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- 15302 discussions
15 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/75be6c49a65d/
Changeset: 75be6c49a65d
User: guerler
Date: 2014-05-15 04:49:44
Summary: Charts: Fix style
Affected #: 2 files
diff -r ac52aab8cb0e0ae989b3429b895743849dfb7e3a -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c config/plugins/visualizations/charts/static/app.css
--- a/config/plugins/visualizations/charts/static/app.css
+++ b/config/plugins/visualizations/charts/static/app.css
@@ -39,9 +39,7 @@
.charts-viewport .info {
position: absolute;
- margin-left: 10px;
- margin-top: 10px;
- margin-bottom: 50px;
+ margin: 10px 20px 50px 10px;
}
.charts-viewport .text {
diff -r ac52aab8cb0e0ae989b3429b895743849dfb7e3a -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -62,10 +62,10 @@
$container.show()
break;
case 'failed':
- $icon.addClass('fa fa-warning');
+ $icon.addClass('icon fa fa-warning');
break;
default:
- $icon.addClass('fa fa-spinner fa-spin');
+ $icon.addClass('icon fa fa-spinner fa-spin');
}
});
},
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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15 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ac52aab8cb0e/
Changeset: ac52aab8cb0e
User: guerler
Date: 2014-05-15 04:21:36
Summary: Charts: Update panel
Affected #: 1 file
diff -r f05fe632cbc70d4694b5a4aa5e30b4f003952aa1 -r ac52aab8cb0e0ae989b3429b895743849dfb7e3a config/plugins/visualizations/charts/static/views/types.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/views/types.js
@@ -0,0 +1,133 @@
+define(['utils/utils', 'plugin/library/ui'], function(Utils, Ui) {
+
+return Backbone.View.extend(
+{
+ // defaults options
+ optionsDefault: {
+ onchange : null,
+ ondblclick : null
+ },
+
+ // events
+ events : {
+ 'click' : '_onclick',
+ 'dblclick' : '_ondblclick'
+ },
+
+ // initialize
+ initialize : function(app, options) {
+
+ // link app
+ this.app = app;
+
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ var $el = $('<div class="charts-grid"/>');
+
+ // set element
+ this.setElement($el);
+
+ // load chart types into categories
+ var categories = {};
+ var types = app.types.attributes;
+ for (var id in types) {
+ var type = types[id];
+ var category = type.category;
+ if (!categories[category]) {
+ categories[category] = {};
+ }
+ categories[category][id] = type;
+ }
+
+ // add categories and charts to screen
+ for (var category in categories) {
+ // create empty element
+ var $el = $('<div style="clear: both;"/>')
+
+ // add header label
+ $el.append(Utils.wrap(this._template_header({title: category})));
+
+ // add chart types
+ for (var id in categories[category]) {
+ var type = categories[category][id];
+ $el.append(Utils.wrap(this._template_item({
+ id : id,
+ title : type.title,
+ url : config.app_root + 'charts/' + id + '/logo.png'
+ })));
+ }
+
+ // add to view
+ this.$el.append(Utils.wrap($el));
+ }
+ },
+
+ // value
+ value: function(new_value) {
+ // get current element
+ var before = this.$el.find('.current').attr('id');
+
+ // check if new_value is defined
+ if (new_value !== undefined) {
+
+ // remove current class
+ this.$el.find('.current').removeClass('current');
+
+ // add current class
+ this.$el.find('#' + new_value).addClass('current');
+ }
+
+ // get current id/value
+ var after = this.$el.find('.current').attr('id');
+ if(after === undefined) {
+ return null;
+ } else {
+ // fire onchange
+ if (after != before && this.options.onchange) {
+ this.options.onchange(new_value);
+ }
+
+ // return current value
+ return after;
+ }
+ },
+
+ // onclick
+ _onclick: function(e) {
+ var old_value = this.value();
+ var new_value = $(e.target).closest('.item').attr('id');
+ if (new_value != '') {
+ if (new_value && old_value != new_value) {
+ this.value(new_value);
+ }
+ }
+ },
+
+ // ondblclick
+ _ondblclick: function(e) {
+ var value = this.value();
+ if (value && this.options.ondblclick) {
+ this.options.ondblclick(value);
+ }
+ },
+
+ // template
+ _template_header: function(options) {
+ return '<div class="header">' +
+ '• ' + options.title +
+ '<div>';
+ },
+
+ // template
+ _template_item: function(options) {
+ return '<div id="' + options.id + '" class="item">' +
+ '<img class="image" src="' + options.url + '">' +
+ '<div class="title">' + options.title + '</div>' +
+ '<div>';
+ }
+
+});
+
+});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts: Update boxplots and stacked bar
by commits-noreply＠bitbucket.org 15 May '14
by commits-noreply＠bitbucket.org 15 May '14
15 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f05fe632cbc7/
Changeset: f05fe632cbc7
User: guerler
Date: 2014-05-15 04:18:17
Summary: Charts: Update boxplots and stacked bar
Affected #: 5 files
diff -r 2b4c26870efbc19441f02da19659c830cc8b591a -r f05fe632cbc70d4694b5a4aa5e30b4f003952aa1 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png
Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed
diff -r 2b4c26870efbc19441f02da19659c830cc8b591a -r f05fe632cbc70d4694b5a4aa5e30b4f003952aa1 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js
@@ -0,0 +1,122 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // highcharts configuration
+ hc_config : {
+ chart: {
+ type: 'boxplot'
+ },
+
+ title: {
+ text: ''
+ },
+
+ legend: {
+ enabled: false
+ },
+
+ credits: {
+ enabled: false
+ },
+
+ plotOptions: {
+ series: {
+ animation: false
+ }
+ },
+
+ xAxis: {
+ categories: [],
+ title: {
+ text: ''
+ }
+ },
+
+ yAxis: {
+ title: {
+ text: ''
+ }
+ },
+
+ series: [{
+ name: 'Details:',
+ data: [],
+ tooltip: {
+ headerFormat: '<em>{point.key}</em><br/>'
+ }
+ }]
+ },
+
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 0;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = null;
+ group.columns = {
+ x: {
+ index: index++
+ }
+ }
+ }
+
+ // set axis labels
+ this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label');
+ this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label');
+
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function() {
+
+ // reset data/categories
+ var data = [];
+ var categories = [];
+
+ // loop through data groups
+ for (var key in request_dictionary.groups) {
+ // get group
+ var group = request_dictionary.groups[key];
+
+ // add category
+ categories.push(group.key);
+
+ // format chart data
+ var point = [];
+ for (var key in group.values) {
+ point.push(group.values[key].x);
+ }
+
+ // add to data
+ data.push (point);
+ }
+
+ // categories
+ self.hc_config.xAxis.categories = categories;
+
+ // update data
+ self.hc_config.series[0].data = data;
+
+ // draw plot
+ self.options.canvas[0].highcharts(self.hc_config);
+
+ // set chart state
+ chart.state('ok', 'Box plot drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 2b4c26870efbc19441f02da19659c830cc8b591a -r f05fe632cbc70d4694b5a4aa5e30b4f003952aa1 config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js
@@ -0,0 +1,8 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Stacked',
+ category : 'Bar diagrams'
+});
+
+});
\ No newline at end of file
diff -r 2b4c26870efbc19441f02da19659c830cc8b591a -r f05fe632cbc70d4694b5a4aa5e30b4f003952aa1 config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/logo.png has changed
diff -r 2b4c26870efbc19441f02da19659c830cc8b591a -r f05fe632cbc70d4694b5a4aa5e30b4f003952aa1 config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/wrapper.js
@@ -0,0 +1,23 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary, function(nvd3_model) {
+ nvd3_model.stacked(true);
+ });
+ }
+});
+
