map containing overrides to the pagination default options
+ */
+ Pagination.prototype.init = function _init( $element, options ){
+ options = options || {};
+ this.$element = $element;
+ this.options = jQuery.extend( true, {}, this.defaults, options );
+
+ this.currPage = this.options.startingPage;
+ if( this.options.totalDataSize !== null ){
+ this.numPages = Math.ceil( this.options.totalDataSize / this.options.perPage );
+ // limit currPage by numPages
+ if( this.currPage >= this.numPages ){
+ this.currPage = this.numPages - 1;
+ }
+ }
+ //console.debug( 'Pagination.prototype.init:', this.$element, this.currPage );
+ //console.debug( JSON.stringify( this.options ) );
+
+ // bind to data of element
+ this.$element.data( Pagination.prototype.DATA_KEY, this );
+
+ this._render();
+ return this;
+ };
+
+ /** helper to create a simple li + a combo */
+ function _make$Li( contents ){
+ return $([
+ '<li><a href="javascript:void(0);">', contents, '</a></li>'
+ ].join( '' ));
+ }
+
+ /** render previous and next pagination buttons */
+ Pagination.prototype._render = function __render(){
+ // no data - no pagination
+ if( this.options.totalDataSize === 0 ){ return this; }
+ // only one page
+ if( this.numPages === 1 ){ return this; }
+
+ // when the number of pages are known, render each page as a link
+ if( this.numPages > 0 ){
+ this._renderPages();
+ this._scrollToActivePage();
+
+ // when the number of pages is not known, render previous or next
+ } else {
+ this._renderPrevNext();
+ }
+ return this;
+ };
+
+ /** render previous and next pagination buttons */
+ Pagination.prototype._renderPrevNext = function __renderPrevNext(){
+ var pagination = this,
+ $prev = _make$Li( 'Prev' ),
+ $next = _make$Li( 'Next' ),
+ $paginationContainer = $( '<ul/>' ).addClass( 'pagination pagination-prev-next' );
+
+ // disable if it either end
+ if( this.currPage === 0 ){
+ $prev.addClass( 'disabled' );
+ } else {
+ $prev.click( function(){ pagination.prevPage(); });
+ }
+ if( ( this.numPages && this.currPage === ( this.numPages - 1 ) )
+ || ( this.options.currDataSize && this.options.currDataSize < this.options.perPage ) ){
+ $next.addClass( 'disabled' );
+ } else {
+ $next.click( function(){ pagination.nextPage(); });
+ }
+
+ this.$element.html( $paginationContainer.append([ $prev, $next ]) );
+ //console.debug( this.$element, this.$element.html() );
+ return this.$element;
+ };
+
+ /** render page links for each possible page (if we can) */
+ Pagination.prototype._renderPages = function __renderPages(){
+ // it's better to scroll the control and let the user see all pages
+ // than to force her/him to change pages in order to find the one they want (as traditional << >> does)
+ var pagination = this,
+ $scrollingContainer = $( '<div>' ).addClass( 'pagination-scroll-container' ),
+ $paginationContainer = $( '<ul/>' ).addClass( 'pagination pagination-page-list' ),
+ page$LiClick = function( ev ){
+ pagination.goToPage( $( this ).data( 'page' ) );
+ };
+
+ for( var i=0; i<this.numPages; i+=1 ){
+ // add html5 data tag 'page' for later click event handler use
+ var $pageLi = _make$Li( i + 1 ).attr( 'data-page', i ).click( page$LiClick );
+ // highlight the current page
+ if( i === this.currPage ){
+ $pageLi.addClass( 'active' );
+ }
+ //console.debug( '\t', $pageLi );
+ $paginationContainer.append( $pageLi );
+ }
+ return this.$element.html( $scrollingContainer.html( $paginationContainer ) );
+ };
+
+ /** scroll scroll-container (if any) to show the active page */
+ Pagination.prototype._scrollToActivePage = function __scrollToActivePage(){
+ // scroll to show active page in center of scrollable area
+ var $container = this.$element.find( '.pagination-scroll-container' );
+ // no scroll container : don't scroll
+ if( !$container.size() ){ return this; }
+
+ var $activePage = this.$element.find( 'li.active' ),
+ midpoint = $container.width() / 2;
+ //console.debug( $container, $activePage, midpoint );
+ $container.scrollLeft( $container.scrollLeft() + $activePage.position().left - midpoint );
+ return this;
+ };
+
+ /** go to a certain page */
+ Pagination.prototype.goToPage = function goToPage( page ){
+ if( page <= 0 ){ page = 0; }
+ if( this.numPages && page >= this.numPages ){ page = this.numPages - 1; }
+ if( page === this.currPage ){ return this; }
+
+ //console.debug( '\t going to page ' + page )
+ this.currPage = page;
+ this.$element.trigger( 'pagination.page-change', this.currPage );
+ //console.info( 'pagination:page-change', this.currPage );
+ this._render();
+ return this;
+ };
+
+ /** go to the previous page */
+ Pagination.prototype.prevPage = function prevPage(){
+ return this.goToPage( this.currPage - 1 );
+ };
+
+ /** go to the next page */
+ Pagination.prototype.nextPage = function nextPage(){
+ return this.goToPage( this.currPage + 1 );
+ };
+
+ /** return the current page */
+ Pagination.prototype.page = function page(){
+ return this.currPage;
+ };
+
+ // alternate constructor invocation
+ Pagination.create = function _create( $element, options ){
+ return new Pagination( $element, options );
+ };
+
+ // as jq plugin
+ jQuery.fn.extend({
+ pagination : function $pagination( options ){
+ var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 );
+
+ // if passed an object - use that as an options map to create pagination for each selected
+ if( jQuery.type( options ) === 'object' ){
+ return this.map( function(){
+ Pagination.create( $( this ), options );
+ return this;
+ });
+ }
+
+ // (other invocations only work on the first element in selected)
+ var $firstElement = $( this[0] ),
+ previousControl = $firstElement.data( Pagination.prototype.DATA_KEY );
+ // if a pagination control was found for this element, either...
+ if( previousControl ){
+ // invoke a function on the pagination object if passed a string (the function name)
+ if( jQuery.type( options ) === 'string' ){
+ var fn = previousControl[ options ];
+ if( jQuery.type( fn ) === 'function' ){
+ return fn.apply( previousControl, nonOptionsArgs );
+ }
+
+ // if passed nothing, return the previously set control
+ } else {
+ return previousControl;
+ }
+ }
+ // if there is no control already set, return undefined
+ return undefined;
+ }
+ });
+}());
+
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1390,6 +1390,12 @@
.quota-meter-bar-warn{background-color:#bf822c}
.quota-meter-bar-error{background-color:#b93e3a}
.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000;white-space:nowrap}
+.pagination{margin:0px}
+.pagination-scroll-container{overflow:auto;background-color:#F8F8F8;border-radius:3px;border:1px solid #BFBFBF}
+.pagination-scroll-container .pagination-page-list{margin:3px 0px 3px 0px}
+.pagination-scroll-container .pagination-page-list>li:first-child>a,.pagination-scroll-container .pagination-page-list>li:first-child>span{border-radius:0px;border-left:0px}
+.pagination-scroll-container .pagination-page-list>li:last-child>a,.pagination-scroll-container .pagination-page-list>li:last-child>span{border-radius:0px}
+.pagination-scroll-container .pagination-page-list>li>a{float:none;position:static;border:1px solid #BFBFBF;border-width:0px 0px 0px 1px}
div.metadataForm{border:solid #aaaaaa 1px}
div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px}
div.metadataFormBody{background:#FFFFFF;padding:5px 0}
diff -r f199022e48088ab4fd71701e07899b729496b005 -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 static/style/src/less/base.less
--- a/static/style/src/less/base.less
+++ b/static/style/src/less/base.less
@@ -508,6 +508,39 @@
white-space: nowrap;
}
+// ---------------------------------------------------------------------------- pagination & scrolling pagination
+.pagination {
+ margin: 0px;
+}
+
+.pagination-scroll-container {
+ overflow : auto;
+ background-color: #F8F8F8;
+ border-radius : 3px;
+ border : 1px solid #BFBFBF;
+}
+
+.pagination-scroll-container .pagination-page-list {
+ margin : 3px 0px 3px 0px;
+}
+
+.pagination-scroll-container .pagination-page-list > li:first-child > a,
+.pagination-scroll-container .pagination-page-list > li:first-child > span {
+ border-radius : 0px;
+ border-left : 0px;
+}
+
+.pagination-scroll-container .pagination-page-list > li:last-child > a,
+.pagination-scroll-container .pagination-page-list > li:last-child > span {
+ border-radius : 0px;
+}
+
+.pagination-scroll-container .pagination-page-list > li > a {
+ float : none;
+ position : static;
+ border : 1px solid #BFBFBF;
+ border-width : 0px 0px 0px 1px;
+}
// ==== Tool form styles ====
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e088f2dc8b07/
Changeset: e088f2dc8b07
Branch: stable
User: jmchilton
Date: 2014-02-13 18:15:10
Summary: Fix tool shed install and test framework to work with API driven tests.
