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October 2014
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commit/galaxy-central: jmchilton: Update and fix the version of node-http-proxy used by dynamic proxy.
by commits-noreply＠bitbucket.org 31 Oct '14
by commits-noreply＠bitbucket.org 31 Oct '14
31 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ddf23ee62758/
Changeset: ddf23ee62758
User: jmchilton
Date: 2014-10-31 18:41:30+00:00
Summary: Update and fix the version of node-http-proxy used by dynamic proxy.
Upgrade with:
% cd lib/galaxy/web/proxy/js
% npm install
Hoping to fix problems encountered by Bjoern or at least eliminate differences in our respective environments.
Affected #: 1 file
diff -r a0061d1183cbac2308357dcc43276ac8c3bce3fe -r ddf23ee6275837e3ca25ca5c51c43ec68a7432d8 lib/galaxy/web/proxy/js/package.json
--- a/lib/galaxy/web/proxy/js/package.json
+++ b/lib/galaxy/web/proxy/js/package.json
@@ -11,7 +11,7 @@
"url": "https://bitbucket.org/galaxy/galaxy-central"
},
"dependencies": {
- "http-proxy": "~1.1",
+ "http-proxy": "1.6.0",
"commander": "~2.2",
"sqlite3": "3.0.2"
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
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1
0
commit/galaxy-central: guerler: Charts: Fix storage call
by commits-noreply＠bitbucket.org 31 Oct '14
by commits-noreply＠bitbucket.org 31 Oct '14
31 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a0061d1183cb/
Changeset: a0061d1183cb
User: guerler
Date: 2014-10-31 16:15:26+00:00
Summary: Charts: Fix storage call
Affected #: 5 files
diff -r dcd77603b24da934ba6f0fae63da8ddfea55d10b -r a0061d1183cbac2308357dcc43276ac8c3bce3fe client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -142,8 +142,8 @@
if (batch_n === -1) {
batch_n = n;
} else {
- if (batch_n !== n) {
- this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
+ if (batch_n !== n && n != 1) {
+ this._foundError(input_id, 'Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
return false;
}
}
diff -r dcd77603b24da934ba6f0fae63da8ddfea55d10b -r a0061d1183cbac2308357dcc43276ac8c3bce3fe 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.
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o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#portlet-title-text");var n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-title-text" class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),errorText:"No data available.",waitText:"Please wait..."},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$message=$("<div/>"),this.$options=$(this._template(t)),this.$el.append(this.$message),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},wait:function(){this._size()==0&&(this._messageShow(this.options.waitText,"info"),this.$options.hide())},unwait:function(){this._messageHide(),this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.errorText,"danger"),this.$options.hide()):(this._messageHide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,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._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){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.$el)),f.append(r.wrap(this.types.$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.$el}),this.portlet.append(this.message.$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="Data label"),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});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_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()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{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:"0"}]},separator_y:{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",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{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:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),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/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r dcd77603b24da934ba6f0fae63da8ddfea55d10b -r a0061d1183cbac2308357dcc43276ac8c3bce3fe config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -110,7 +110,7 @@
chart.set('dataset_id_job', job.id);
// save
- this.app.storage.save();
+ self.app.storage.save();
// wait for job completion
self._wait(chart, success, error);
diff -r dcd77603b24da934ba6f0fae63da8ddfea55d10b -r a0061d1183cbac2308357dcc43276ac8c3bce3fe static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -142,8 +142,8 @@
if (batch_n === -1) {
batch_n = n;
} else {
- if (batch_n !== n) {
- this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
+ if (batch_n !== n && n != 1) {
+ this._foundError(input_id, 'Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
return false;
}
}
diff -r dcd77603b24da934ba6f0fae63da8ddfea55d10b -r a0061d1183cbac2308357dcc43276ac8c3bce3fe static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g&&g!=1){this._foundError(l,"Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Improve wait message for options
by commits-noreply＠bitbucket.org 31 Oct '14
by commits-noreply＠bitbucket.org 31 Oct '14
31 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dcd77603b24d/
Changeset: dcd77603b24d
User: guerler
Date: 2014-10-31 13:21:59+00:00
Summary: ToolForm: Improve wait message for options
Affected #: 17 files
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -96,15 +96,15 @@
console.debug(current_state);
// activates/disables spinner for dynamic fields to indicate that they are currently being updated
- function wait(activate) {
+ function wait(active) {
for (var i in self.input_list) {
var field = self.field_list[i];
var input = self.input_list[i];
- if (input.is_dynamic && field.wait && field.show) {
- if (activate) {
+ if (input.is_dynamic && field.wait && field.unwait) {
+ if (active) {
field.wait();
} else {
- field.show();
+ field.unwait();
}
}
}
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b client/galaxy/scripts/mvc/tools/tools-input.js
--- a/client/galaxy/scripts/mvc/tools/tools-input.js
+++ b/client/galaxy/scripts/mvc/tools/tools-input.js
@@ -6,7 +6,10 @@
// input field element wrapper
return Backbone.View.extend({
// initialize input wrapper
- initialize: function(options) {
+ initialize: function(app, options) {
+ // link app
+ this.app = app;
+
// link field
this.field = options.field;
@@ -61,10 +64,10 @@
/** Refresh element
*/
_refresh: function() {
- // show/hide field element
if (!this.field.skip) {
this.$field.fadeIn('fast');
this.$title_optional.html('Disable');
+ this.app.refresh();
} else {
this.$field.hide();
this.$title_optional.html('Enable');
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -192,7 +192,7 @@
}
// create input field wrapper
- var input_element = new InputElement({
+ var input_element = new InputElement(this.app, {
label : input_def.title,
help : input_def.help,
field : repeat
@@ -302,7 +302,7 @@
this.app.field_list[id] = field;
// create input field wrapper
- var input_element = new InputElement({
+ var input_element = new InputElement(this.app, {
label : input_def.label,
optional : input_def.optional,
help : input_def.help,
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b client/galaxy/scripts/mvc/ui/ui-options.js
--- a/client/galaxy/scripts/mvc/ui/ui-options.js
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -11,7 +11,8 @@
visible : true,
data : [],
id : Utils.uuid(),
- empty : 'No data available'
+ errorText : 'No data available.',
+ waitText : 'Please wait...'