+});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts: Add new selection panel, improve modularity, activate basic heat map
by commits-noreply＠bitbucket.org 15 May '14
by commits-noreply＠bitbucket.org 15 May '14
15 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2b4c26870efb/
Changeset: 2b4c26870efb
User: guerler
Date: 2014-05-15 04:11:59
Summary: Charts: Add new selection panel, improve modularity, activate basic heat map
Affected #: 67 files
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/app.css
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/app.css
@@ -0,0 +1,69 @@
+.charts-grid .item {
+ padding: 5px;
+ margin: 5px;
+ float: left;
+ cursor: pointer;
+ border-radius:5px
+}
+
+.charts-grid .current {
+ border-color:#66afe9;
+ background-color:#EEEEFF;
+ outline:0;
+ -webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
+ box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
+}
+
+.charts-grid .image {
+ padding: 10px;
+ width: 100px;
+}
+
+.charts-grid .title {
+ text-align: center;
+ font-size: 0.9em;
+ word-wrap: break-work;
+ font-weight: bold;
+ width: 100px;
+}
+
+.charts-grid .header {
+ font-size: 0.9em;
+ font-weight: bold;
+}
+
+.charts-viewport {
+ height: inherit;
+ min-height: 50px;
+}
+
+.charts-viewport .info {
+ position: absolute;
+ margin-left: 10px;
+ margin-top: 10px;
+ margin-bottom: 50px;
+}
+
+.charts-viewport .text {
+ position: relative;
+ margin-left: 5px;
+ top: -1px;
+ font-size: 1.0em;
+}
+
+.charts-viewport .icon {
+ font-size: 1.2em;
+ display: inline-block;
+}
+
+.charts-viewport .container {
+ float: left;
+ display: block;
+ height: 100%;
+}
+
+.charts-viewport .canvas {
+ display: block;
+ width:100%;
+ height: inherit;
+}
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),s=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),a=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:i,Icon:s,ButtonIcon:o,Input:h,Anchor:u,Message:a,Searchbox:f,Title:l,Text:r,Select:t,ButtonMenu:c}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="float: left; display: block; width:'+t+'%; height: 100%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas" style="display: block; width:100%; height: inherit;">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the charts tool available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","nvd3_bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bardiagram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/nvd3_linewithfocus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/nvd3_piechart/config",[],function(){return{title:"Pie chart",library:"nvd3.js",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var 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- No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others"})}),define("plugin/charts/nvd3_line_focus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others"})}),define("plugin/charts/nvd3_pie/config",[],function(){return{title:"Pie chart",library:"nvd3.js",category:"Area charts",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bar/config","plugin/charts/nvd3_bar_stacked/config","plugin/charts/nvd3_bar_horizontal/config","plugin/charts/nvd3_bar_horizontal_stacked/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:f,nvd3_stackedarea_full:l,nvd3_stackedarea_stream:c,nvd3_line:s,nvd3_line_focus:o,nvd3_scatter:a,nvd3_pie:u,nvd3_histogram:i,highcharts_boxplot:h,heatmap:p}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/config.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js
@@ -2,6 +2,7 @@
return {
title : 'Heatmap',
+ category : 'Data processing (requires \'charts\' tool from Toolshed)',
library : '',
tag : 'div',
use_panels : true,
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js
+++ /dev/null
@@ -1,71 +0,0 @@
-// dependencies
-define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'],
-function(Utils, HeatmapPlugin, HeatmapParameters) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // link this
- var self = this;
-
- // loop through data groups
- var index = 0;
- for (var group_index in request_dictionary.groups) {
-
- // configure request
- for (var i in request_dictionary.groups) {
- var group = request_dictionary.groups[i];
- group.columns = null;
- group.columns = {
- row_label: {
- index : index++,
- is_label : true
- },
- col_label: {
- index : index++,
- is_label : true
- },
- value: {
- index : index++
- }
- }
- }
-
- // request data
- this.app.datasets.request(request_dictionary, function() {
-
- // get group
- var group = request_dictionary.groups[group_index];
- var div = self.options.canvas[group_index];
-
- // draw plot
- var heatmap = new HeatmapPlugin({
- 'title' : group.key,
- 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')],
- 'data' : group.values,
- 'div' : div
- });
-
- // check if done
- if (group_index == request_dictionary.groups.length - 1) {
- // set chart state
- chart.state('ok', 'Heat map drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- }
- });
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/logo.png
Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js
@@ -0,0 +1,71 @@
+// dependencies
+define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'],
+function(Utils, HeatmapPlugin, HeatmapParameters) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // link this
+ var self = this;
+
+ // loop through data groups
+ var index = 0;
+ for (var group_index in request_dictionary.groups) {
+
+ // configure request
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = null;
+ group.columns = {
+ row_label: {
+ index : index++,
+ is_label : true
+ },
+ col_label: {
+ index : index++,
+ is_label : true
+ },
+ value: {
+ index : index++
+ }
+ }
+ }
+
+ // request data
+ this.app.datasets.request(request_dictionary, function() {
+
+ // get group
+ var group = request_dictionary.groups[group_index];
+ var div = self.options.canvas[group_index];
+
+ // draw plot
+ var heatmap = new HeatmapPlugin({
+ 'title' : group.key,
+ 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')],
+ 'data' : group.values,
+ 'div' : div
+ });
+
+ // check if done
+ if (group_index == request_dictionary.groups.length - 1) {
+ // set chart state
+ chart.state('ok', 'Heat map drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ }
+ });
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
--- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
@@ -1,16 +1,17 @@
define([], function() {
return {
- title : 'Box plot',
- library : 'highcharts.js',
- tag : 'div',
- execute : 'boxplot',
- columns : {
+ title : 'Box plot',
+ category : 'Data processing (requires \'charts\' tool from Toolshed)',
+ library : 'highcharts.js',
+ tag : 'div',
+ execute : 'boxplot',
+ columns : {
y : {
title : 'Observations'
}
},
- settings : {
+ settings : {
separator_label : {
title : 'X axis',
type : 'separator'
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
--- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
+++ /dev/null
@@ -1,122 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // highcharts configuration
- hc_config : {
- chart: {
- type: 'boxplot'
- },
-
- title: {
- text: ''
- },
-
- legend: {
- enabled: false
- },
-
- credits: {
- enabled: false
- },
-
- plotOptions: {
- series: {
- animation: false
- }
- },
-
- xAxis: {
- categories: [],
- title: {
- text: ''
- }
- },
-
- yAxis: {
- title: {
- text: ''
- }
- },
-
- series: [{
- name: 'Details:',
- data: [],
- tooltip: {
- headerFormat: '<em>{point.key}</em><br/>'
- }
- }]
- },
-
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // configure request
- var index = 0;
- for (var i in request_dictionary.groups) {