Affected #: 1 file
diff -r 3691fd3e12ef8160ae993cef5ebd51ddeee95da1 -r e088f2dc8b070d13e9fb7319463786d7ff4f5024 test/install_and_test_tool_shed_repositories/base/util.py
--- a/test/install_and_test_tool_shed_repositories/base/util.py
+++ b/test/install_and_test_tool_shed_repositories/base/util.py
@@ -138,7 +138,7 @@
default_galaxy_test_host = '127.0.0.1'
# The following should be an actual value (not None). If developers manually specify their
# tests to use the API it will not work unless a master API key is specified.
-default_galaxy_master_api_key = 123456
+default_galaxy_master_api_key = '123456'
testing_single_repository_dict = {}
if 'repository_name' in os.environ and 'repository_owner' in os.environ:
https://bitbucket.org/galaxy/galaxy-central/commits/6d1dd4a389fd/
Changeset: 6d1dd4a389fd
User: jmchilton
Date: 2014-02-13 18:15:23
Summary: Merge latest stable.
Affected #: 1 file
diff -r 784f02de9effb43eafa84b5253af62091e6f2f36 -r 6d1dd4a389fd4a17fd9a7dc928860a1f0e01c214 test/install_and_test_tool_shed_repositories/base/util.py
--- a/test/install_and_test_tool_shed_repositories/base/util.py
+++ b/test/install_and_test_tool_shed_repositories/base/util.py
@@ -138,7 +138,7 @@
default_galaxy_test_host = '127.0.0.1'
# The following should be an actual value (not None). If developers manually specify their
# tests to use the API it will not work unless a master API key is specified.
-default_galaxy_master_api_key = 123456
+default_galaxy_master_api_key = '123456'
testing_single_repository_dict = {}
if 'repository_name' in os.environ and 'repository_owner' in os.environ:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/784f02de9eff/
Changeset: 784f02de9eff
User: guerler
Date: 2014-02-13 17:27:25
Summary: Merge
Affected #: 1 file
diff -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 -r 784f02de9effb43eafa84b5253af62091e6f2f36 lib/galaxy/webapps/reports/controllers/jobs.py
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -29,7 +29,7 @@
return job.tool_id
class CreateTimeColumn( grids.DateTimeColumn ):
def get_value( self, trans, grid, job ):
- return job.create_time.isoformat()
+ return job.create_time.strftime("%b %d, %Y, %H:%M:%S")
class UserColumn( grids.GridColumn ):
def get_value( self, trans, grid, job ):
if job.user:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Reports: Fix time format in grids
by commits-noreply＠bitbucket.org 14 Feb '14
by commits-noreply＠bitbucket.org 14 Feb '14
14 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef/
Changeset: 3691fd3e12ef
Branch: stable
User: guerler
Date: 2014-02-13 17:19:54
Summary: Reports: Fix time format in grids
Affected #: 1 file
diff -r b463c73f334811d4c48298c40de9ac489261c32d -r 3691fd3e12ef8160ae993cef5ebd51ddeee95da1 lib/galaxy/webapps/reports/controllers/jobs.py
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -29,7 +29,7 @@
return job.tool_id
class CreateTimeColumn( grids.DateTimeColumn ):
def get_value( self, trans, grid, job ):
- return job.create_time
+ return job.create_time.strftime("%b %d, %Y, %H:%M:%S")
class UserColumn( grids.GridColumn ):
def get_value( self, trans, grid, job ):
if job.user:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Ui: Apply naming convention
by commits-noreply＠bitbucket.org 13 Feb '14
by commits-noreply＠bitbucket.org 13 Feb '14
13 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/75a8d88ba728/
Changeset: 75a8d88ba728
User: guerler
Date: 2014-02-13 10:21:06
Summary: Ui: Apply naming convention
Affected #: 12 files
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/popover.js
--- a/static/scripts/mvc/ui/popover.js
+++ /dev/null
@@ -1,169 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-var View = Backbone.View.extend({
-
- // default options
- optionsDefault: {
- with_close : true,
- container : 'body',
- title : null,
- placement : 'top'
- },
-
- // visibility flag
- visible: false,
-
- // initialize
- initialize: function (options) {
-
- // link this
- var self = this;
-
- // update options
- this.options = _.defaults(options, this.optionsDefault);
-
- // set element
- this.setElement(this._template(this.options));
-
- // attach popover to parent
- this.options.container.parent().append(this.$el);
-
- // attach close
- if (this.options.with_close) {
- this.$el.find('#close').on('click', function() { self.hide(); });
- }
-
- // generate unique id
- this.uuid = Utils.uuid();
-
- // add event to hide if click is outside of popup
- var self = this;
- $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) });
- },
-
- // title
- title: function(val) {
- if (val !== undefined) {
- this.$el.find('.popover-title-label').html(val);
- }
- },
-
- // show
- show: function () {
- // show popover
- this.$el.show();
- this.visible = true;
-
- // calculate position
- var position = this._get_placement(this.options.placement);
-
- // set position
- this.$el.css(position);
- },
-
- // calculate position and error
- _get_placement: function(placement) {
- // get popover dimensions
- var width = this._get_width(this.$el);
- var height = this.$el.height();
-
- // get container details
- var $container = this.options.container;
- var container_width = this._get_width($container);
- var container_height = this._get_height($container);
- var container_position = $container.position();
-
- // initialize position
- var top = 0;
- var left = 0;
-
- // calculate position
- if (placement == 'top' || placement == 'bottom') {
- left = container_position.left - width + (container_width + width) / 2;
- if (placement == 'top') {
- top = container_position.top - height - 5;
- } else {
- top = container_position.top + container_height + 5;
- }
- }
-
- // return
- return {top: top, left: left};
- },
-
- // width
- _get_width: function($el) {
- return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right'))
- },
-
- // heigth
- _get_height: function($el) {
- return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom'))
- },
-
- // hide
- hide: function () {
- this.$el.hide();
- this.visible = false;
- },
-
- // append
- append: function($el) {
- this.$el.find('.popover-content').append($el);
- },
-
- // empty
- empty: function($el) {
- this.$el.find('.popover-content').empty();
- },
-
- // remove
- remove: function() {
- // remove event handler
- $('body').off('mousedown.' + this.uuid);
-
- // remove element from dom
- this.$el.remove();
- },
-
- // remove
- _hide : function(e) {
- //the 'is' for buttons that trigger popups
- //the 'has' for icons within a button that triggers a popup
- if (!$(this.options.container).is(e.target) &&
- !$(this.el).is(e.target) &&
- $(this.el).has(e.target).length === 0) {
- this.hide();
- }
- },
-
- // template
- _template: function(options) {
- var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' +
- '<div class="arrow"></div>' +
- '<div class="popover-title">' +
- '<div class="popover-title-label">' +
- options.title +
- '</div>';
-
- // add close icon
- if (options.with_close) {
- tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>';
- }
-
- // finalize
- tmpl += '</div>' +
- '<div class="popover-content"></div>' +
- '</div>';
-
- // return
- return tmpl;
- }
-});
-
-return {
- View: View
-}
-
-});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/select.js
--- a/static/scripts/mvc/ui/select.js
+++ /dev/null
@@ -1,193 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- css : '',
- placeholder : 'No data available',
- data : []
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add to dom
- this.options.container.append(this.$el);
-
- // link selection dictionary
- this.select_data = this.options.data;
-
- // refresh
- this._refresh();
-
- // initial value
- if (this.options.value) {
- this._setValue(this.options.value);
- }
-
- // add change event
- var self = this;
- if (this.options.onchange) {
- this.$el.on('change', function() {
- self.options.onchange(self.value());
- });
- }
- },
-
- // value
- value : function (new_value) {
- // get current id/value
- var before = this._getValue();
-
- // check if new_value is defined
- if (new_value !== undefined) {
- this._setValue(new_value);
- }
-
- // get current id/value
- var after = this._getValue();
- if(after === undefined) {
- return null;
- } else {
- // fire onchange
- if ((after != before && this.options.onchange)) {
- this.options.onchange(after);
- }
-
- // return current value
- return after;
- }
- },
-
- // label
- text : function () {
- return this.$el.select2('data').text;
- },
-
- // disabled
- disabled: function() {
- return !this.$el.select2('enable');
- },
-
- // enable
- enable: function() {