};
// configure options
@@ -21,11 +22,11 @@
this.setElement('<div/>');
// create elements
- this.$error = $(this._templateError(options));
+ this.$message = $('<div/>');
this.$options = $(this._template(options));
// append
- this.$el.append(this.$error);
+ this.$el.append(this.$message);
this.$el.append(this.$options);
// hide input field
@@ -121,6 +122,22 @@
return true;
},
+ /** Wait message during request processing
+ */
+ wait: function() {
+ if (this._size() == 0) {
+ this._messageShow(this.options.waitText, 'info');
+ this.$options.hide();
+ }
+ },
+
+ /** Hide wait message
+ */
+ unwait: function() {
+ this._messageHide();
+ this._refresh();
+ },
+
/** Trigger custom onchange callback function
*/
_change: function() {
@@ -132,13 +149,11 @@
/** Refresh options view
*/
_refresh: function() {
- // count remaining options
- var remaining = this.$el.find('.ui-option').length;
- if (remaining == 0) {
- this.$error.show();
+ if (this._size() == 0) {
+ this._messageShow(this.options.errorText, 'danger');
this.$options.hide();
} else {
- this.$error.hide();
+ this._messageHide();
this.$options.css('display', 'inline-block');
}
},
@@ -163,9 +178,26 @@
return selected.val();
}
},
+
+ /** Returns the number of options
+ */
+ _size: function() {
+ return this.$el.find('.ui-option').length;
+ },
- _templateError: function(options) {
- return '<div class="ui-error" style="display: none;">' + options.empty + '</div>';
+ /** Show message instead if options
+ */
+ _messageShow: function(text, status) {
+ this.$message.show();
+ this.$message.removeClass();
+ this.$message.addClass('ui-message alert alert-' + status);
+ this.$message.html(text);
+ },
+
+ /** Hide message
+ */
+ _messageHide: function() {
+ this.$message.hide();
}
});
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b client/galaxy/scripts/mvc/ui/ui-select-default.js
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -107,8 +107,7 @@
/** Show the select field
*/
show: function() {
- this.$icon.removeClass();
- this.$icon.addClass('fa fa-caret-down');
+ this.unwait();
this.$select.show();
this.$el.show();
},
@@ -126,6 +125,13 @@
this.$icon.addClass('fa fa-spinner fa-spin');
},
+ /** Hide spinner indicating that the request has been completed
+ */
+ unwait: function() {
+ this.$icon.removeClass();
+ this.$icon.addClass('fa fa-caret-down');
+ },
+
/** Returns true if the field is disabled
*/
disabled: function() {
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -96,15 +96,15 @@
console.debug(current_state);
// activates/disables spinner for dynamic fields to indicate that they are currently being updated
- function wait(activate) {
+ function wait(active) {
for (var i in self.input_list) {
var field = self.field_list[i];
var input = self.input_list[i];
- if (input.is_dynamic && field.wait && field.show) {
- if (activate) {
+ if (input.is_dynamic && field.wait && field.unwait) {
+ if (active) {
field.wait();
} else {
- field.show();
+ field.unwait();
}
}
}
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/mvc/tools/tools-input.js
--- a/static/scripts/mvc/tools/tools-input.js
+++ b/static/scripts/mvc/tools/tools-input.js
@@ -6,7 +6,10 @@
// input field element wrapper
return Backbone.View.extend({
// initialize input wrapper
- initialize: function(options) {
+ initialize: function(app, options) {
+ // link app
+ this.app = app;
+
// link field
this.field = options.field;
@@ -61,10 +64,10 @@
/** Refresh element
*/
_refresh: function() {
- // show/hide field element
if (!this.field.skip) {
this.$field.fadeIn('fast');
this.$title_optional.html('Disable');
+ this.app.refresh();
} else {
this.$field.hide();
this.$title_optional.html('Enable');
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -192,7 +192,7 @@
}
// create input field wrapper
- var input_element = new InputElement({
+ var input_element = new InputElement(this.app, {
label : input_def.title,
help : input_def.help,
field : repeat
@@ -302,7 +302,7 @@
this.app.field_list[id] = field;
// create input field wrapper
- var input_element = new InputElement({
+ var input_element = new InputElement(this.app, {
label : input_def.label,
optional : input_def.optional,
help : input_def.help,
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/mvc/ui/ui-options.js
--- a/static/scripts/mvc/ui/ui-options.js
+++ b/static/scripts/mvc/ui/ui-options.js
@@ -11,7 +11,8 @@
visible : true,
data : [],
id : Utils.uuid(),
- empty : 'No data available'
+ errorText : 'No data available.',
+ waitText : 'Please wait...'
};
// configure options
@@ -21,11 +22,11 @@
this.setElement('<div/>');
// create elements
- this.$error = $(this._templateError(options));
+ this.$message = $('<div/>');
this.$options = $(this._template(options));
// append
- this.$el.append(this.$error);
+ this.$el.append(this.$message);
this.$el.append(this.$options);
// hide input field
@@ -121,6 +122,22 @@
return true;
},
+ /** Wait message during request processing
+ */
+ wait: function() {
+ if (this._size() == 0) {
+ this._messageShow(this.options.waitText, 'info');
+ this.$options.hide();
+ }
+ },
+
+ /** Hide wait message
+ */
+ unwait: function() {
+ this._messageHide();
+ this._refresh();
+ },
+
/** Trigger custom onchange callback function
*/
_change: function() {
@@ -132,13 +149,11 @@
/** Refresh options view
*/
_refresh: function() {
- // count remaining options
- var remaining = this.$el.find('.ui-option').length;
- if (remaining == 0) {
- this.$error.show();
+ if (this._size() == 0) {
+ this._messageShow(this.options.errorText, 'danger');
this.$options.hide();
} else {
- this.$error.hide();
+ this._messageHide();
this.$options.css('display', 'inline-block');
}
},
@@ -163,9 +178,26 @@
return selected.val();
}
},
+
+ /** Returns the number of options
+ */
+ _size: function() {
+ return this.$el.find('.ui-option').length;
+ },
- _templateError: function(options) {
- return '<div class="ui-error" style="display: none;">' + options.empty + '</div>';
+ /** Show message instead if options
+ */
+ _messageShow: function(text, status) {
+ this.$message.show();
+ this.$message.removeClass();
+ this.$message.addClass('ui-message alert alert-' + status);
+ this.$message.html(text);
+ },
+
+ /** Hide message
+ */
+ _messageHide: function() {
+ this.$message.hide();
}
});
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/mvc/ui/ui-select-default.js
--- a/static/scripts/mvc/ui/ui-select-default.js
+++ b/static/scripts/mvc/ui/ui-select-default.js
@@ -107,8 +107,7 @@
/** Show the select field
*/
show: function() {
- this.$icon.removeClass();
- this.$icon.addClass('fa fa-caret-down');