- var group = request_dictionary.groups[i];
- group.columns = null;
- group.columns = {
- x: {
- index: index++
- }
- }
- }
-
- // set axis labels
- this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label');
- this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label');
-
- // request data
- var self = this;
- this.app.datasets.request(request_dictionary, function() {
-
- // reset data/categories
- var data = [];
- var categories = [];
-
- // loop through data groups
- for (var key in request_dictionary.groups) {
- // get group
- var group = request_dictionary.groups[key];
-
- // add category
- categories.push(group.key);
-
- // format chart data
- var point = [];
- for (var key in group.values) {
- point.push(group.values[key].x);
- }
-
- // add to data
- data.push (point);
- }
-
- // categories
- self.hc_config.xAxis.categories = categories;
-
- // update data
- self.hc_config.series[0].data = data;
-
- // draw plot
- self.options.canvas[0].highcharts(self.hc_config);
-
- // set chart state
- chart.state('ok', 'Box plot drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js
@@ -2,6 +2,7 @@
return {
title : '',
+ category : '',
library : 'nvd3.js',
tag : 'svg',
columns : {
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
@@ -31,9 +31,7 @@
.axisLabelDistance(30);
// controls
- if (chart.groups.length == 1) {
- nvd3_model.options({ showControls: false });
- }
+ nvd3_model.options({showControls: false});
// legend
var legend_visible = true;
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js
@@ -0,0 +1,8 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Regular',
+ category : 'Bar diagrams'
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar/wrapper.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js
@@ -0,0 +1,13 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Horizontal',
+ category : 'Bar diagrams',
+ settings : {
+ x_axis_type : {
+ init : 'hide'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/wrapper.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js
@@ -0,0 +1,13 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Stacked horizontal',
+ category : 'Bar diagrams',
+ settings : {
+ x_axis_type : {
+ init : 'hide'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/wrapper.js
@@ -0,0 +1,23 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary, function(nvd3_model) {
+ nvd3_model.stacked(true);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Bar diagram',
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/nvd3_bardiagram.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/nvd3_bardiagram.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js
@@ -1,14 +1,16 @@
+
define(['plugin/charts/nvd3/config'], function(nvd3_config) {
return $.extend(true, {}, nvd3_config, {
- title : 'Histogram',
- execute : 'histogram',
- columns : {
+ title : 'Histogram',
+ category : 'Data processing (requires \'charts\' tool from Toolshed)',
+ execute : 'histogram',
+ columns : {
y : {
title : 'Observations'
}
},
- settings : {
+ settings : {
x_axis_label : {
init : 'Breaks'
},
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_histogram/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/nvd3_histogram.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram/nvd3_histogram.js
+++ /dev/null
@@ -1,39 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // configure request
- var index = 1;
- for (var i in request_dictionary.groups) {
- var group = request_dictionary.groups[i];
- group.columns = {
- x: {
- index: 0
- },
- y: {
- index: index++
- },
- }
- }
-
- // link this
- var self = this;
-
- // load nvd3
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js
@@ -0,0 +1,41 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 1;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = {
+ x: {
+ index: 0
+ },
+ y: {
+ index: index++
+ },
+ }
+ }
+
+ // link this
+ var self = this;
+
+ // load nvd3
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary, function(nvd3_model) {
+ nvd3_model.options({showControls: true});
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js
@@ -0,0 +1,28 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Histogram',
+ category : 'Histograms',
+ execute : 'histogram_discrete',
+ columns : {
+ y : {
+ title : 'Observations'
+ }
+ },
+ settings : {
+ x_axis_label : {
+ init : 'Breaks'
+ },
+ y_axis_label : {
+ init : 'Density'
+ },
+ y_axis_type : {
+ init : 'f'
+ },
+ y_axis_tick : {
+ init : '.2'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js
@@ -0,0 +1,39 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 1;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = {
+ x: {
+ index: 0
+ },
+ y: {
+ index: index++
+ },
+ }
+ }
+
+ // link this
+ var self = this;
+
+ // load nvd3
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_horizontal/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_horizontal/config.js
+++ /dev/null
@@ -1,12 +0,0 @@
-define(['plugin/charts/nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Bar diagram (horizontal)',
- settings : {
- x_axis_type : {
- init : 'hide'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_horizontal/nvd3_horizontal.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_horizontal/nvd3_horizontal.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
@@ -1,7 +1,8 @@
define(['plugin/charts/nvd3/config'], function(nvd3_config) {
return $.extend(true, {}, nvd3_config, {
- title : 'Line chart',
+ title : 'Line chart',
+ category : 'Others'
});
});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_line/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/nvd3_line.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_line/nvd3_line.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/wrapper.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js
@@ -0,0 +1,8 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Line with focus',
+ category : 'Others'
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line_focus/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_line_focus/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line_focus/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/wrapper.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Line with focus',
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/nvd3_linewithfocus.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/nvd3_linewithfocus.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js
@@ -0,0 +1,115 @@
+define([], function() {
+
+return {
+ title : 'Pie chart',
+ library : 'nvd3.js',
+ category : 'Area charts',
+ tag : 'svg',
+ use_panels : true,
+ columns : {
+ label : {
+ title : 'Labels',
+ is_label : true
+ },
+ y : {
+ title : 'Values'
+ }
+ },
+
+ settings : {
+ show_legend : {
+ title : 'Show legend',
+ info : 'Would you like to add a legend?',
+ type : 'select',
+ init : 'false',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ },
+
+ donut_ratio : {
+ title : 'Donut ratio',
+ info : 'Determine how large the donut hole will be.',
+ type : 'select',
+ init : '0.5',
+ data : [
+ {
+ label : '50%',
+ value : '0.5'
+ },
+ {
+ label : '25%',
+ value : '0.25'
+ },
+ {
+ label : '10%',
+ value : '0.10'
+ },
+ {
+ label : '0%',
+ value : '0'
+ }
+ ]
+ },
+
+ label_separator : {
+ type : 'separator',
+ title : 'Label settings'
+ },
+
+ label_type : {
+ title : 'Donut label',
+ info : 'What would you like to show for each slice?',
+ type : 'select',
+ init : 'percent',
+ data : [
+ {
+ label : '-- Nothing --',
+ value : 'hide',
+ hide : 'label_outside'
+ },
+ {
+ label : 'Label column',
+ value : 'key',
+ show : 'label_outside'
+ },