- this.$el.select2('enable', true);
- },
-
- // disable
- disable: function() {
- this.$el.select2('enable', false);
- },
-
- // add
- add: function(options) {
- // add options
- this.select_data.push({
- id : options.id,
- text : options.text
- });
-
- // refresh
- this._refresh();
- },
-
- // remove
- del: function(id) {
- // search option
- var index = this._getIndex(id);
-
- // check if found
- if (index != -1) {
- // remove options
- this.select_data.splice(index, 1);
-
- // refresh
- this._refresh();
- }
- },
-
- // remove
- remove: function() {
- this.$el.select2('destroy');
- },
-
- // update
- update: function(options) {
- // copy options
- this.select_data = [];
- for (var key in options.data) {
- this.select_data.push(options.data[key]);
- }
-
- // refresh
- this._refresh();
- },
-
- // refresh
- _refresh: function() {
-
- // link select data
- var select_data = this.select_data;
- if (!select_data || select_data.length == 0) {
- select_data = [];
- }
-
- // selected
- var selected = this._getValue();
-
- // add select2 data
- this.$el.select2({
- data : select_data,
- containerCssClass : this.options.css,
- placeholder : this.options.placeholder
- });
-
- // select
- var index = this._getIndex(selected);
- if (index != -1) {
- this._setValue(selected);
- }
- },
-
- // get index
- _getIndex: function(value) {
- // search index
- for (var key in this.select_data) {
- if (this.select_data[key].id == value) {
- return key;
- }
- }
-
- // not found
- return -1;
- },
-
- // get value
- _getValue: function() {
- return this.$el.select2('val');
- },
-
- // set value
- _setValue: function(new_value) {
- this.$el.select2('val', new_value);
- },
-
- // element
- _template: function(options) {
- return '<input type="hidden"/>';
- }
-});
-
-return {
- View : View
-}
-
-});
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/ui-popover.js
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-popover.js
@@ -0,0 +1,169 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+var View = Backbone.View.extend({
+
+ // default options
+ optionsDefault: {
+ with_close : true,
+ container : 'body',
+ title : null,
+ placement : 'top'
+ },
+
+ // visibility flag
+ visible: false,
+
+ // initialize
+ initialize: function (options) {
+
+ // link this
+ var self = this;
+
+ // update options
+ this.options = _.defaults(options, this.optionsDefault);
+
+ // set element
+ this.setElement(this._template(this.options));
+
+ // attach popover to parent
+ this.options.container.parent().append(this.$el);
+
+ // attach close
+ if (this.options.with_close) {
+ this.$el.find('#close').on('click', function() { self.hide(); });
+ }
+
+ // generate unique id
+ this.uuid = Utils.uuid();
+
+ // add event to hide if click is outside of popup
+ var self = this;
+ $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) });
+ },
+
+ // title
+ title: function(val) {
+ if (val !== undefined) {
+ this.$el.find('.popover-title-label').html(val);
+ }
+ },
+
+ // show
+ show: function () {
+ // show popover
+ this.$el.show();
+ this.visible = true;
+
+ // calculate position
+ var position = this._get_placement(this.options.placement);
+
+ // set position
+ this.$el.css(position);
+ },
+
+ // calculate position and error
+ _get_placement: function(placement) {
+ // get popover dimensions
+ var width = this._get_width(this.$el);
+ var height = this.$el.height();
+
+ // get container details
+ var $container = this.options.container;
+ var container_width = this._get_width($container);
+ var container_height = this._get_height($container);
+ var container_position = $container.position();
+
+ // initialize position
+ var top = 0;
+ var left = 0;
+
+ // calculate position
+ if (placement == 'top' || placement == 'bottom') {
+ left = container_position.left - width + (container_width + width) / 2;
+ if (placement == 'top') {
+ top = container_position.top - height - 5;
+ } else {
+ top = container_position.top + container_height + 5;
+ }
+ }
+
+ // return
+ return {top: top, left: left};
+ },
+
+ // width
+ _get_width: function($el) {
+ return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right'))
+ },
+
+ // heigth
+ _get_height: function($el) {
+ return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom'))
+ },
+
+ // hide
+ hide: function () {
+ this.$el.hide();
+ this.visible = false;
+ },
+
+ // append
+ append: function($el) {
+ this.$el.find('.popover-content').append($el);
+ },
+
+ // empty
+ empty: function($el) {
+ this.$el.find('.popover-content').empty();
+ },
+
+ // remove
+ remove: function() {
+ // remove event handler
+ $('body').off('mousedown.' + this.uuid);
+
+ // remove element from dom
+ this.$el.remove();
+ },
+
+ // remove
+ _hide : function(e) {
+ //the 'is' for buttons that trigger popups
+ //the 'has' for icons within a button that triggers a popup
+ if (!$(this.options.container).is(e.target) &&
+ !$(this.el).is(e.target) &&
+ $(this.el).has(e.target).length === 0) {
+ this.hide();
+ }
+ },
+
+ // template
+ _template: function(options) {
+ var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' +
+ '<div class="arrow"></div>' +
+ '<div class="popover-title">' +
+ '<div class="popover-title-label">' +
+ options.title +
+ '</div>';
+
+ // add close icon
+ if (options.with_close) {
+ tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>';
+ }
+
+ // finalize
+ tmpl += '</div>' +
+ '<div class="popover-content"></div>' +
+ '</div>';
+
+ // return
+ return tmpl;
+ }
+});
+
+return {
+ View: View
+}
+
+});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/ui-select.js
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-select.js
@@ -0,0 +1,193 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend(
+{
+ // options
+ optionsDefault: {
+ css : '',
+ placeholder : 'No data available',
+ data : []
+ },
+
+ // initialize
+ initialize : function(options) {
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+
+ // add to dom
+ this.options.container.append(this.$el);
+
+ // link selection dictionary
+ this.select_data = this.options.data;
+
+ // refresh
+ this._refresh();
+
+ // initial value
+ if (this.options.value) {
+ this._setValue(this.options.value);
+ }
+
+ // add change event
+ var self = this;
+ if (this.options.onchange) {
+ this.$el.on('change', function() {
+ self.options.onchange(self.value());
+ });
+ }
+ },
+
+ // value
+ value : function (new_value) {
+ // get current id/value
+ var before = this._getValue();
+
+ // check if new_value is defined
+ if (new_value !== undefined) {
+ this._setValue(new_value);
+ }
+
+ // get current id/value
+ var after = this._getValue();
+ if(after === undefined) {
+ return null;
+ } else {
+ // fire onchange
+ if ((after != before && this.options.onchange)) {
+ this.options.onchange(after);
+ }
+
+ // return current value
+ return after;
+ }
+ },
+
+ // label
+ text : function () {
+ return this.$el.select2('data').text;
+ },
+
+ // disabled
+ disabled: function() {
+ return !this.$el.select2('enable');
+ },
+
+ // enable
+ enable: function() {
+ this.$el.select2('enable', true);
+ },
+
+ // disable
+ disable: function() {
+ this.$el.select2('enable', false);
+ },
+
+ // add
+ add: function(options) {
+ // add options
+ this.select_data.push({
+ id : options.id,
+ text : options.text
+ });
+
+ // refresh
+ this._refresh();
+ },
+
+ // remove
+ del: function(id) {
+ // search option
+ var index = this._getIndex(id);
+
+ // check if found
+ if (index != -1) {
+ // remove options
+ this.select_data.splice(index, 1);
+
+ // refresh
+ this._refresh();
+ }
+ },
+
+ // remove
+ remove: function() {
+ this.$el.select2('destroy');
+ },
+
+ // update
+ update: function(options) {
+ // copy options
+ this.select_data = [];
+ for (var key in options.data) {
+ this.select_data.push(options.data[key]);
+ }
+
+ // refresh
+ this._refresh();
+ },
+
+ // refresh
+ _refresh: function() {
+
+ // link select data
+ var select_data = this.select_data;
+ if (!select_data || select_data.length == 0) {
+ select_data = [];
+ }
+
+ // selected
+ var selected = this._getValue();
+
+ // add select2 data
+ this.$el.select2({
+ data : select_data,
+ containerCssClass : this.options.css,
+ placeholder : this.options.placeholder
+ });
+
+ // select
+ var index = this._getIndex(selected);
+ if (index != -1) {
+ this._setValue(selected);
+ }
+ },
+
+ // get index
+ _getIndex: function(value) {
+ // search index
+ for (var key in this.select_data) {
+ if (this.select_data[key].id == value) {
+ return key;
+ }
+ }
+
+ // not found
+ return -1;
+ },
+
+ // get value
+ _getValue: function() {