+ this.unwait();
this.$select.show();
this.$el.show();
},
@@ -126,6 +125,13 @@
this.$icon.addClass('fa fa-spinner fa-spin');
},
+ /** Hide spinner indicating that the request has been completed
+ */
+ unwait: function() {
+ this.$icon.removeClass();
+ this.$icon.addClass('fa fa-caret-down');
+ },
+
/** Returns true if the field is disabled
*/
disabled: function() {
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(p){if(p.values.length>0&&p.values[0]&&p.values[0].src==="hda"){return m.content.get({id:p.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);function o(r){for(var q in m.input_list){var s=m.field_list[q];var p=m.input_list[q];if(p.is_dynamic&&s.wait&&s.show){if(r){s.wait()}else{s.show()}}}}o(true);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(p){m._rebuildForm(p);o(false);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(p)},error:function(p){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(p)}})},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(p){if(p.values.length>0&&p.values[0]&&p.values[0].src==="hda"){return m.content.get({id:p.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);function o(s){for(var q in m.input_list){var r=m.field_list[q];var p=m.input_list[q];if(p.is_dynamic&&r.wait&&r.unwait){if(s){r.wait()}else{r.unwait()}}}}o(true);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(p){m._rebuildForm(p);o(false);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(p)},error:function(p){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(p)}})},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/packed/mvc/tools/tools-input.js
--- a/static/scripts/packed/mvc/tools/tools-input.js
+++ b/static/scripts/packed/mvc/tools/tools-input.js
@@ -1,1 +1,1 @@
-define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
+define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.refresh()}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var l=this._addRow("conditional",h);for(var k in h.cases){var j=h.id+"-section-"+k;var m=new f(this.app,{inputs:h.cases[k].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(j)}l.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return i},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var l=this._addRow("conditional",h);for(var k in h.cases){var j=h.id+"-section-"+k;var m=new f(this.app,{inputs:h.cases[k].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(j)}l.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return i},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/packed/mvc/ui/ui-options.js
--- a/static/scripts/packed/mvc/ui/ui-options.js
+++ b/static/scripts/packed/mvc/ui/ui-options.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
+define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/scripts/packed/mvc/ui/ui-select-default.js
--- a/static/scripts/packed/mvc/ui/ui-select-default.js
+++ b/static/scripts/packed/mvc/ui/ui-select-default.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},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")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}});
\ No newline at end of file
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1292,7 +1292,7 @@
.ui-table-form-info{clear:both !important}
.ui-table-form-separator{font-weight:bold;font-size:0.9em}
.ui-label{font-weight:bold}
-.ui-message{padding:2px 2px 2px 10px}
+.ui-message{padding:2px 2px 2px 10px;margin-bottom:5px}
.ui-icon{font-size:1.2em}
.ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px}
.ui-button-icon .button{margin-right:5px;margin-left:5px}.ui-button-icon .button .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px}
diff -r 06970f2cfee91d60b981308483d56a9ebb3afb55 -r dcd77603b24da934ba6f0fae63da8ddfea55d10b static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -81,6 +81,7 @@
.ui-message {
padding: 2px 2px 2px 10px;
+ margin-bottom: 5px;
}
.ui-icon {
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1
0
commit/galaxy-central: guerler: ToolForm: Fix conditional parameter mapping
by commits-noreply＠bitbucket.org 30 Oct '14
by commits-noreply＠bitbucket.org 30 Oct '14
30 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/06970f2cfee9/
Changeset: 06970f2cfee9
User: guerler
Date: 2014-10-30 19:49:05+00:00
Summary: ToolForm: Fix conditional parameter mapping
Affected #: 3 files
diff -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da -r 06970f2cfee91d60b981308483d56a9ebb3afb55 client/galaxy/scripts/mvc/tools/tools-tree.js
--- a/client/galaxy/scripts/mvc/tools/tools-tree.js
+++ b/client/galaxy/scripts/mvc/tools/tools-tree.js
@@ -169,7 +169,12 @@
}
} else {
if (node.type == 'conditional') {
- search (index, node.inputs);
+ var value = node.test_param && node.test_param.value;
+ for (var j in node.cases) {
+ if (node.cases[j].value == value) {
+ search (index, node.cases[j].inputs);
+ }
+ }
} else {
var input_id = self.app.tree.job_ids[index];
if (input_id) {
diff -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da -r 06970f2cfee91d60b981308483d56a9ebb3afb55 static/scripts/mvc/tools/tools-tree.js
--- a/static/scripts/mvc/tools/tools-tree.js
+++ b/static/scripts/mvc/tools/tools-tree.js
@@ -169,7 +169,12 @@
}
} else {
if (node.type == 'conditional') {
- search (index, node.inputs);
+ var value = node.test_param && node.test_param.value;
+ for (var j in node.cases) {
+ if (node.cases[j].value == value) {
+ search (index, node.cases[j].inputs);
+ }
+ }
} else {
var input_id = self.app.tree.job_ids[index];
if (input_id) {
diff -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da -r 06970f2cfee91d60b981308483d56a9ebb3afb55 static/scripts/packed/mvc/tools/tools-tree.js
--- a/static/scripts/packed/mvc/tools/tools-tree.js
+++ b/static/scripts/packed/mvc/tools/tools-tree.js
@@ -1,1 +1,1 @@
-define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(n,l){for(var k in l){var m=l[k];var h=m.name;if(n!=""){h=n+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){d(h,m.inputs)}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})});
\ No newline at end of file
+define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(o,l){for(var k in l){var m=l[k];var h=m.name;if(o!=""){h=o+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){var n=m.test_param&&m.test_param.value;for(var g in m.cases){if(m.cases[g].value==n){d(h,m.cases[g].inputs)}}}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Add spinner to dynamic select fields
by commits-noreply＠bitbucket.org 30 Oct '14
by commits-noreply＠bitbucket.org 30 Oct '14
30 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d1c4ff95fad8/
Changeset: d1c4ff95fad8