+ {
+ label : 'Value column',
+ value : 'value',
+ show : 'label_outside'
+ },
+ {
+ label : 'Percentage',
+ value : 'percent',
+ show : 'label_outside'
+ }
+ ],
+ },
+
+ label_outside : {
+ title : 'Show outside',
+ info : 'Would you like to show labels outside the donut?',
+ type : 'select',
+ init : 'false',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_pie/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_pie/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_pie/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_pie/wrapper.js
@@ -0,0 +1,115 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function() {
+
+ // loop through data groups
+ for (var group_index in request_dictionary.groups) {
+ // get group
+ var group = request_dictionary.groups[group_index];
+
+ // draw group
+ self._draw_group(chart, group, self.options.canvas[group_index]);
+ }
+
+ // set chart state
+ chart.state('ok', 'Pie chart has been drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ },
+
+ // draw group
+ _draw_group: function(chart, group, canvas) {
+
+ // add title
+ var title = canvas.append('text');
+
+ // configure title attributes
+ this._fix_title(chart, canvas, title, group.key);
+
+ // format chart data
+ var pie_data = [];
+ for (var key in group.values) {
+ var value = group.values[key];
+ pie_data.push ({
+ y : value.y,
+ x : value.label
+ });
+ }
+
+ // add graph to screen
+ var self = this;
+ nv.addGraph(function() {
+ // legend
+ var legend_visible = true;
+ if (chart.settings.get('show_legend') == 'false') {
+ legend_visible = false;
+ }
+
+ // legend
+ var label_outside = true;
+ if (chart.settings.get('label_outside') == 'false') {
+ label_outside = false;
+ }
+
+ // label type
+ var label_type = chart.settings.get('label_type');
+
+ // ratio
+ var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
+
+ // create chart model
+ var chart_3d = nv.models.pieChart()
+ .donut(true)
+ .labelThreshold(.05)
+ .showLegend(legend_visible)
+ .labelType(label_type)
+ .donutRatio(donut_ratio)
+ .donutLabelsOutside(label_outside);
+
+ // add data to canvas
+ canvas.datum(pie_data)
+ .call(chart_3d);
+
+ // add resize trigger
+ nv.utils.windowResize(function() {
+ // update chart
+ chart_3d.update();
+
+ // fix title
+ self._fix_title(chart, canvas, title, group.key);
+ });
+ });
+ },
+
+ // fix title
+ _fix_title: function(chart, canvas, title_element, title_text) {
+ // update title
+ var width = parseInt(canvas.style('width'));
+ var height = parseInt(canvas.style('height'));
+
+ // add title
+ title_element.attr('x', width / 2)
+ .attr('y', height - 10)
+ .attr('text-anchor', 'middle')
+ .text(title_text);
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js
+++ /dev/null
@@ -1,114 +0,0 @@
-define([], function() {
-
-return {
- title : 'Pie chart',
- library : 'nvd3.js',
- tag : 'svg',
- use_panels : true,
- columns : {
- label : {
- title : 'Labels',
- is_label : true
- },
- y : {
- title : 'Values'
- }
- },
-
- settings : {
- show_legend : {
- title : 'Show legend',
- info : 'Would you like to add a legend?',
- type : 'select',
- init : 'false',
- data : [
- {
- label : 'Yes',
- value : 'true'
- },
- {
- label : 'No',
- value : 'false'
- }
- ]
- },
-
- donut_ratio : {
- title : 'Donut ratio',
- info : 'Determine how large the donut hole will be.',
- type : 'select',
- init : '0.5',
- data : [
- {
- label : '50%',
- value : '0.5'
- },
- {
- label : '25%',
- value : '0.25'
- },
- {
- label : '10%',
- value : '0.10'
- },
- {
- label : '0%',
- value : '0'
- }
- ]
- },
-
- label_separator : {
- type : 'separator',
- title : 'Label settings'
- },
-
- label_type : {
- title : 'Donut label',
- info : 'What would you like to show for each slice?',
- type : 'select',
- init : 'percent',
- data : [
- {
- label : '-- Nothing --',
- value : 'hide',
- hide : 'label_outside'
- },
- {
- label : 'Label column',
- value : 'key',
- show : 'label_outside'
- },
- {
- label : 'Value column',
- value : 'value',
- show : 'label_outside'
- },
- {
- label : 'Percentage',
- value : 'percent',
- show : 'label_outside'
- }
- ],
- },
-
- label_outside : {
- title : 'Show outside',
- info : 'Would you like to show labels outside the donut?',
- type : 'select',
- init : 'false',
- data : [
- {
- label : 'Yes',
- value : 'true'
- },
- {
- label : 'No',
- value : 'false'
- }
- ]
- }
- }
-};
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js
+++ /dev/null
@@ -1,115 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // request data
- var self = this;
- this.app.datasets.request(request_dictionary, function() {
-
- // loop through data groups
- for (var group_index in request_dictionary.groups) {
- // get group
- var group = request_dictionary.groups[group_index];
-
- // draw group
- self._draw_group(chart, group, self.options.canvas[group_index]);
- }
-
- // set chart state
- chart.state('ok', 'Pie chart has been drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- });
- },
-
- // draw group
- _draw_group: function(chart, group, canvas) {
-
- // add title
- var title = canvas.append('text');
-
- // configure title attributes
- this._fix_title(chart, canvas, title, group.key);
-
- // format chart data
- var pie_data = [];
- for (var key in group.values) {
- var value = group.values[key];
- pie_data.push ({
- y : value.y,
- x : value.label
- });
- }
-
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- // legend
- var legend_visible = true;
- if (chart.settings.get('show_legend') == 'false') {
- legend_visible = false;
- }
-
- // legend
- var label_outside = true;
- if (chart.settings.get('label_outside') == 'false') {
- label_outside = false;
- }
-
- // label type
- var label_type = chart.settings.get('label_type');
-
- // ratio
- var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
-
- // create chart model
- var chart_3d = nv.models.pieChart()
- .donut(true)
- .labelThreshold(.05)
- .showLegend(legend_visible)
- .labelType(label_type)
- .donutRatio(donut_ratio)
- .donutLabelsOutside(label_outside);
-
- // add data to canvas
- canvas.datum(pie_data)
- .call(chart_3d);
-
- // add resize trigger
- nv.utils.windowResize(function() {
- // update chart
- chart_3d.update();
-
- // fix title
- self._fix_title(chart, canvas, title, group.key);
- });
- });
- },
-
- // fix title
- _fix_title: function(chart, canvas, title_element, title_text) {
- // update title
- var width = parseInt(canvas.style('width'));
- var height = parseInt(canvas.style('height'));
-
- // add title
- title_element.attr('x', width / 2)
- .attr('y', height - 10)
- .attr('text-anchor', 'middle')
- .text(title_text);
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js
@@ -0,0 +1,13 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Scatter plot',
+ category : 'Others',
+ columns : {
+ x : {
+ title : 'Values for x-axis'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatter/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_scatter/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatter/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatter/wrapper.js
@@ -0,0 +1,25 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) {
+ nvd3_model.showDistX(true)
+ .showDistY(true)
+ .color(d3.scale.category10().range());
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/config.js
+++ /dev/null
@@ -1,12 +0,0 @@
-define(['plugin/charts/nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Scatter plot',
- columns : {
- x : {
- title : 'Values for x-axis'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/nvd3_scatterplot.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/nvd3_scatterplot.js