+ return this.$el.select2('val');
+ },
+
+ // set value
+ _setValue: function(new_value) {
+ this.$el.select2('val', new_value);
+ },
+
+ // element
+ _template: function(options) {
+ return '<input type="hidden"/>';
+ }
+});
+
+return {
+ View : View
+}
+
+});
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/upload/upload-row.js
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -3,8 +3,8 @@
'mvc/upload/upload-model',
'mvc/upload/upload-extensions',
'mvc/upload/upload-settings',
- 'mvc/ui/popover',
- 'mvc/ui/select'],
+ 'mvc/ui/ui-popover',
+ 'mvc/ui/ui-select'],
function( Utils,
UploadModel,
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/upload/upload-view.js
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -5,7 +5,7 @@
"mvc/upload/upload-model",
"mvc/upload/upload-row",
"mvc/upload/upload-ftp",
- "mvc/ui/popover",
+ "mvc/ui/ui-popover",
"mvc/ui",
"utils/uploadbox"],
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/popover.js
--- a/static/scripts/packed/mvc/ui/popover.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/select.js
--- a/static/scripts/packed/mvc/ui/select.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/ui-popover.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/ui-popover.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/ui-select.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/ui-select.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/upload/upload-row.js
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/popover","mvc/ui/select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/upload/upload-view.js
--- a/static/scripts/packed/mvc/upload/upload-view.js
+++ b/static/scripts/packed/mvc/upload/upload-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
+define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Ui: Move ui classes into a separate directory
by commits-noreply＠bitbucket.org 13 Feb '14
by commits-noreply＠bitbucket.org 13 Feb '14
13 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b6acb69067f8/
Changeset: b6acb69067f8
User: guerler
Date: 2014-02-13 10:12:41
Summary: Ui: Move ui classes into a separate directory
Affected #: 12 files
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui.popover.js
--- a/static/scripts/mvc/ui.popover.js
+++ /dev/null
@@ -1,169 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-var View = Backbone.View.extend({
-
- // default options
- optionsDefault: {
- with_close : true,
- container : 'body',
- title : null,
- placement : 'top'
- },
-
- // visibility flag
- visible: false,
-
- // initialize
- initialize: function (options) {
-
- // link this
- var self = this;
-
- // update options
- this.options = _.defaults(options, this.optionsDefault);
-
- // set element
- this.setElement(this._template(this.options));
-
- // attach popover to parent
- this.options.container.parent().append(this.$el);
-
- // attach close
- if (this.options.with_close) {
- this.$el.find('#close').on('click', function() { self.hide(); });
- }
-
- // generate unique id
- this.uuid = Utils.uuid();
-
- // add event to hide if click is outside of popup
- var self = this;
- $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) });
- },
-
- // title
- title: function(val) {
- if (val !== undefined) {
- this.$el.find('.popover-title-label').html(val);
- }
- },
-
- // show
- show: function () {
- // show popover
- this.$el.show();
- this.visible = true;
-
- // calculate position
- var position = this._get_placement(this.options.placement);
-
- // set position
- this.$el.css(position);
- },
-
- // calculate position and error
- _get_placement: function(placement) {
- // get popover dimensions
- var width = this._get_width(this.$el);
- var height = this.$el.height();
-
- // get container details
- var $container = this.options.container;
- var container_width = this._get_width($container);
- var container_height = this._get_height($container);
- var container_position = $container.position();
-
- // initialize position
- var top = 0;
- var left = 0;
-
- // calculate position
- if (placement == 'top' || placement == 'bottom') {
- left = container_position.left - width + (container_width + width) / 2;
- if (placement == 'top') {
- top = container_position.top - height - 5;
- } else {
- top = container_position.top + container_height + 5;
- }
- }
-
- // return
- return {top: top, left: left};
- },
-
- // width
- _get_width: function($el) {
- return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right'))
- },
-
- // heigth
- _get_height: function($el) {
- return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom'))
- },
-
- // hide
- hide: function () {
- this.$el.hide();
- this.visible = false;
- },
-
- // append
- append: function($el) {
- this.$el.find('.popover-content').append($el);
- },
-
- // empty
- empty: function($el) {
- this.$el.find('.popover-content').empty();
- },
-
- // remove
- remove: function() {
- // remove event handler
- $('body').off('mousedown.' + this.uuid);
-
- // remove element from dom
- this.$el.remove();
- },
-
- // remove
- _hide : function(e) {
- //the 'is' for buttons that trigger popups
- //the 'has' for icons within a button that triggers a popup
- if (!$(this.options.container).is(e.target) &&
- !$(this.el).is(e.target) &&
- $(this.el).has(e.target).length === 0) {
- this.hide();
- }
- },
-
- // template
- _template: function(options) {
- var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' +
- '<div class="arrow"></div>' +
- '<div class="popover-title">' +
- '<div class="popover-title-label">' +
- options.title +
- '</div>';
-
- // add close icon
- if (options.with_close) {
- tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>';
- }
-
- // finalize
- tmpl += '</div>' +
- '<div class="popover-content"></div>' +
- '</div>';
-
- // return
- return tmpl;
- }
-});
-
-return {
- View: View
-}
-
-});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui.select.js
--- a/static/scripts/mvc/ui.select.js
+++ /dev/null
@@ -1,193 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- css : '',
- placeholder : 'No data available',
- data : []
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add to dom
- this.options.container.append(this.$el);
-
- // link selection dictionary
- this.select_data = this.options.data;
-
- // refresh
- this._refresh();
-
- // initial value
- if (this.options.value) {
- this._setValue(this.options.value);
- }
-
- // add change event
- var self = this;
- if (this.options.onchange) {
- this.$el.on('change', function() {
- self.options.onchange(self.value());
- });
- }
- },
-
- // value
- value : function (new_value) {
- // get current id/value
- var before = this._getValue();
-
- // check if new_value is defined
- if (new_value !== undefined) {
- this._setValue(new_value);
- }
-
- // get current id/value
- var after = this._getValue();
- if(after === undefined) {
- return null;
- } else {
- // fire onchange
- if ((after != before && this.options.onchange)) {
- this.options.onchange(after);
- }
-
- // return current value
- return after;
- }
- },
-
- // label
- text : function () {
- return this.$el.select2('data').text;
- },
-
- // disabled
- disabled: function() {
- return !this.$el.select2('enable');
- },
-
- // enable
- enable: function() {
- this.$el.select2('enable', true);
- },
-
- // disable
- disable: function() {
- this.$el.select2('enable', false);
- },
-
- // add
- add: function(options) {
- // add options
- this.select_data.push({
- id : options.id,
- text : options.text
- });
-
- // refresh
- this._refresh();
- },
-
- // remove
- del: function(id) {
- // search option
- var index = this._getIndex(id);
-
- // check if found
- if (index != -1) {
- // remove options
- this.select_data.splice(index, 1);
-
- // refresh
- this._refresh();
- }
- },
-
- // remove
- remove: function() {
- this.$el.select2('destroy');
- },
-
- // update
- update: function(options) {
- // copy options
- this.select_data = [];
- for (var key in options.data) {
- this.select_data.push(options.data[key]);
- }
-
- // refresh
- this._refresh();
- },
-
- // refresh
- _refresh: function() {
-
- // link select data
- var select_data = this.select_data;
- if (!select_data || select_data.length == 0) {
- select_data = [];
- }
-
- // selected
- var selected = this._getValue();
-
- // add select2 data
- this.$el.select2({
- data : select_data,
- containerCssClass : this.options.css,
- placeholder : this.options.placeholder
- });
-
- // select
- var index = this._getIndex(selected);
- if (index != -1) {
- this._setValue(selected);
- }
- },
-
- // get index
- _getIndex: function(value) {