User: guerler
Date: 2014-10-30 18:39:44+00:00
Summary: ToolForm: Add spinner to dynamic select fields
Affected #: 6 files
diff -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -95,6 +95,24 @@
console.debug('tools-form::_refreshForm() - Refreshing states.');
console.debug(current_state);
+ // activates/disables spinner for dynamic fields to indicate that they are currently being updated
+ function wait(activate) {
+ for (var i in self.input_list) {
+ var field = self.field_list[i];
+ var input = self.input_list[i];
+ if (input.is_dynamic && field.wait && field.show) {
+ if (activate) {
+ field.wait();
+ } else {
+ field.show();
+ }
+ }
+ }
+ }
+
+ // set wait mode
+ wait(true);
+
// post job
Utils.request({
type : 'GET',
@@ -104,6 +122,9 @@
// rebuild form
self._rebuildForm(response);
+ // unset wait mode
+ wait(false);
+
// log success
console.debug('tools-form::_refreshForm() - States refreshed.');
console.debug(response);
diff -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -82,7 +82,7 @@
input_def.value = input_def.test_param.value;
// build options field
- var table_row = this._addRow('conditional', input_def);
+ var field = this._addRow('conditional', input_def);
// add fields
for (var i in input_def.cases) {
@@ -104,6 +104,9 @@
// append to table
this.table.append(sub_section_id);
}
+
+ // trigger refresh on conditional input field after all input elements have been created
+ field.trigger('change');
},
/** Add a repeat block
@@ -315,8 +318,8 @@
// append to table
this.table.append(id);
- // return table row
- return this.table.get(id)
+ // return created field
+ return field;
},
/** Conditional input field selector
diff -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -95,6 +95,24 @@
console.debug('tools-form::_refreshForm() - Refreshing states.');
console.debug(current_state);
+ // activates/disables spinner for dynamic fields to indicate that they are currently being updated
+ function wait(activate) {
+ for (var i in self.input_list) {
+ var field = self.field_list[i];
+ var input = self.input_list[i];
+ if (input.is_dynamic && field.wait && field.show) {
+ if (activate) {
+ field.wait();
+ } else {
+ field.show();
+ }
+ }
+ }
+ }
+
+ // set wait mode
+ wait(true);
+
// post job
Utils.request({
type : 'GET',
@@ -104,6 +122,9 @@
// rebuild form
self._rebuildForm(response);
+ // unset wait mode
+ wait(false);
+
// log success
console.debug('tools-form::_refreshForm() - States refreshed.');
console.debug(response);
diff -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -82,7 +82,7 @@
input_def.value = input_def.test_param.value;
// build options field
- var table_row = this._addRow('conditional', input_def);
+ var field = this._addRow('conditional', input_def);
// add fields
for (var i in input_def.cases) {
@@ -104,6 +104,9 @@
// append to table
this.table.append(sub_section_id);
}
+
+ // trigger refresh on conditional input field after all input elements have been created
+ field.trigger('change');
},
/** Add a repeat block
@@ -315,8 +318,8 @@
// append to table
this.table.append(id);
- // return table row
- return this.table.get(id)
+ // return created field
+ return field;
},
/** Conditional input field selector
diff -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(p){if(p.values.length>0&&p.values[0]&&p.values[0].src==="hda"){return m.content.get({id:p.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);function o(r){for(var q in m.input_list){var s=m.field_list[q];var p=m.input_list[q];if(p.is_dynamic&&s.wait&&s.show){if(r){s.wait()}else{s.show()}}}}o(true);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(p){m._rebuildForm(p);o(false);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(p)},error:function(p){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(p)}})},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
diff -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 -r d1c4ff95fad8e27ec2ea1cd3f5a3d7fa764e24da static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var l=this._addRow("conditional",h);for(var k in h.cases){var j=h.id+"-section-"+k;var m=new f(this.app,{inputs:h.cases[k].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(j)}l.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return i},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Reduce number of refreshing events
by commits-noreply＠bitbucket.org 30 Oct '14
by commits-noreply＠bitbucket.org 30 Oct '14
30 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/08d0cdb2a351/
Changeset: 08d0cdb2a351
User: guerler
Date: 2014-10-30 18:17:51+00:00
Summary: ToolForm: Reduce number of refreshing events
Affected #: 6 files
diff -r 713526cf328d41f0248ce85860e1d33db779482f -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -64,18 +64,55 @@
}
},
- // refresh
+ // rebuild underlying data structure representation for the tool form
+ // this happens i.e. when repeat blocks are added or removed and on initialization
+ rebuild: function() {
+ this.tree.refresh();
+ console.debug('tools-form::refresh() - Refreshed form structure.');
+ },
+
+ // refreshes input states i.e. for dynamic parameters
refresh: function() {
- // recreate tree structure
- this.tree.refresh();
+ // link this
+ var self = this;
- // trigger change
- for (var id in this.field_list) {
- this.field_list[id].trigger('change');
+ // only refresh the state if the form contains dynamic parameters
+ if (!this.is_dynamic) {
+ return;
}
- // log
- console.debug('tools-form::refresh() - Recreated data structure. Refresh.');
+ // finalize data
+ var current_state = this.tree.finalize({
+ data : function(dict) {
+ if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') {
+ return self.content.get({id: dict.values[0].id}).dataset_id;
+ }
+ return null;
+ }
+ });
+
+ // log tool state
+ console.debug('tools-form::_refreshForm() - Refreshing states.');
+ console.debug(current_state);
+
+ // post job
+ Utils.request({
+ type : 'GET',
+ url : galaxy_config.root + 'api/tools/' + this.options.id + '/build',
+ data : current_state,
+ success : function(response) {
+ // rebuild form
+ self._rebuildForm(response);
+
+ // log success
+ console.debug('tools-form::_refreshForm() - States refreshed.');
+ console.debug(response);
+ },
+ error : function(response) {
+ console.debug('tools-form::_refreshForm() - Refresh request failed.');
+ console.debug(response);
+ }
+ });
},
// build tool model through api call
@@ -123,50 +160,6 @@
});
},
- // refresh form data
- rebuild: function() {
- // link this
- var self = this;
-
- // only refresh the state if the form contains dynamic parameters