+++ /dev/null
@@ -1,25 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) {
- nvd3_model.showDistX(true)
- .showDistY(true)
- .color(d3.scale.category10().range());
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
@@ -1,7 +1,8 @@
define(['plugin/charts/nvd3/config'], function(nvd3_config) {
return $.extend(true, {}, nvd3_config, {
- title : 'Stacked area'
+ title : 'Regular',
+ category : 'Area charts'
});
});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/nvd3_stackedarea.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/nvd3_stackedarea.js
+++ /dev/null
@@ -1,26 +0,0 @@
-// dependencies
-define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
- // make plot
- nvd3_model.x(function(d) { return d.x })
- .y(function(d) { return d.y })
- .clipEdge(true);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/wrapper.js
@@ -0,0 +1,26 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
+ // make plot
+ nvd3_model.x(function(d) { return d.x })
+ .y(function(d) { return d.y })
+ .clipEdge(true);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js
@@ -0,0 +1,8 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Expanded',
+ category : 'Area charts'
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/wrapper.js
@@ -0,0 +1,27 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
+ // make plot
+ nvd3_model.x(function(d) { return d.x })
+ .y(function(d) { return d.y })
+ .clipEdge(true)
+ .style('expand');
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js
@@ -0,0 +1,8 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Stream',
+ category : 'Area charts'
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/logo.png
Binary file config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/logo.png has changed
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/wrapper.js
@@ -0,0 +1,27 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
+ // make plot
+ nvd3_model.x(function(d) { return d.x })
+ .y(function(d) { return d.y })
+ .clipEdge(true)
+ .style('stream');
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -1,22 +1,30 @@
// dependencies
-define(['plugin/charts/nvd3_bardiagram/config',
+define(['plugin/charts/nvd3_bar/config',
+ 'plugin/charts/nvd3_bar_stacked/config',
+ 'plugin/charts/nvd3_bar_horizontal/config',
+ 'plugin/charts/nvd3_bar_horizontal_stacked/config',
'plugin/charts/nvd3_histogram/config',
- 'plugin/charts/nvd3_horizontal/config',
'plugin/charts/nvd3_line/config',
- 'plugin/charts/nvd3_linewithfocus/config',
- 'plugin/charts/nvd3_piechart/config',
- 'plugin/charts/nvd3_scatterplot/config',
+ 'plugin/charts/nvd3_line_focus/config',
+ 'plugin/charts/nvd3_pie/config',
+ 'plugin/charts/nvd3_scatter/config',
'plugin/charts/nvd3_stackedarea/config',
+ 'plugin/charts/nvd3_stackedarea_full/config',
+ 'plugin/charts/nvd3_stackedarea_stream/config',
'plugin/charts/highcharts_boxplot/config',
'plugin/charts/heatmap/config',
- ], function(nvd3_bardiagram,
+ ], function(nvd3_bar,
+ nvd3_bar_stacked,
+ nvd3_bar_horizontal,
+ nvd3_bar_horizontal_stacked,
nvd3_histogram,
- nvd3_horizontal,
nvd3_line,
- nvd3_linewithfocus,
- nvd3_piechart,
- nvd3_scatterplot,
+ nvd3_line_focus,
+ nvd3_pie,
+ nvd3_scatter,
nvd3_stackedarea,
+ nvd3_stackedarea_full,
+ nvd3_stackedarea_stream,
highcharts_boxplot,
heatmap
) {
@@ -26,16 +34,20 @@
{
// types
defaults: {
- 'nvd3_bardiagram' : nvd3_bardiagram,
- 'nvd3_horizontal' : nvd3_horizontal,
- //'heatmap' : heatmap,
- 'nvd3_histogram' : nvd3_histogram,
- 'nvd3_line' : nvd3_line,
- 'nvd3_linewithfocus' : nvd3_linewithfocus,
- 'nvd3_piechart' : nvd3_piechart,
- 'nvd3_scatterplot' : nvd3_scatterplot,
- 'nvd3_stackedarea' : nvd3_stackedarea,
- 'highcharts_boxplot' : highcharts_boxplot
+ 'nvd3_bar' : nvd3_bar,
+ 'nvd3_bar_stacked' : nvd3_bar_stacked,
+ 'nvd3_bar_horizontal' : nvd3_bar_horizontal,
+ 'nvd3_bar_horizontal_stacked' : nvd3_bar_horizontal_stacked,
+ 'nvd3_stackedarea' : nvd3_stackedarea,
+ 'nvd3_stackedarea_full' : nvd3_stackedarea_full,
+ 'nvd3_stackedarea_stream' : nvd3_stackedarea_stream,
+ 'nvd3_line' : nvd3_line,
+ 'nvd3_line_focus' : nvd3_line_focus,
+ 'nvd3_scatter' : nvd3_scatter,
+ 'nvd3_pie' : nvd3_pie,
+ 'nvd3_histogram' : nvd3_histogram,
+ 'highcharts_boxplot' : highcharts_boxplot,
+ 'heatmap' : heatmap
}
});
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/library/deferred.js
--- a/config/plugins/visualizations/charts/static/library/deferred.js
+++ b/config/plugins/visualizations/charts/static/library/deferred.js
@@ -76,11 +76,7 @@
// ready
ready: function() {
- if (this.counter == 0) {
- return true;
- } else {
- return false;
- }
+ return (this.counter == 0);
}
});
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/library/ui-table.js
--- a/config/plugins/visualizations/charts/static/library/ui-table.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table.js
@@ -162,13 +162,14 @@
// get values
var old_value = this.value();
var new_value = $(e.target).closest('tr').attr('id');
-
- // check equality
- if (new_value && old_value != new_value) {
- if (this.options.onconfirm) {
- this.options.onconfirm(new_value);
- } else {
- this.value(new_value);
+ if (new_value != ''){
+ // check equality
+ if (new_value && old_value != new_value) {
+ if (this.options.onconfirm) {
+ this.options.onconfirm(new_value);
+ } else {
+ this.value(new_value);
+ }
}
}
},
diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/library/ui.js
--- a/config/plugins/visualizations/charts/static/library/ui.js
+++ b/config/plugins/visualizations/charts/static/library/ui.js
@@ -2,11 +2,35 @@
define(['utils/utils', 'plugin/library/ui-select'], function(Utils, Select) {
// plugin
+var Image = Backbone.View.extend(
+{
+ // options
+ optionsDefault: {
+ url : ''
+ },
+
+ // initialize
+ initialize : function(options) {
+ // get options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+ },
+
+ // template
+ _template: function(options) {
+ return '<img src="' + options.url + '"/>';
+ }
+});
+
+// plugin
var Label = Backbone.View.extend(
{
// options
optionsDefault: {
- title : ''
+ title : '',
+ cls : ''
},
// initialize
@@ -25,7 +49,7 @@
// template
_template: function(options) {
- return '<label><b>' + options.title + '</b></label>';
+ return '<label class="' + options.cls + '"><b>' + options.title + '</b></label>';
},
// value
@@ -108,39 +132,6 @@
});
// plugin
-var Icon = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- float : 'right',
- icon : '',
- tooltip : '',
- placement : 'bottom',
- title : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- return '<div>' +
- '<span class="fa ' + options.icon + '" style="font-size: 1.2em;"/> ' +
- options.title +
- '</div>';
- }
-});
-
-// plugin
var ButtonIcon = Backbone.View.extend(
{
// options
@@ -194,6 +185,39 @@
});
// plugin
+var Icon = Backbone.View.extend(
+{
+ // options
+ optionsDefault: {
+ float : 'right',
+ icon : '',
+ tooltip : '',
+ placement : 'bottom',
+ title : ''
+ },
+
+ // initialize
+ initialize : function(options) {
+ // get options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+
+ // add tooltip
+ $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
+ },
+
+ // element
+ _template: function(options) {
+ return '<div>' +
+ '<span class="fa ' + options.icon + '" style="font-size: 1.2em;"/> ' +
+ options.title +
+ '</div>';
+ }
+});
+
+// plugin
var Anchor = Backbone.View.extend(
{
// options
@@ -552,6 +576,7 @@
// return
return {
Label : Label,
+ Image : Image,
Button : Button,
Icon : Icon,
ButtonIcon : ButtonIcon,
This diff is so big that we needed to truncate the remainder.