- // search index
- for (var key in this.select_data) {
- if (this.select_data[key].id == value) {
- return key;
- }
- }
-
- // not found
- return -1;
- },
-
- // get value
- _getValue: function() {
- return this.$el.select2('val');
- },
-
- // set value
- _setValue: function(new_value) {
- this.$el.select2('val', new_value);
- },
-
- // element
- _template: function(options) {
- return '<input type="hidden"/>';
- }
-});
-
-return {
- View : View
-}
-
-});
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui/popover.js
--- /dev/null
+++ b/static/scripts/mvc/ui/popover.js
@@ -0,0 +1,169 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+var View = Backbone.View.extend({
+
+ // default options
+ optionsDefault: {
+ with_close : true,
+ container : 'body',
+ title : null,
+ placement : 'top'
+ },
+
+ // visibility flag
+ visible: false,
+
+ // initialize
+ initialize: function (options) {
+
+ // link this
+ var self = this;
+
+ // update options
+ this.options = _.defaults(options, this.optionsDefault);
+
+ // set element
+ this.setElement(this._template(this.options));
+
+ // attach popover to parent
+ this.options.container.parent().append(this.$el);
+
+ // attach close
+ if (this.options.with_close) {
+ this.$el.find('#close').on('click', function() { self.hide(); });
+ }
+
+ // generate unique id
+ this.uuid = Utils.uuid();
+
+ // add event to hide if click is outside of popup
+ var self = this;
+ $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) });
+ },
+
+ // title
+ title: function(val) {
+ if (val !== undefined) {
+ this.$el.find('.popover-title-label').html(val);
+ }
+ },
+
+ // show
+ show: function () {
+ // show popover
+ this.$el.show();
+ this.visible = true;
+
+ // calculate position
+ var position = this._get_placement(this.options.placement);
+
+ // set position
+ this.$el.css(position);
+ },
+
+ // calculate position and error
+ _get_placement: function(placement) {
+ // get popover dimensions
+ var width = this._get_width(this.$el);
+ var height = this.$el.height();
+
+ // get container details
+ var $container = this.options.container;
+ var container_width = this._get_width($container);
+ var container_height = this._get_height($container);
+ var container_position = $container.position();
+
+ // initialize position
+ var top = 0;
+ var left = 0;
+
+ // calculate position
+ if (placement == 'top' || placement == 'bottom') {
+ left = container_position.left - width + (container_width + width) / 2;
+ if (placement == 'top') {
+ top = container_position.top - height - 5;
+ } else {
+ top = container_position.top + container_height + 5;
+ }
+ }
+
+ // return
+ return {top: top, left: left};
+ },
+
+ // width
+ _get_width: function($el) {
+ return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right'))
+ },
+
+ // heigth
+ _get_height: function($el) {
+ return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom'))
+ },
+
+ // hide
+ hide: function () {
+ this.$el.hide();
+ this.visible = false;
+ },
+
+ // append
+ append: function($el) {
+ this.$el.find('.popover-content').append($el);
+ },
+
+ // empty
+ empty: function($el) {
+ this.$el.find('.popover-content').empty();
+ },
+
+ // remove
+ remove: function() {
+ // remove event handler
+ $('body').off('mousedown.' + this.uuid);
+
+ // remove element from dom
+ this.$el.remove();
+ },
+
+ // remove
+ _hide : function(e) {
+ //the 'is' for buttons that trigger popups
+ //the 'has' for icons within a button that triggers a popup
+ if (!$(this.options.container).is(e.target) &&
+ !$(this.el).is(e.target) &&
+ $(this.el).has(e.target).length === 0) {
+ this.hide();
+ }
+ },
+
+ // template
+ _template: function(options) {
+ var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' +
+ '<div class="arrow"></div>' +
+ '<div class="popover-title">' +
+ '<div class="popover-title-label">' +
+ options.title +
+ '</div>';
+
+ // add close icon
+ if (options.with_close) {
+ tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>';
+ }
+
+ // finalize
+ tmpl += '</div>' +
+ '<div class="popover-content"></div>' +
+ '</div>';
+
+ // return
+ return tmpl;
+ }
+});
+
+return {
+ View: View
+}
+
+});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui/select.js
--- /dev/null
+++ b/static/scripts/mvc/ui/select.js
@@ -0,0 +1,193 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend(
+{
+ // options
+ optionsDefault: {
+ css : '',
+ placeholder : 'No data available',
+ data : []
+ },
+
+ // initialize
+ initialize : function(options) {
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+
+ // add to dom
+ this.options.container.append(this.$el);
+
+ // link selection dictionary
+ this.select_data = this.options.data;
+
+ // refresh
+ this._refresh();
+
+ // initial value
+ if (this.options.value) {
+ this._setValue(this.options.value);
+ }
+
+ // add change event
+ var self = this;
+ if (this.options.onchange) {
+ this.$el.on('change', function() {
+ self.options.onchange(self.value());
+ });
+ }
+ },
+
+ // value
+ value : function (new_value) {
+ // get current id/value
+ var before = this._getValue();
+
+ // check if new_value is defined
+ if (new_value !== undefined) {
+ this._setValue(new_value);
+ }
+
+ // get current id/value
+ var after = this._getValue();
+ if(after === undefined) {
+ return null;
+ } else {
+ // fire onchange
+ if ((after != before && this.options.onchange)) {
+ this.options.onchange(after);
+ }
+
+ // return current value
+ return after;
+ }
+ },
+
+ // label
+ text : function () {
+ return this.$el.select2('data').text;
+ },
+
+ // disabled
+ disabled: function() {
+ return !this.$el.select2('enable');
+ },
+
+ // enable
+ enable: function() {
+ this.$el.select2('enable', true);
+ },
+
+ // disable
+ disable: function() {
+ this.$el.select2('enable', false);
+ },
+
+ // add
+ add: function(options) {
+ // add options
+ this.select_data.push({
+ id : options.id,
+ text : options.text
+ });
+
+ // refresh
+ this._refresh();
+ },
+
+ // remove
+ del: function(id) {
+ // search option
+ var index = this._getIndex(id);
+
+ // check if found
+ if (index != -1) {
+ // remove options
+ this.select_data.splice(index, 1);
+
+ // refresh
+ this._refresh();
+ }
+ },
+
+ // remove
+ remove: function() {
+ this.$el.select2('destroy');
+ },
+
+ // update
+ update: function(options) {
+ // copy options
+ this.select_data = [];
+ for (var key in options.data) {
+ this.select_data.push(options.data[key]);
+ }
+
+ // refresh
+ this._refresh();
+ },
+
+ // refresh
+ _refresh: function() {
+
+ // link select data
+ var select_data = this.select_data;
+ if (!select_data || select_data.length == 0) {
+ select_data = [];
+ }
+
+ // selected
+ var selected = this._getValue();
+
+ // add select2 data
+ this.$el.select2({
+ data : select_data,
+ containerCssClass : this.options.css,
+ placeholder : this.options.placeholder
+ });
+
+ // select
+ var index = this._getIndex(selected);
+ if (index != -1) {
+ this._setValue(selected);
+ }
+ },
+
+ // get index
+ _getIndex: function(value) {
+ // search index
+ for (var key in this.select_data) {
+ if (this.select_data[key].id == value) {
+ return key;
+ }
+ }
+
+ // not found
+ return -1;
+ },
+
+ // get value
+ _getValue: function() {
+ return this.$el.select2('val');
+ },
+
+ // set value
+ _setValue: function(new_value) {
+ this.$el.select2('val', new_value);
+ },
+
+ // element
+ _template: function(options) {
+ return '<input type="hidden"/>';
+ }
+});
+
+return {
+ View : View
+}
+
+});
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/upload/upload-row.js
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -3,8 +3,8 @@
'mvc/upload/upload-model',
'mvc/upload/upload-extensions',
'mvc/upload/upload-settings',
- 'mvc/ui.popover',
- 'mvc/ui.select'],
+ 'mvc/ui/popover',
+ 'mvc/ui/select'],
function( Utils,
UploadModel,
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/upload/upload-view.js
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -5,7 +5,7 @@
"mvc/upload/upload-model",
"mvc/upload/upload-row",
"mvc/upload/upload-ftp",
- "mvc/ui.popover",
+ "mvc/ui/popover",
"mvc/ui",
"utils/uploadbox"],
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui.popover.js
--- a/static/scripts/packed/mvc/ui.popover.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui.select.js
--- a/static/scripts/packed/mvc/ui.select.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui/popover.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/popover.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui/select.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/select.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/upload/upload-row.js