- if (!this.is_dynamic) {
- return;
- }
-
- // finalize data
- var current_state = this.tree.finalize({
- data : function(dict) {
- if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') {
- return self.content.get({id: dict.values[0].id}).dataset_id;
- }
- return null;
- }
- });
-
- // log tool state
- console.debug('tools-form::_refreshForm() - Refreshing states.');
- console.debug(current_state);
-
- // post job
- Utils.request({
- type : 'GET',
- url : galaxy_config.root + 'api/tools/' + this.options.id + '/build',
- data : current_state,
- success : function(response) {
- // rebuild form
- self._rebuildForm(response);
-
- // log success
- console.debug('tools-form::_refreshForm() - States refreshed.');
- console.debug(response);
- },
- error : function(response) {
- console.debug('tools-form::_refreshForm() - Refresh request failed.');
- console.debug(response);
- }
- });
- },
-
// rebuild the form elements
_rebuildForm: function(new_model) {
var self = this;
@@ -177,7 +170,7 @@
// backup new options
input.options = node.options;
- // get/update field (currently only done for select fields)
+ // get/update field
var field = self.field_list[input_id];
if (field.update && input.type != 'data') {
var new_options = [];
@@ -296,7 +289,6 @@
cls : 'btn btn-primary',
floating : 'clear',
onclick : function() {
- //self.rebuild();
self.job_handler.submit();
}
})
@@ -328,8 +320,8 @@
// append tool section
this.portlet.append(this.section.$el);
- // trigger refresh
- this.refresh();
+ // rebuild the underlying data structure
+ this.rebuild();
}
});
diff -r 713526cf328d41f0248ce85860e1d33db779482f -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -131,6 +131,7 @@
repeat.retitle(input_def.title);
// trigger refresh
+ self.app.rebuild();
self.app.refresh();
}
}
@@ -164,6 +165,7 @@
create(input_def.inputs, true);
// trigger refresh
+ self.app.rebuild();
self.app.refresh();
}
});
@@ -366,6 +368,9 @@
section_row.hide();
}
}
+
+ // refresh form inputs
+ self.app.refresh();
}
});
},
@@ -378,8 +383,8 @@
id : 'field-' + input_def.id,
extensions : input_def.extensions,
multiple : input_def.multiple,
- onchange : function(dict) {
- self.app.rebuild();
+ onchange : function() {
+ self.app.refresh();
}
});
},
@@ -415,7 +420,7 @@
data : options,
multiple: input_def.multiple,
onchange: function() {
- self.app.rebuild();
+ self.app.refresh();
}
});
},
diff -r 713526cf328d41f0248ce85860e1d33db779482f -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -64,18 +64,55 @@
}
},
- // refresh
+ // rebuild underlying data structure representation for the tool form
+ // this happens i.e. when repeat blocks are added or removed and on initialization
+ rebuild: function() {
+ this.tree.refresh();
+ console.debug('tools-form::refresh() - Refreshed form structure.');
+ },
+
+ // refreshes input states i.e. for dynamic parameters
refresh: function() {
- // recreate tree structure
- this.tree.refresh();
+ // link this
+ var self = this;
- // trigger change
- for (var id in this.field_list) {
- this.field_list[id].trigger('change');
+ // only refresh the state if the form contains dynamic parameters
+ if (!this.is_dynamic) {
+ return;
}
- // log
- console.debug('tools-form::refresh() - Recreated data structure. Refresh.');
+ // finalize data
+ var current_state = this.tree.finalize({
+ data : function(dict) {
+ if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') {
+ return self.content.get({id: dict.values[0].id}).dataset_id;
+ }
+ return null;
+ }
+ });
+
+ // log tool state
+ console.debug('tools-form::_refreshForm() - Refreshing states.');
+ console.debug(current_state);
+
+ // post job
+ Utils.request({
+ type : 'GET',
+ url : galaxy_config.root + 'api/tools/' + this.options.id + '/build',
+ data : current_state,
+ success : function(response) {
+ // rebuild form
+ self._rebuildForm(response);
+
+ // log success
+ console.debug('tools-form::_refreshForm() - States refreshed.');
+ console.debug(response);
+ },
+ error : function(response) {
+ console.debug('tools-form::_refreshForm() - Refresh request failed.');
+ console.debug(response);
+ }
+ });
},
// build tool model through api call
@@ -123,50 +160,6 @@
});
},
- // refresh form data
- rebuild: function() {
- // link this
- var self = this;
-
- // only refresh the state if the form contains dynamic parameters
- if (!this.is_dynamic) {
- return;
- }
-
- // finalize data
- var current_state = this.tree.finalize({
- data : function(dict) {
- if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') {
- return self.content.get({id: dict.values[0].id}).dataset_id;
- }
- return null;
- }
- });
-
- // log tool state
- console.debug('tools-form::_refreshForm() - Refreshing states.');
- console.debug(current_state);
-
- // post job
- Utils.request({
- type : 'GET',
- url : galaxy_config.root + 'api/tools/' + this.options.id + '/build',
- data : current_state,
- success : function(response) {
- // rebuild form
- self._rebuildForm(response);
-
- // log success
- console.debug('tools-form::_refreshForm() - States refreshed.');
- console.debug(response);
- },
- error : function(response) {
- console.debug('tools-form::_refreshForm() - Refresh request failed.');
- console.debug(response);
- }
- });
- },
-
// rebuild the form elements
_rebuildForm: function(new_model) {
var self = this;
@@ -177,7 +170,7 @@
// backup new options
input.options = node.options;
- // get/update field (currently only done for select fields)
+ // get/update field
var field = self.field_list[input_id];
if (field.update && input.type != 'data') {
var new_options = [];
@@ -296,7 +289,6 @@
cls : 'btn btn-primary',
floating : 'clear',
onclick : function() {
- //self.rebuild();
self.job_handler.submit();
}
})
@@ -328,8 +320,8 @@
// append tool section
this.portlet.append(this.section.$el);
- // trigger refresh
- this.refresh();
+ // rebuild the underlying data structure
+ this.rebuild();
}
});
diff -r 713526cf328d41f0248ce85860e1d33db779482f -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -131,6 +131,7 @@
repeat.retitle(input_def.title);
// trigger refresh
+ self.app.rebuild();
self.app.refresh();
}
}
@@ -164,6 +165,7 @@
create(input_def.inputs, true);
// trigger refresh
+ self.app.rebuild();
self.app.refresh();
}
});
@@ -366,6 +368,9 @@
section_row.hide();
}
}
+
+ // refresh form inputs
+ self.app.refresh();
}
});
},
@@ -378,8 +383,8 @@
id : 'field-' + input_def.id,
extensions : input_def.extensions,
multiple : input_def.multiple,
- onchange : function(dict) {
- self.app.rebuild();
+ onchange : function() {
+ self.app.refresh();
}