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/954789571b9d/
Changeset: 954789571b9d
User: jmchilton
Date: 2014-05-15 01:25:50
Summary: Bugfix: Small fix for running workflows with subcollection mapping steps.
Affected #: 1 file
diff -r 9a1415f8108f6283181c7a5b564118920359decc -r 954789571b9d7c2c2ea2d1651d50f13aefaced7e lib/galaxy/dataset_collections/structure.py
--- a/lib/galaxy/dataset_collections/structure.py
+++ b/lib/galaxy/dataset_collections/structure.py
@@ -42,7 +42,7 @@
if substructure.is_leaf:
yield dict_map( element, collection_dict )
else:
- sub_collections = dict_map( lambda collection: element( collection ).child_collection )
+ sub_collections = dict_map( lambda collection: element( collection ).child_collection, collection_dict )
for element in substructure._walk_collections( sub_collections ):
yield element
https://bitbucket.org/galaxy/galaxy-central/commits/31e5817ba7d3/
Changeset: 31e5817ba7d3
User: jmchilton
Date: 2014-05-15 01:25:50
Summary: Bugfix: Yet another bug fix for workflow extraction with collection operations.
Fail, fail, fail.
Affected #: 2 files
diff -r 954789571b9d7c2c2ea2d1651d50f13aefaced7e -r 31e5817ba7d36a039c432205b32958e190cbabbc lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2864,6 +2864,13 @@
def dataset( self ):
return self.dataset_instance.dataset
+ def first_dataset_instance( self ):
+ element_object = self.element_object
+ if isinstance( element_object, DatasetCollection ):
+ return element_object.dataset_instances[ 0 ]
+ else:
+ return element_object
+
def copy_to_collection( self, collection ):
new_element = DatasetCollectionElement(
element=self.element_object,
diff -r 954789571b9d7c2c2ea2d1651d50f13aefaced7e -r 31e5817ba7d36a039c432205b32958e190cbabbc lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -293,6 +293,8 @@
# HACK: Nested associations are not yet working, but we
# still need to clean them up so we can serialize
# if not( prefix ):
+ if isinstance( tmp, model.DatasetCollectionElement ):
+ tmp = tmp.first_dataset_instance()
if tmp: # this is false for a non-set optional dataset
if not isinstance(tmp, list):
associations.append( ( tmp.hid, prefix + key ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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15 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9a1415f8108f/
Changeset: 9a1415f8108f
User: greg
Date: 2014-05-15 00:13:33
Summary: Enhance the galaxy API for the Tool Shed to retrieve the latest installable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner.
Affected #: 3 files
diff -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f -r 9a1415f8108f6283181c7a5b564118920359decc lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -66,6 +66,50 @@
exported_workflows.append( display_dict )
return exported_workflows
+ @web.expose_api
+ def get_latest_installable_revision( self, trans, payload, **kwd ):
+ """
+ POST /api/tool_shed_repositories/get_latest_installable_revision
+ Get the latest installable revision of a specified repository from a specified Tool Shed.
+
+ :param key: the current Galaxy admin user's API key
+
+ The following parameters are included in the payload.
+ :param tool_shed_url (required): the base URL of the Tool Shed from which to retrieve the Repository revision.
+ :param name (required): the name of the Repository
+ :param owner (required): the owner of the Repository
+ """
+ # Get the information about the repository to be installed from the payload.
+ tool_shed_url = payload.get( 'tool_shed_url', '' )
+ if not tool_shed_url:
+ raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." )
+ name = payload.get( 'name', '' )
+ if not name:
+ raise HTTPBadRequest( detail="Missing required parameter 'name'." )
+ owner = payload.get( 'owner', '' )
+ if not owner:
+ raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
+ # Make sure the current user's API key proves he is an admin user in this Galaxy instance.
+ if not trans.user_is_admin():
+ raise HTTPForbidden( detail='You are not authorized to request the latest installable revision for a repository in this Galaxy instance.' )
+ params = '?name=%s&owner=%s' % ( name, owner )
+ url = common_util.url_join( tool_shed_url,
+ 'api/repositories/get_ordered_installable_revisions%s' % params )
+ try:
+ raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
+ except Exception, e:
+ message = "Error attempting to retrieve the latest installable revision from tool shed %s for repository %s owned by %s: %s" % \
+ ( str( tool_shed_url ), str( name ), str( owner ), str( e ) )
+ log.debug( message )
+ return dict( status='error', error=message )
+ if raw_text:
+ # If successful, the response from get_ordered_installable_revisions will be a list of
+ # changeset_revision hash strings.
+ changeset_revisions = json.from_json_string( raw_text )
+ if len( changeset_revisions ) >= 1:
+ return changeset_revisions[ -1 ]
+ return suc.INITIAL_CHANGELOG_HASH
+
def __get_value_mapper( self, trans, tool_shed_repository ):
value_mapper={ 'id' : trans.security.encode_id( tool_shed_repository.id ),
'error_message' : tool_shed_repository.error_message or '' }
diff -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f -r 9a1415f8108f6283181c7a5b564118920359decc lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -321,7 +321,8 @@
'exported_workflows' : 'GET',
'import_workflow' : 'POST',
'import_workflows' : 'POST' },
- collection={ 'reset_metadata_on_installed_repositories' : 'POST' },
+ collection={ 'get_latest_installable_revision' : 'POST',
+ 'reset_metadata_on_installed_repositories' : 'POST' },
controller='tool_shed_repositories',
name_prefix='tool_shed_repository_',
path_prefix='/api',
diff -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f -r 9a1415f8108f6283181c7a5b564118920359decc scripts/api/install_tool_shed_repositories.py
--- a/scripts/api/install_tool_shed_repositories.py
+++ b/scripts/api/install_tool_shed_repositories.py
@@ -1,8 +1,12 @@
#!/usr/bin/env python
"""
-Install a specified repository revision from a specified tool shed into Galaxy. This example demonstrates installation of a repository that contains
-valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section.