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/popover","mvc/ui/select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/upload/upload-view.js
--- a/static/scripts/packed/mvc/upload/upload-view.js
+++ b/static/scripts/packed/mvc/upload/upload-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
+define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Improve select style
by commits-noreply＠bitbucket.org 13 Feb '14
by commits-noreply＠bitbucket.org 13 Feb '14
13 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0ef8c71a3ed1/
Changeset: 0ef8c71a3ed1
User: guerler
Date: 2014-02-13 09:33:39
Summary: Upload: Improve select style
Affected #: 2 files
diff -r e8810dcb7d7295fc61288c338c2ea9e36b083225 -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1264,6 +1264,7 @@
.upload-box .table td{margin:0px;paddign:0px}
.upload-box .upload-item .select2-arrow b{background-position:0 -3px}
.upload-box .upload-item .select2-choice{max-height:20px;line-height:18px;background:transparent}
+.upload-box .upload-item .select2-container-disabled .select2-arrow{background:transparent}
.upload-box .mode{float:left;font-size:1.2em;width:1.2em;color:#555}
.upload-box .title{width:130px;word-wrap:break-word;font-size:11px;float:left}
.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit;color:#000}
@@ -1684,15 +1685,15 @@
div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-paused .state-icon:before{content:"\f04c"}
div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-new .state-icon:before{content:"\f071"}
div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important}
-div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px}
-div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px}
-div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px}
-div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px}
-div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px}
-div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px}
-div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px}
-div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px}
-div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px}
+div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px;height:16px}
+div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px;height:16px}
div.historyItemBody div{padding-top:2px}
pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#5f6990}
pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px}
diff -r e8810dcb7d7295fc61288c338c2ea9e36b083225 -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 static/style/src/less/upload.less
--- a/static/style/src/less/upload.less
+++ b/static/style/src/less/upload.less
@@ -95,6 +95,12 @@
line-height: 18px;
background: transparent;
}
+
+ .select2-container-disabled {
+ .select2-arrow {
+ background: transparent;
+ }
+ }
}
.mode {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Fix select removal
by commits-noreply＠bitbucket.org 13 Feb '14
by commits-noreply＠bitbucket.org 13 Feb '14
13 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e8810dcb7d72/
Changeset: e8810dcb7d72
User: guerler
Date: 2014-02-13 09:14:26
Summary: Upload: Fix select removal
Affected #: 4 files
diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/mvc/ui.select.js
--- a/static/scripts/mvc/ui.select.js
+++ b/static/scripts/mvc/ui.select.js
@@ -100,7 +100,7 @@
},
// remove
- remove: function(id) {
+ del: function(id) {
// search option
var index = this._getIndex(id);
@@ -114,6 +114,11 @@
}
},
+ // remove
+ remove: function() {
+ this.$el.select2('destroy');
+ },
+
// update
update: function(options) {
// copy options
diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/mvc/upload/upload-row.js
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -195,6 +195,16 @@
}
},
+ // remove
+ remove: function() {
+ // trigger remove event
+ this.select_genome.remove();
+ this.select_extension.remove();
+
+ // call the base class remove method
+ Backbone.View.prototype.remove.apply(this);
+ },
+
//
// handle model events
//
diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/packed/mvc/ui.select.js
--- a/static/scripts/packed/mvc/ui.select.js
+++ b/static/scripts/packed/mvc/ui.select.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},remove:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/packed/mvc/upload/upload-row.js
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Add select2 selection fields, add select2 backbone wrapper
by commits-noreply＠bitbucket.org 13 Feb '14
by commits-noreply＠bitbucket.org 13 Feb '14
13 Feb '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/086352011e07/
Changeset: 086352011e07
User: guerler
Date: 2014-02-13 08:37:10
Summary: Upload: Add select2 selection fields, add select2 backbone wrapper
Affected #: 8 files
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/mvc/ui.select.js
--- /dev/null
+++ b/static/scripts/mvc/ui.select.js
@@ -0,0 +1,188 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend(
+{
+ // options
+ optionsDefault: {
+ css : '',
+ placeholder : 'No data available',
+ data : []
+ },
+
+ // initialize
+ initialize : function(options) {
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+
+ // add to dom
+ this.options.container.append(this.$el);
+
+ // link selection dictionary
+ this.select_data = this.options.data;
+
+ // refresh
+ this._refresh();
+
+ // initial value
+ if (this.options.value) {
+ this._setValue(this.options.value);
+ }
+
+ // add change event
+ var self = this;
+ if (this.options.onchange) {
+ this.$el.on('change', function() {
+ self.options.onchange(self.value());
+ });
+ }
+ },
+
+ // value
+ value : function (new_value) {
+ // get current id/value
+ var before = this._getValue();
+
+ // check if new_value is defined
+ if (new_value !== undefined) {
+ this._setValue(new_value);
+ }
+
+ // get current id/value
+ var after = this._getValue();
+ if(after === undefined) {
+ return null;
+ } else {
+ // fire onchange
+ if ((after != before && this.options.onchange)) {
+ this.options.onchange(after);
+ }
+
+ // return current value
+ return after;
+ }
+ },
+
+ // label
+ text : function () {
+ return this.$el.select2('data').text;
+ },
+
+ // disabled
+ disabled: function() {
+ return !this.$el.select2('enable');
+ },
+
+ // enable
+ enable: function() {
+ this.$el.select2('enable', true);
+ },
+
+ // disable
+ disable: function() {
+ this.$el.select2('enable', false);
+ },
+
+ // add
+ add: function(options) {
+ // add options
+ this.select_data.push({
+ id : options.id,
+ text : options.text
+ });
+
+ // refresh
+ this._refresh();
+ },
+
+ // remove
+ remove: function(id) {
+ // search option
+ var index = this._getIndex(id);
+
+ // check if found
+ if (index != -1) {
+ // remove options
+ this.select_data.splice(index, 1);
+
+ // refresh
+ this._refresh();
+ }
+ },
+
+ // update
+ update: function(options) {
+ // copy options
+ this.select_data = [];
+ for (var key in options.data) {
+ this.select_data.push(options.data[key]);
+ }
+
+ // refresh
+ this._refresh();
+ },
+
+ // refresh
+ _refresh: function() {
+
+ // link select data
+ var select_data = this.select_data;
+ if (!select_data || select_data.length == 0) {
+ select_data = [];
+ }
+
+ // selected
+ var selected = this._getValue();
+
+ // add select2 data
+ this.$el.select2({
+ data : select_data,
+ containerCssClass : this.options.css,
+ placeholder : this.options.placeholder
+ });
+
+ // select
+ var index = this._getIndex(selected);
+ if (index != -1) {
+ this._setValue(selected);
+ }
+ },
+
+ // get index
+ _getIndex: function(value) {
+ // search index
+ for (var key in this.select_data) {
+ if (this.select_data[key].id == value) {
+ return key;
+ }
+ }
+
+ // not found
+ return -1;
+ },
+
+ // get value
+ _getValue: function() {
+ return this.$el.select2('val');
+ },
+
+ // set value
+ _setValue: function(new_value) {
+ this.$el.select2('val', new_value);
+ },
+
+ // element
+ _template: function(options) {
+ return '<input type="hidden"/>';
+ }
+});
+
+return {
+ View : View
+}
+
+});
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/mvc/upload/upload-row.js
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -3,13 +3,15 @@
'mvc/upload/upload-model',
'mvc/upload/upload-extensions',
'mvc/upload/upload-settings',
- 'mvc/ui.popover'],
+ 'mvc/ui.popover',
+ 'mvc/ui.select'],
function( Utils,
UploadModel,
UploadExtensions,
UploadSettings,
- Popover
+ Popover,
+ Select
) {
// item view
@@ -31,6 +33,12 @@
// handle for settings popover
settings: null,
+ // genome selector