});
},
@@ -415,7 +420,7 @@
data : options,
multiple: input_def.multiple,
onchange: function() {
- self.app.rebuild();
+ self.app.refresh();
}
});
},
diff -r 713526cf328d41f0248ce85860e1d33db779482f -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
diff -r 713526cf328d41f0248ce85860e1d33db779482f -r 08d0cdb2a3514cf3c1782e1195d2b85a4dbffa17 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(j){i.app.rebuild()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.rebuild()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Activate dynamic parameter handling
by commits-noreply＠bitbucket.org 30 Oct '14
by commits-noreply＠bitbucket.org 30 Oct '14
30 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/713526cf328d/
Changeset: 713526cf328d
User: guerler
Date: 2014-10-30 15:27:26+00:00
Summary: ToolForm: Activate dynamic parameter handling
Affected #: 7 files
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -128,6 +128,11 @@
// link this
var self = this;
+ // only refresh the state if the form contains dynamic parameters
+ if (!this.is_dynamic) {
+ return;
+ }
+
// finalize data
var current_state = this.tree.finalize({
data : function(dict) {
@@ -139,7 +144,7 @@
});
// log tool state
- console.debug('tools-form::_refreshForm() - Refreshing inputs/states.');
+ console.debug('tools-form::_refreshForm() - Refreshing states.');
console.debug(current_state);
// post job
@@ -152,7 +157,7 @@
self._rebuildForm(response);
// log success
- console.debug('tools-form::_refreshForm() - Refreshed inputs/states.');
+ console.debug('tools-form::_refreshForm() - States refreshed.');
console.debug(response);
},
error : function(response) {
@@ -174,7 +179,7 @@
// get/update field (currently only done for select fields)
var field = self.field_list[input_id];
- if (field.update && input.type == 'select') {
+ if (field.update && input.type != 'data') {
var new_options = [];
for (var i in node.options) {
var opt = node.options[i];
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -231,7 +231,6 @@
// data column
case 'data_column':
- input_def.is_dynamic = false;
field = this._fieldSelect(input_def);
break;
@@ -285,7 +284,7 @@
// deactivate dynamic fields
if (input_def.is_dynamic) {
- this.app.incompatible = true;
+ //this.app.incompatible = true;
this.app.is_dynamic = true;
}
@@ -374,119 +373,13 @@
/** Data input field
*/
_fieldData : function(input_def) {
- // link this
var self = this;
-
- // get element id
- var id = input_def.id;
-
- // select field
return new SelectContent.View(this.app, {
- id : 'field-' + id,
+ id : 'field-' + input_def.id,
extensions : input_def.extensions,
multiple : input_def.multiple,
onchange : function(dict) {
- // rebuild the form
- if (self.app.is_dynamic) {
- self.app.rebuild();
- }
-
- // pick the first content only (todo: maybe collect multiple meta information)
- var content_def = dict.values[0];
- var content_id = content_def.id;
- var content_src = content_def.src;
-
- // get referenced columns
- var column_list = self.app.tree.references(id, 'data_column');
-
- // check data column list
- if (column_list.length <= 0) {
- console.debug('tool-form::field_data() - Data column parameters unavailable.');
- return;
- }
-
- // set wait mode
- for (var i in column_list) {
- var column_field = self.app.field_list[column_list[i]];
- column_field.wait && column_field.wait();
- }
-
- // find selected content
- self.app.content.getDetails({
- id : content_id,
- src : content_src,
- success : function(content) {
- // meta data
- var meta = null;
-
- // check content
- if (content) {
- // log selection
- console.debug('tool-form::field_data() - Selected content ' + content_id + '.');
-
- // select the first dataset to represent collections
- if (content_src == 'hdca' && content.elements && content.elements.length > 0) {
- content = content.elements[0].object;
- }
-
- // get meta data
- meta = content.metadata_column_types;
-
- // check meta data
- if (!meta) {
- console.debug('tool-form::field_data() - FAILED: Could not find metadata for content ' + content_id + '.');
- }
- } else {
- console.debug('tool-form::field_data() - FAILED: Could not find content ' + content_id + '.');
- }
-
- // update referenced columns
- for (var i in column_list) {
- // get column input/field
- var column_input = self.app.input_list[column_list[i]];
- var column_field = self.app.field_list[column_list[i]];
- if (!column_input || !column_field) {
- console.debug('tool-form::field_data() - FAILED: Column not found.');
- }
-
- // is numerical?
- var numerical = column_input.numerical;
-
- // identify column options
- var columns = [];
- for (var key in meta) {
- // get column type
- var column_type = meta[key];
-
- // column index
- var column_index = (parseInt(key) + 1);
-
- // column type label
- var column_label = 'Text';
- if (column_type == 'int' || column_type == 'float') {
- column_label = 'Number';
- }
-
- // add to selection
- if (column_type == 'int' || column_type == 'float' || !numerical) {
- columns.push({
- 'label' : 'Column: ' + column_index + ' [' + column_label + ']',
- 'value' : column_index
- });
- }
- }
-
- // update field
- if (column_field) {
- column_field.update(columns);
- if (!column_field.exists(column_field.value())) {
- column_field.value(column_field.first());
- }
- column_field.show();
- }
- }
- }
- });
+ self.app.rebuild();
}
});
},
@@ -516,10 +409,14 @@
}
// select field
+ var self = this;
return new SelectClass.View({
id : 'field-' + input_def.id,
data : options,
- multiple: input_def.multiple
+ multiple: input_def.multiple,
+ onchange: function() {
+ self.app.rebuild();
+ }
});
},
@@ -535,7 +432,6 @@
/** Slider field
*/
_fieldSlider: function(input_def) {
- // create slider
return new Ui.Slider.View({
id : 'field-' + input_def.id,
precise : input_def.type == 'float',
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1242,7 +1242,7 @@
if type(col) == type(()) and len(col) == 2: # fiddled
options.append((col[1],col[0],False))
else:
- options.append( ( 'c' + col, col, False ) )
+ options.append( ( 'Column: ' + col, col, False ) )
return options
def get_initial_value( self, trans, context, history=None ):
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -128,6 +128,11 @@
// link this
var self = this;
+ // only refresh the state if the form contains dynamic parameters
+ if (!this.is_dynamic) {
+ return;
+ }
+
// finalize data
var current_state = this.tree.finalize({
data : function(dict) {
@@ -139,7 +144,7 @@
});
// log tool state
- console.debug('tools-form::_refreshForm() - Refreshing inputs/states.');