-You can choose if tool dependencies or repository dependencies should be installed, use --repository-deps or --tool-deps.
+If a repository name, owner and revision are specified,install the revision from a specified tool shed into Galaxy.
+Specifying a revision is optional, if it is no specified, the latest installable revision will automatically be installed.
+However, the name and owner are required.
+
+This example demonstrates installation of a repository that contains valid tools, loading them into a section of the
+Galaxy tool panel or creating a new tool panel section. You can choose if tool dependencies or repository dependencies
+should be installed, use --repository-deps or --tool-deps.
This example requires a tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain a tool panel section like the following:
@@ -10,7 +14,7 @@
</section>
Here is a working example of how to use this script to install a repository from the test tool shed.
-./install_tool_shed_repositories.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb --tool-deps
+./install_tool_shed_repositories.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --tool-deps
"""
import os
@@ -25,7 +29,20 @@
data[ 'tool_shed_url' ] = options.tool_shed_url
data[ 'name' ] = options.name
data[ 'owner' ] = options.owner
- data[ 'changeset_revision' ] = options.changeset_revision
+ if options.changeset_revision:
+ data[ 'changeset_revision' ] = options.changeset_revision
+ else:
+ # If the changeset_revision is not specified, default to the latest installable revision.
+ revision_data = {}
+ revision_data[ 'tool_shed_url' ] = options.tool_shed_url.rstrip( '/' )
+ revision_data[ 'name' ] = options.name
+ revision_data[ 'owner' ] = options.owner
+ revision_url = '%s%s' % ( options.local_url.rstrip( '/' ), '/api/tool_shed_repositories/get_latest_installable_revision' )
+ latest_installable_revision = submit( options.api,
+ revision_url,
+ revision_data,
+ return_formatted=False )
+ data[ 'changeset_revision' ] = latest_installable_revision
if options.tool_panel_section_id:
data[ 'tool_panel_section_id' ] = options.tool_panel_section_id
elif options.new_tool_panel_section_label:
@@ -34,7 +51,7 @@
data[ 'install_repository_dependencies' ] = options.install_repository_dependencies
if options.install_tool_dependencies:
data[ 'install_tool_dependencies' ] = options.install_tool_dependencies
- submit( options.api, '%s%s' % ( options.local_url.strip( '/' ), '/api/tool_shed_repositories/new/install_repository_revision' ), data )
+ submit( options.api, '%s%s' % ( options.local_url.rstrip( '/' ), '/api/tool_shed_repositories/new/install_repository_revision' ), data )
if __name__ == '__main__':
parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' )
@@ -43,7 +60,7 @@
parser.add_argument( "-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance." )
parser.add_argument( "-n", "--name", required=True, help="Repository name." )
parser.add_argument( "-o", "--owner", required=True, help="Repository owner." )
- parser.add_argument( "-r", "--revision", dest="changeset_revision", required=True, help="Repository owner." )
+ parser.add_argument( "-r", "--revision", dest="changeset_revision", help="Repository revision." )
parser.add_argument( "--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section." )
parser.add_argument( "--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created." )
parser.add_argument( "--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]")
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Add a config option for controlling the AMQP consumer timeout, catch socket.error and attempt to recover from it.
by commits-noreply＠bitbucket.org 14 May '14
by commits-noreply＠bitbucket.org 14 May '14
14 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/22ec0ac1ebcd/
Changeset: 22ec0ac1ebcd
User: natefoo
Date: 2014-05-14 23:34:15
Summary: Add a config option for controlling the AMQP consumer timeout, catch socket.error and attempt to recover from it.
Affected #: 4 files
diff -r a24a928c3b8c4e49bad89fb95496c6b1f78c23bc -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -51,6 +51,12 @@
<!-- <param id="amqp_connect_ssl_keyfile">/path/to/key.pem</param> --><!-- <param id="amqp_connect_ssl_certfile">/path/to/cert.pem</param> --><!-- <param id="amqp_connect_ssl_cert_reqs">cert_required</param> -->
+ <!-- By default, the AMQP consumer uses a nonblocking connection with
+ a 0.2 second timeout. In testing, this works fine for
+ unencrypted AMQP connections, but with SSL it will cause the
+ client to reconnect to the server after each timeout. Set to a
+ higher value (in seconds) (or `None` to use blocking connections). -->
+ <!-- <param id="amqp_consumer_timeout">None</param> --></plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" />
diff -r a24a928c3b8c4e49bad89fb95496c6b1f78c23bc -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f lib/galaxy/jobs/runners/lwr.py
--- a/lib/galaxy/jobs/runners/lwr.py
+++ b/lib/galaxy/jobs/runners/lwr.py
@@ -47,10 +47,16 @@
self._init_monitor_thread()
self._init_worker_threads()
amqp_connect_ssl_args = {}
+ amqp_consumer_timeout = False
for kwd in kwds.keys():
if kwd.startswith('amqp_connect_ssl_'):
amqp_connect_ssl_args[kwd] = kwds[kwd]
client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None}
+ if 'amqp_consumer_timeout' in kwds:
+ if kwds['amqp_consumer_timeout'] == 'None':
+ client_manager_kwargs['amqp_consumer_timeout'] = None
+ else:
+ client_manager_kwargs['amqp_consumer_timeout'] = float(kwds['amqp_consumer_timeout'])
self.galaxy_url = galaxy_url
self.client_manager = build_client_manager(**client_manager_kwargs)
diff -r a24a928c3b8c4e49bad89fb95496c6b1f78c23bc -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
--- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
+++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
@@ -6,6 +6,7 @@
import socket
import logging
+from time import sleep
log = logging.getLogger(__name__)
@@ -47,13 +48,18 @@
def consume(self, queue_name, callback, check=True, connection_kwargs={}):
queue = self.__queue(queue_name)
- with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection:
- with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']):
- while check:
- try:
- connection.drain_events(timeout=self.__timeout)
- except socket.timeout:
- pass
+ while check:
+ try:
+ with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection:
+ with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']):
+ while check and connection.connected:
+ try:
+ connection.drain_events(timeout=self.__timeout)
+ except socket.timeout:
+ pass
+ except socket.error, exc:
+ log.warning('Got socket.error, will retry: %s', exc)
+ sleep(1)
def publish(self, name, payload):
with self.connection(self.__url, ssl=self.__connect_ssl) as connection:
diff -r a24a928c3b8c4e49bad89fb95496c6b1f78c23bc -r 22ec0ac1ebcd1cc5ae5fda4ec70723043e8d5c5f lib/galaxy/jobs/runners/lwr_client/manager.py
--- a/lib/galaxy/jobs/runners/lwr_client/manager.py
+++ b/lib/galaxy/jobs/runners/lwr_client/manager.py
@@ -78,7 +78,11 @@
self.url = kwds.get('url')
self.manager_name = kwds.get("manager", "_default_")
self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None))
- self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl)
+ timeout = kwds.get('amqp_consumer_timeout', False)
+ if timeout is False:
+ self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl)
+ else:
+ self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl, timeout=timeout)
self.status_cache = {}
self.callback_lock = threading.Lock()
self.callback_thread = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Fix for setting metadata when uploading directly to a library.
by commits-noreply＠bitbucket.org 14 May '14
by commits-noreply＠bitbucket.org 14 May '14
14 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a24a928c3b8c/
Changeset: a24a928c3b8c
User: dan
Date: 2014-05-14 23:26:41
Summary: Fix for setting metadata when uploading directly to a library.