+ select_genome : null,
+
+ // extension selector
+ select_extension : null,
+
// render
initialize: function(app, options) {
// link app
@@ -55,6 +63,28 @@
placement : 'bottom'
});
+ // select genomes
+ this.select_genome = new Select.View({
+ css: 'genome',
+ onchange : function() {
+ self.model.set('genome', self.select_genome.value());
+ },
+ data: self.app.list_genomes,
+ container: it.find('#genome'),
+ value: self.model.get('genome')
+ });
+
+ // select extension
+ this.select_extension = new Select.View({
+ css: 'extension',
+ onchange : function() {
+ self.model.set('extension', self.select_extension.value());
+ },
+ data: self.app.list_extensions,
+ container: it.find('#extension'),
+ value: self.model.get('extension')
+ });
+
//
// ui events
//
@@ -76,16 +106,6 @@
self.model.set('file_size', $(e.target).val().length);
});
- // handle genome selection
- it.find('#genome').on('change', function(e) {
- self.model.set('genome', $(e.target).val());
- });
-
- // handle extension selection
- it.find('#extension').on('change', function(e) {
- self.model.set('extension', $(e.target).val());
- });
-
// handle space to tabs button
it.find('#space_to_tabs').on('change', function(e) {
self.model.set('space_to_tabs', $(e.target).prop('checked'));
@@ -100,9 +120,6 @@
this.model.on('change:status', function() {
self._refreshStatus();
});
- this.model.on('change:extension', function() {
- self._destroyExtensionInfo();
- });
this.model.on('change:info', function() {
self._refreshInfo();
});
@@ -113,11 +130,9 @@
self._refreshFileSize();
});
this.model.on('remove', function() {
- self._destroyExtensionInfo();
self.remove();
});
this.app.collection.on('reset', function() {
- self._destroyExtensionInfo();
self.remove();
});
},
@@ -189,7 +204,7 @@
{
// update genome info on screen
var genome = this.model.get('genome');
- this.$el.find('#genome').val(genome);
+ this.select_genome.value(genome);
},
// progress
@@ -231,17 +246,23 @@
// set new status class
sy.addClass(status_class);
-
+
// enable form fields
if (status == 'init') {
+ // select fields
+ this.select_genome.enable();
+ this.select_extension.enable();
+
+ // default fields
it.find('#text-content').attr('disabled', false);
- it.find('#genome').attr('disabled', false);
- it.find('#extension').attr('disabled', false);
it.find('#space_to_tabs').attr('disabled', false);
} else {
+ // select fields
+ this.select_genome.disable();
+ this.select_extension.disable();
+
+ // default fields
it.find('#text-content').attr('disabled', true);
- it.find('#genome').attr('disabled', true);
- it.find('#extension').attr('disabled', true);
it.find('#space_to_tabs').attr('disabled', true);
}
@@ -275,7 +296,6 @@
// only remove from queue if not in processing line
if (status == 'init' || status == 'success' || status == 'error') {
- // remove from collection
this.app.collection.remove(this.model);
}
},
@@ -286,7 +306,7 @@
// initialize
var $el = $(this.el).find('#extension-info');
var extension = this.model.get('extension');
- var title = $(this.el).find('#extension').find('option:selected').text();
+ var title = this.select_extension.text();
// create popup
if (!this.extension_popup) {
@@ -323,66 +343,43 @@
}
},
- // attach file info popup
- _destroyExtensionInfo : function()
- {
- this.$el.find('#extension-info').popover('destroy');
- },
-
// template
_template: function(options)
{
- // link this
- var self = this;
-
- // construct template
- var tmpl = '<tr id="upload-item-' + options.id + '" class="upload-item">' +
- '<td>' +
- '<div style="position: relative;">' +
- '<div id="mode"></div>' +
- '<div id="title" class="title"></div>' +
- '<div id="text" class="text">' +
- '<div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div>' +
- '<textarea id="text-content" class="text-content form-control"></textarea>' +
- '</div>' +
+ return '<tr id="upload-item-' + options.id + '" class="upload-item">' +
+ '<td>' +
+ '<div style="position: relative;">' +
+ '<div id="mode"></div>' +
+ '<div id="title" class="title"></div>' +
+ '<div id="text" class="text">' +
+ '<div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div>' +
+ '<textarea id="text-content" class="text-content form-control"></textarea>' +
'</div>' +
- '</td>' +
- '<td>' +
- '<div id="size" class="size"></div>' +
- '</td>';
-
- // add file type selectore
- tmpl += '<td>' +
- '<select id="extension" class="extension">';
- for (key in self.app.select_extension)
- tmpl += '<option value="' + self.app.select_extension[key][1] + '">' + self.app.select_extension[key][0] + '</option>';
- tmpl += '</select>' +
- ' <i id="extension-info" class="upload-icon-button fa fa-search"/>' +
- '</td>';
-
- // add genome selector
- tmpl += '<td>' +
- '<select id="genome" class="genome">';
- for (key in self.app.select_genome)
- tmpl += '<option value="' + self.app.select_genome[key][1] + '">' + self.app.select_genome[key][0] + '</option>';
- tmpl += '</select>' +
- '</td>';
-
- // add next row
- tmpl += '<td><div id="settings" class="upload-icon-button fa fa-gear"></div>' +
- '<td>' +
- '<div id="info" class="info">' +
- '<div class="progress">' +
- '<div class="progress-bar progress-bar-success"></div>' +
- '<div id="percentage" class="percentage">0%</div>' +
- '</div>' +
+ '</div>' +
+ '</td>' +
+ '<td>' +
+ '<div id="size" class="size"></div>' +
+ '</td>' +
+ '<td>' +
+ '<div id="extension" class="extension" style="float: left;"/>  ' +
+ '<div id="extension-info" class="upload-icon-button fa fa-search"/>' +
+ '</td>' +
+ '<td>' +
+ '<div id="genome" class="genome" />' +
+ '</td>' +
+ '<td><div id="settings" class="upload-icon-button fa fa-gear"></div>' +
+ '<td>' +
+ '<div id="info" class="info">' +
+ '<div class="progress">' +
+ '<div class="progress-bar progress-bar-success"></div>' +
+ '<div id="percentage" class="percentage">0%</div>' +
'</div>' +
- '</td>' +
- '<td><div id="symbol" class="' + this.status_classes.init + '"></div></td>' +
- '</tr>';
-
- // return html string
- return tmpl;
+ '</div>' +
+ '</td>' +
+ '<td>' +
+ '<div id="symbol" class="' + this.status_classes.init + '"></div>' +
+ '</td>' +
+ '</tr>';
}
});
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/mvc/upload/upload-view.js
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -42,10 +42,10 @@
upload_size: 0,
// extension types
- select_extension :[['Auto-detect', 'auto']],
+ list_extensions :[{id: 'auto', text: 'Auto-detect'}],
// genomes
- select_genome : [['Unspecified (?)', '?']],
+ list_genomes : [],
// collection
collection : new UploadModel.Collection(),
@@ -107,32 +107,30 @@
var self = this;
Utils.jsonFromUrl(galaxy_config.root + "api/datatypes?upload_only=True",
function(datatypes) {
- for (key in datatypes)
- self.select_extension.push([datatypes[key], datatypes[key]]);
+ for (key in datatypes) {
+ self.list_extensions.push({
+ id : datatypes[key],
+ text : datatypes[key]
+ });
+ }
});
// load genomes
Utils.jsonFromUrl(galaxy_config.root + "api/genomes",
function(genomes) {
- // backup default
- var def = self.select_genome[0];
-
- // fill array
- self.select_genome = [];
- for (key in genomes)
- if (genomes[key].length > 1)
- if (genomes[key][1] !== def[1])
- self.select_genome.push(genomes[key]);
-
+ for (key in genomes) {
+ self.list_genomes.push({
+ id : genomes[key][1],
+ text : genomes[key][0]
+ });
+ }
+
// sort
- self.select_genome.sort(function(a, b) {
- return a[0] > b[0] ? 1 : a[0] < b[0] ? -1 : 0;
+ self.list_genomes.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
});
-
- // insert default back to array
- self.select_genome.unshift(def);
});
-
+
// read in options
if (options) {
this.options = _.defaults(options, this.options);
@@ -296,9 +294,6 @@
// configure uploadbox
this.uploadbox.configure({url : this.options.nginx_upload_path});
- // configure tool
- tool_input = {};
-
// local files
if (file_mode == 'local') {
this.uploadbox.configure({paramname : 'files_0|file_data'});
@@ -306,6 +301,9 @@
this.uploadbox.configure({paramname : null});
}
+ // configure tool
+ tool_input = {};
+
// new files
if (file_mode == 'new') {
tool_input['files_0|url_paste'] = url_paste;
@@ -313,7 +311,6 @@
// files from ftp
if (file_mode == 'ftp') {
- // add to tool configuration
tool_input['files_0|ftp_files'] = file_path;
}
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/packed/mvc/ui.select.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui.select.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},remove:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}});
\ No newline at end of file
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/packed/mvc/upload/upload-row.js