+ console.debug('tools-form::_refreshForm() - Refreshing states.');
console.debug(current_state);
// post job
@@ -152,7 +157,7 @@
self._rebuildForm(response);
// log success
- console.debug('tools-form::_refreshForm() - Refreshed inputs/states.');
+ console.debug('tools-form::_refreshForm() - States refreshed.');
console.debug(response);
},
error : function(response) {
@@ -174,7 +179,7 @@
// get/update field (currently only done for select fields)
var field = self.field_list[input_id];
- if (field.update && input.type == 'select') {
+ if (field.update && input.type != 'data') {
var new_options = [];
for (var i in node.options) {
var opt = node.options[i];
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -231,7 +231,6 @@
// data column
case 'data_column':
- input_def.is_dynamic = false;
field = this._fieldSelect(input_def);
break;
@@ -285,7 +284,7 @@
// deactivate dynamic fields
if (input_def.is_dynamic) {
- this.app.incompatible = true;
+ //this.app.incompatible = true;
this.app.is_dynamic = true;
}
@@ -374,119 +373,13 @@
/** Data input field
*/
_fieldData : function(input_def) {
- // link this
var self = this;
-
- // get element id
- var id = input_def.id;
-
- // select field
return new SelectContent.View(this.app, {
- id : 'field-' + id,
+ id : 'field-' + input_def.id,
extensions : input_def.extensions,
multiple : input_def.multiple,
onchange : function(dict) {
- // rebuild the form
- if (self.app.is_dynamic) {
- self.app.rebuild();
- }
-
- // pick the first content only (todo: maybe collect multiple meta information)
- var content_def = dict.values[0];
- var content_id = content_def.id;
- var content_src = content_def.src;
-
- // get referenced columns
- var column_list = self.app.tree.references(id, 'data_column');
-
- // check data column list
- if (column_list.length <= 0) {
- console.debug('tool-form::field_data() - Data column parameters unavailable.');
- return;
- }
-
- // set wait mode
- for (var i in column_list) {
- var column_field = self.app.field_list[column_list[i]];
- column_field.wait && column_field.wait();
- }
-
- // find selected content
- self.app.content.getDetails({
- id : content_id,
- src : content_src,
- success : function(content) {
- // meta data
- var meta = null;
-
- // check content
- if (content) {
- // log selection
- console.debug('tool-form::field_data() - Selected content ' + content_id + '.');
-
- // select the first dataset to represent collections
- if (content_src == 'hdca' && content.elements && content.elements.length > 0) {
- content = content.elements[0].object;
- }
-
- // get meta data
- meta = content.metadata_column_types;
-
- // check meta data
- if (!meta) {
- console.debug('tool-form::field_data() - FAILED: Could not find metadata for content ' + content_id + '.');
- }
- } else {
- console.debug('tool-form::field_data() - FAILED: Could not find content ' + content_id + '.');
- }
-
- // update referenced columns
- for (var i in column_list) {
- // get column input/field
- var column_input = self.app.input_list[column_list[i]];
- var column_field = self.app.field_list[column_list[i]];
- if (!column_input || !column_field) {
- console.debug('tool-form::field_data() - FAILED: Column not found.');
- }
-
- // is numerical?
- var numerical = column_input.numerical;
-
- // identify column options
- var columns = [];
- for (var key in meta) {
- // get column type
- var column_type = meta[key];
-
- // column index
- var column_index = (parseInt(key) + 1);
-
- // column type label
- var column_label = 'Text';
- if (column_type == 'int' || column_type == 'float') {
- column_label = 'Number';
- }
-
- // add to selection
- if (column_type == 'int' || column_type == 'float' || !numerical) {
- columns.push({
- 'label' : 'Column: ' + column_index + ' [' + column_label + ']',
- 'value' : column_index
- });
- }
- }
-
- // update field
- if (column_field) {
- column_field.update(columns);
- if (!column_field.exists(column_field.value())) {
- column_field.value(column_field.first());
- }
- column_field.show();
- }
- }
- }
- });
+ self.app.rebuild();
}
});
},
@@ -516,10 +409,14 @@
}
// select field
+ var self = this;
return new SelectClass.View({
id : 'field-' + input_def.id,
data : options,
- multiple: input_def.multiple
+ multiple: input_def.multiple,
+ onchange: function() {
+ self.app.rebuild();
+ }
});
},
@@ -535,7 +432,6 @@
/** Slider field
*/
_fieldSlider: function(input_def) {
- // create slider
return new Ui.Slider.View({
id : 'field-' + input_def.id,
precise : input_def.type == 'float',
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type=="select"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
diff -r 55c20724a69cacf121a756594d1ba112e5ae56d5 -r 713526cf328d41f0248ce85860e1d33db779482f static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.incompatible=true;this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(j){i.app.rebuild()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.rebuild()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1
0
[galaxyproject/usegalaxy-playbook] 335b4b: Allocate static ~64 GB for wigToBigWig.
by GitHub 29 Oct '14
by GitHub 29 Oct '14
29 Oct '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 335b4bcd32d3cbcc7773a476f27f97336f2b7615
https://github.com/galaxyproject/usegalaxy-playbook/commit/335b4bcd32d3cbcc…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2014-10-29 (Wed, 29 Oct 2014)
Changed paths:
M files/galaxy/test.galaxyproject.org/dynamic_rules/single_dynamic_memory.py
M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml
M files/galaxy/usegalaxy.org/dynamic_rules/single_dynamic_memory.py
M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
Log Message:
-----------
Allocate static ~64 GB for wigToBigWig.
1
0
commit/galaxy-central: guerler: Charts: Update query limits
by commits-noreply＠bitbucket.org 29 Oct '14
by commits-noreply＠bitbucket.org 29 Oct '14
29 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/55c20724a69c/
Changeset: 55c20724a69c
User: guerler
Date: 2014-10-29 17:37:33+00:00
Summary: Charts: Update query limits
Affected #: 11 files
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 client/galaxy/scripts/mvc/tools/tools-template.js
--- a/client/galaxy/scripts/mvc/tools/tools-template.js
+++ b/client/galaxy/scripts/mvc/tools/tools-template.js
@@ -11,10 +11,6 @@
'</div>';
},
- citations: function() {
- return '<div id="citations"></div>';
- },
-
success: function(response) {
// check
if (!response.jobs || !response.jobs.length) {
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 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.