Affected #: 1 file
diff -r c9ad7f354f48f546e11879ba864b60c48d6d52f8 -r a24a928c3b8c4e49bad89fb95496c6b1f78c23bc lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1309,7 +1309,7 @@
config_file = self.app.config.config_file
if datatypes_config is None:
datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs
- return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ],
+ return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets + job.output_library_datasets ],
self.sa_session,
exec_dir=exec_dir,
tmp_dir=tmp_dir,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Remove stray log statements in previous commit.
by commits-noreply＠bitbucket.org 14 May '14
by commits-noreply＠bitbucket.org 14 May '14
14 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c9ad7f354f48/
Changeset: c9ad7f354f48
User: jmchilton
Date: 2014-05-14 23:13:32
Summary: Remove stray log statements in previous commit.
Affected #: 1 file
diff -r 170e2294712a2db7a703df8df62ace9a27fa1c9c -r c9ad7f354f48f546e11879ba864b60c48d6d52f8 lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -99,8 +99,6 @@
raise AssertionError( "Attempt to create workflow with job not connected to current history" )
job = jobs_by_id[ job_id ]
tool_inputs, associations = step_inputs( trans, job )
- log.info("job %s has tool_inputs %s" % (job.id, tool_inputs) )
- log.info("associations are %s" % associations)
step = model.WorkflowStep()
step.type = 'tool'
step.tool_id = job.tool_id
@@ -114,7 +112,6 @@
input_collection = an_implicit_output_collection.find_implicit_input_collection( input_name )
if input_collection:
other_hid = input_collection.hid
- log.info("For input_name %s, have hid %s" % ( input_name, other_hid ) )
if other_hid in hid_to_output_pair:
other_step, other_name = hid_to_output_pair[ other_hid ]
conn = model.WorkflowStepConnection()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Bugfixes: More bug fixes for extracting collection-y workflows from a history.
by commits-noreply＠bitbucket.org 14 May '14
by commits-noreply＠bitbucket.org 14 May '14
14 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/170e2294712a/
Changeset: 170e2294712a
User: jmchilton
Date: 2014-05-14 23:06:33
Summary: Bugfixes: More bug fixes for extracting collection-y workflows from a history.
The embarrassment continues...
Affected #: 1 file
diff -r c0eb8b472f3ccabdfd1b0396dbf92c34f3140200 -r 170e2294712a2db7a703df8df62ace9a27fa1c9c lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -5,6 +5,7 @@
from galaxy import model
from galaxy.tools.parameters.basic import (
DataToolParameter,
+ DataCollectionToolParameter,
DrillDownSelectToolParameter,
SelectToolParameter,
UnvalidatedValue
@@ -98,6 +99,8 @@
raise AssertionError( "Attempt to create workflow with job not connected to current history" )
job = jobs_by_id[ job_id ]
tool_inputs, associations = step_inputs( trans, job )
+ log.info("job %s has tool_inputs %s" % (job.id, tool_inputs) )
+ log.info("associations are %s" % associations)
step = model.WorkflowStep()
step.type = 'tool'
step.tool_id = job.tool_id
@@ -111,6 +114,7 @@
input_collection = an_implicit_output_collection.find_implicit_input_collection( input_name )
if input_collection:
other_hid = input_collection.hid
+ log.info("For input_name %s, have hid %s" % ( input_name, other_hid ) )
if other_hid in hid_to_output_pair:
other_step, other_name = hid_to_output_pair[ other_hid ]
conn = model.WorkflowStepConnection()
@@ -190,7 +194,6 @@
# just grab the implicitly mapped jobs and handle in second pass. Second pass is
# needed because cannot allow selection of individual datasets from an implicit
# mapping during extraction - you get the collection or nothing.
- implicit_outputs = []
for content in self.history.active_contents:
if content.history_content_type == "dataset_collection":
hid = content.hid
@@ -200,34 +203,32 @@
job = DatasetCollectionCreationJob( content )
self.jobs[ job ] = [ ( None, content ) ]
else:
- implicit_outputs.append( content )
+ dataset_collection = content
+ # TODO: Optimize db call
+ # TODO: Ensure this is deterministic, must get same job
+ # for each dataset collection.
+ dataset_instance = dataset_collection.collection.dataset_instances[ 0 ]
+ if not self.__check_state( dataset_instance ):
+ # Just checking the state of one instance, don't need more but
+ # makes me wonder if even need this check at all?
+ continue
+
+ job_hda = self.__original_hda( dataset_instance )
+ if not job_hda.creating_job_associations:
+ log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" )
+ job = DatasetCollectionCreationJob( dataset_collection )
+ self.jobs[ job ] = [ ( None, dataset_collection ) ]
+
+ for assoc in job_hda.creating_job_associations:
+ job = assoc.job
+ if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset":
+ self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ]
+ self.implicit_map_jobs.append( job )
+ else:
+ self.jobs[ job ].append( ( assoc.name, dataset_collection ) )
else:
self.__append_dataset( content )
- for dataset_collection in implicit_outputs:
- # TODO: Optimize db call
- # TODO: Ensure this is deterministic, must get same job
- # for each dataset collection.
- dataset_instance = dataset_collection.collection.dataset_instances[ 0 ]
- if not self.__check_state( dataset_instance ):
- # Just checking the state of one instance, don't need more but
- # makes me wonder if even need this check at all?
- continue
-
- job_hda = self.__original_hda( dataset_instance )
- if not job_hda.creating_job_associations:
- log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" )
- job = DatasetCollectionCreationJob( dataset_collection )
- self.jobs[ job ] = [ ( None, dataset_collection ) ]
-
- for assoc in job_hda.creating_job_associations:
- job = assoc.job
- if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset":
- self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ]
- self.implicit_map_jobs.append( job )
- else:
- self.jobs[ job ].append( ( assoc.name, dataset_collection ) )
-
def __append_dataset( self, dataset ):
if not self.__check_state( dataset ):
return
@@ -289,7 +290,7 @@
if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
values[key] = UnvalidatedValue( values[key] )
- if isinstance( input, DataToolParameter ):
+ if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ):
tmp = values[key]
values[key] = None
# HACK: Nested associations are not yet working, but we
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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