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover"],function(d,b,e,a,c){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#genome").on("change",function(j){f.model.set("genome",$(j.target).val())});h.find("#extension").on("change",function(j){f.model.set("extension",$(j.target).val())});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:extension",function(){f._destroyExtensionInfo()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f._destroyExtensionInfo();f.remove()});this.app.collection.on("reset",function(){f._destroyExtensionInfo();f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var f=this.model.get("genome");this.$el.find("#genome").val(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){g.find("#text-content").attr("disabled",false);g.find("#genome").attr("disabled",false);g.find("#extension").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{g.find("#text-content").attr("disabled",true);g.find("#genome").attr("disabled",true);g.find("#extension").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var h=this.model.get("extension");var g=$(this.el).find("#extension").find("option:selected").text();if(!this.extension_popup){this.extension_popup=new c.View({content:e(h),placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(g);this.extension_popup.empty();this.extension_popup.append(e(h));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_destroyExtensionInfo:function(){this.$el.find("#extension-info").popover("destroy")},_template:function(h){var g=this;var f='<tr id="upload-item-'+h.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';f+='<td><select id="extension" class="extension">';for(key in g.app.select_extension){f+='<option value="'+g.app.select_extension[key][1]+'">'+g.app.select_extension[key][0]+"</option>"}f+='</select> <i id="extension-info" class="upload-icon-button fa fa-search"/></td>';f+='<td><select id="genome" class="genome">';for(key in g.app.select_genome){f+='<option value="'+g.app.select_genome[key][1]+'">'+g.app.select_genome[key][0]+"</option>"}f+="</select></td>";f+='<td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return f}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/packed/mvc/upload/upload-view.js
--- a/static/scripts/packed/mvc/upload/upload-view.js
+++ b/static/scripts/packed/mvc/upload/upload-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});tool_input={};if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
+define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1259,16 +1259,17 @@
.upload-icon{font-size:1.2em;width:1.2em}
.upload-icon-button{font-size:1.2em;width:1.2em;cursor:pointer}
.upload-info{font-weight:normal;text-align:center}
-.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .popover{max-width:500px;width:auto}
-.upload-box .table{width:100%}
+.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%}
.upload-box .table th{text-align:center;white-space:nowrap}
.upload-box .table td{margin:0px;paddign:0px}
+.upload-box .upload-item .select2-arrow b{background-position:0 -3px}
+.upload-box .upload-item .select2-choice{max-height:20px;line-height:18px;background:transparent}
.upload-box .mode{float:left;font-size:1.2em;width:1.2em;color:#555}
.upload-box .title{width:130px;word-wrap:break-word;font-size:11px;float:left}
.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit;color:#000}
.upload-box .text .text-info{font-size:11px}
-.upload-box .extension{width:100px;font-size:11px}
-.upload-box .genome{width:150px;font-size:11px}
+.upload-box .extension{width:100px;min-width:100px;font-size:11px}
+.upload-box .genome{width:150px;min-width:150px;font-size:11px}
.upload-box .size{width:60px;white-space:nowrap}
.upload-box .info{width:130px;font-size:11px;line-height:1.2em}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px;line-height:1.55em}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit}
.upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff}
@@ -1683,15 +1684,15 @@
div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-paused .state-icon:before{content:"\f04c"}
div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-new .state-icon:before{content:"\f071"}
div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important}
-div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px;height:16px}
-div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px;height:16px}
+div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px}
+div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px}
+div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px}
+div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px}
+div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px}
+div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px}
+div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px}
+div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px}
+div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px}
div.historyItemBody div{padding-top:2px}
pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#5f6990}
pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px}
diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/style/src/less/upload.less
--- a/static/style/src/less/upload.less
+++ b/static/style/src/less/upload.less
@@ -71,11 +71,6 @@
overflow-x : hidden;
-ms-overflow-style: none;
- .popover {
- max-width: 500px;
- width: auto;
- }
-
.table {
width : 100%;
}
@@ -89,7 +84,19 @@
margin: 0px;
paddign: 0px;
}
-
+
+ .upload-item {
+ .select2-arrow b {
+ background-position: 0 -3px;
+ }
+
+ .select2-choice {
+ max-height: 20px;
+ line-height: 18px;
+ background: transparent;
+ }
+ }
+
.mode {
float: left;
font-size: 1.2em;
@@ -119,20 +126,21 @@
.text-info {
font-size : @font-size-small;
- // color : @gray-light;
}
}
.extension {
width: 100px;
+ min-width: 100px;
font-size : @font-size-small;
}
.genome {
width: 150px;
+ min-width: 150px;
font-size : @font-size-small;
}
-
+
.size {
width: 60px;
white-space: nowrap;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b463c73f3348/
Changeset: b463c73f3348
Branch: stable
User: greg
Date: 2014-02-12 16:17:38
Summary: Fixes for repositories in the tool shed whose repository tip changeset has no files (because they were all deleted) but have valid tools and other utilities in previous changeset revisions.
Affected #: 2 files
diff -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 -r b463c73f334811d4c48298c40de9ac489261c32d lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2312,6 +2312,7 @@
revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False )
metadata = repository_metadata.metadata
is_malicious = repository_metadata.malicious
+ changeset_revision = previous_changeset_revision
if repository_metadata:
skip_tool_test = repository_metadata.skip_tool_tests
if skip_tool_test:
@@ -2719,10 +2720,15 @@
status = "error"
repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository )
changeset_revision = repository.tip( trans.app )
+ metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans,
+ id,
+ changeset_revision,
+ metadata_only=True )
return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako',
repo=repo,
repository=repository,
changeset_revision=changeset_revision,
+ metadata=metadata,
commit_message=commit_message,
repository_type_select_field=repository_type_select_field,
message=message,
diff -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 -r b463c73f334811d4c48298c40de9ac489261c32d templates/webapps/tool_shed/common/repository_actions_menu.mako
--- a/templates/webapps/tool_shed/common/repository_actions_menu.mako
+++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako
@@ -74,7 +74,7 @@
else:
can_rate = False
- if changeset_revision is not None:
+ if metadata is not None and changeset_revision is not None:
if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ):
can_review_repository = True
else:
@@ -177,7 +177,7 @@
<a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository_admins', id=trans.security.encode_id( repository.id ) )}">Manage repository administrators</a>
%endif
%if can_download:
- %if changeset_revision is not None:
+ %if metadata is not None and changeset_revision is not None:
<a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a>
%endif
<a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a>
https://bitbucket.org/galaxy/galaxy-central/commits/64e6873c8825/
Changeset: 64e6873c8825
User: inithello
Date: 2014-02-12 16:19:19
Summary: Merge stable.
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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