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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#portlet-title-text");var n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-title-text" class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},text:function(){return this.$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.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),empty:"No data available"},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$error=$(this._templateError(t)),this.$options=$(this._template(t)),this.$el.append(this.$error),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){var e=this.$el.find(".ui-option").length;e==0?(this.$error.show(),this.$options.hide()):(this.$error.hide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_templateError:function(e){return'<div class="ui-error" style="display: none;">'+e.empty+"</div>"}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,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._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){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.$el)),f.append(r.wrap(this.types.$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.$el}),this.portlet.append(this.message.$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="Data label"),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});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_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()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{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",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{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:"0"}]},separator_y:{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",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};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 class="dropdown-item" href="'+e.href+'" 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o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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\ No newline at end of file
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/charts/forms/default.js
--- a/config/plugins/visualizations/charts/static/charts/forms/default.js
+++ b/config/plugins/visualizations/charts/static/charts/forms/default.js
@@ -6,7 +6,6 @@
library : '',
tag : '',
keywords : '',
- query_limit : 0,
settings : {
separator_x : {
title : 'X axis',
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
@@ -7,7 +7,6 @@
tag : 'div',
zoomable : true,
keywords : 'medium',
- query_limit : 10000,
settings : {
separator_grid : {
title : 'Grids',
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
@@ -4,8 +4,7 @@
category : '',
library : 'NVD3',
tag : 'svg',
- keywords : 'small',
- query_limit : 500
+ keywords : 'small'
});
});
\ No newline at end of file
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
@@ -5,7 +5,6 @@
category : 'Data processing (requires \'charts\' tool from Toolshed)',
execute : 'histogramdiscrete',
keywords : 'small medium large',
- query_limit : 10000,
columns : {
x : {
title : 'Observations',
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
--- a/config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
+++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
@@ -3,7 +3,6 @@
return $.extend(true, {}, config_default, {
title : 'Heatmap',
category : 'Others',
- query_limit : 1000,
library : 'Custom',
tag : 'svg',
keywords : 'small',
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -38,7 +38,6 @@
// query block size
var query_size = this.app.config.get('query_limit');
- var query_timeout = this.app.config.get('query_timeout');
// set range
var query_start = request_dictionary.start || 0;
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -5,7 +5,7 @@
return Backbone.Model.extend({
// options
defaults : {
- query_limit : 5000,
+ query_limit : 10000,
query_timeout : 100
}
});
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 static/scripts/mvc/tools/tools-template.js
--- a/static/scripts/mvc/tools/tools-template.js
+++ b/static/scripts/mvc/tools/tools-template.js
@@ -11,10 +11,6 @@
'</div>';
},
- citations: function() {
- return '<div id="citations"></div>';
- },
-
success: function(response) {
// check
if (!response.jobs || !response.jobs.length) {
diff -r f1fda6a03505414f041f167c8df537f38c95d14c -r 55c20724a69cacf121a756594d1ba112e5ae56d5 static/scripts/packed/mvc/tools/tools-template.js
--- a/static/scripts/packed/mvc/tools/tools-template.js
+++ b/static/scripts/packed/mvc/tools/tools-template.js
@@ -1,1 +1,1 @@
-define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}});
\ No newline at end of file
+define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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29 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f1fda6a03505/
Changeset: f1fda6a03505
User: guerler
Date: 2014-10-29 15:37:04+00:00
Summary: ToolForm: Fix citations
Affected #: 8 files
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -309,15 +309,15 @@
// append citations
if (options.citations) {
- // append html
- this.$el.append(ToolTemplate.citations());
-
// fetch citations
var citations = new CitationModel.ToolCitationCollection();
citations.tool_id = options.id;
var citation_list_view = new CitationView.CitationListView({ collection: citations } );
citation_list_view.render();
citations.fetch();
+
+ // append to element
+ this.$el.append(citation_list_view.$el);
}
// append tool section
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -286,6 +286,7 @@
// deactivate dynamic fields
if (input_def.is_dynamic) {
this.app.incompatible = true;
+ this.app.is_dynamic = true;
}
// set field value
@@ -493,11 +494,6 @@
/** Select/Checkbox/Radio options field
*/
_fieldSelect : function (input_def) {
- // check compatibility
- if (input_def.is_dynamic) {
- this.app.is_dynamic = true;
- }
-
// configure options fields
var options = [];
for (var i in input_def.options) {
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c 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="ui-modal 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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n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};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 class="dropdown-item" 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" 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src="'+e.url+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#portlet-title-text");var n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-title-text" class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},text:function(){return this.$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.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),empty:"No data available"},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$error=$(this._templateError(t)),this.$options=$(this._template(t)),this.$el.append(this.$error),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){var e=this.$el.find(".ui-option").length;e==0?(this.$error.show(),this.$options.hide()):(this.$error.hide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_templateError:function(e){return'<div class="ui-error" style="display: none;">'+e.empty+"</div>"}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,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._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){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.$el)),f.append(r.wrap(this.types.$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.$el}),this.portlet.append(this.message.$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="Data label"),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});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_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()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{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",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{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:"0"}]},separator_y:{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",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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charts",zoomable:!0,keywords:"default small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",query_limit:1e4,settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{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:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),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/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -5,7 +5,7 @@
return Backbone.Model.extend({
// options
defaults : {
- query_limit : 500,
+ query_limit : 5000,
query_timeout : 100
}
});
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -309,15 +309,15 @@
// append citations
if (options.citations) {
- // append html
- this.$el.append(ToolTemplate.citations());
-
// fetch citations
var citations = new CitationModel.ToolCitationCollection();
citations.tool_id = options.id;
var citation_list_view = new CitationView.CitationListView({ collection: citations } );
citation_list_view.render();
citations.fetch();
+
+ // append to element
+ this.$el.append(citation_list_view.$el);
}
// append tool section
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -286,6 +286,7 @@
// deactivate dynamic fields
if (input_def.is_dynamic) {
this.app.incompatible = true;
+ this.app.is_dynamic = true;
}
// set field value
@@ -493,11 +494,6 @@
/** Select/Checkbox/Radio options field
*/
_fieldSelect : function (input_def) {
- // check compatibility
- if (input_def.is_dynamic) {
- this.app.is_dynamic = true;
- }
-
// configure options fields
var options = [];
for (var i in input_def.options) {
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type=="select"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type=="select"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r f1fda6a03505414f041f167c8df537f38c95d14c static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.incompatible=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.incompatible=true;this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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