[galaxy-commits] commit/galaxy-central: natefoo: Merge default to next-stable.

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/e6813f244a2a/ Changeset: e6813f244a2a Branch: next-stable User: natefoo Date: 2014-07-29 21:48:38 Summary: Merge default to next-stable. Affected #: 719 files

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 .hgignore --- a/.hgignore +++ b/.hgignore @@ -11,8 +11,12 @@ scripts/scramble/lib scripts/scramble/archives

+# Python virtualenv +.venv + # Database stuff database/beaker_sessions +database/citations database/community_files database/compiled_templates database/files @@ -35,6 +39,7 @@ tool_shed_webapp.log tool_shed_webapp.pid hgweb.config* +lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml

# Reports Runtime Files reports_webapp.lock @@ -61,6 +66,7 @@ data_manager_conf.xml shed_data_manager_conf.xml object_store_conf.xml +job_metrics_conf.xml config/* static/welcome.html.* static/welcome.html

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,3 +7,6 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 +68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 +7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 +8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -58,6 +58,7 @@ tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/publicbuilds.txt.sample +tool-data/shared/ucsc/ucsc_build_sites.txt.sample "

DIRS="

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -1,3 +1,20 @@ +.charts-tooltip { + position: absolute; + text-align: center; + padding: 3px 5px 3px 5px; + font: 12px sans-serif; + background: white; + border: 1px solid gray; + border-radius: 4px; + pointer-events: none; +} + +.charts-tooltip-first { + font-weight: bold; + text-align: left; + padding-right: 5px; +} + .charts-grid .item { padding: 5px; margin: 5px; @@ -17,6 +34,7 @@ .charts-grid .image { padding: 10px; width: 100px; + height: 86px; }

.charts-grid .title { @@ -47,6 +65,7 @@ margin-left: 5px; top: -1px; font-size: 1.0em; + display: inline; }

.charts-viewport .icon { @@ -63,5 +82,6 @@ .charts-viewport .charts-viewport-canvas { display: block; width:100%; + min-height: 100px; height: inherit; } \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,26 +1,26 @@ // dependencies define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', - 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', + '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( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, + function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, Deferred, ViewerView, EditorView, Config, Chart, Types ) {

-// widget -return Backbone.View.extend( -{ +/** + * Main application class. + */ +return Backbone.View.extend({ // initialize - initialize: function(options) - { + initialize: function(options){ // deactivate all debugs outputs //window.console.debug = function() {};

// link options this.options = options; - + // link galaxy modal or create one if (Galaxy && Galaxy.modal) { this.modal = Galaxy.modal; @@ -41,6 +41,7 @@ this.jobs = new Jobs(this); this.datasets = new Datasets(this); this.storage = new Storage(this); + this.deferred = new Deferred();

// // views @@ -62,7 +63,7 @@

// draw chart var self = this; - this.chart.deferred.execute(function() { + this.deferred.execute(function() { self.chart.trigger('redraw'); }); } @@ -86,17 +87,20 @@ } },

- // execute command - execute: function(options) { - }, - - // unload - onunload: function() { - }, - - // log - log: function(location, message) { - console.log(location + ' ' + message); + // get root path + chartPath: function(chart_type) { + // create path from id + var path = chart_type.split(/_(.+)/); + + // check path + if (path.length >= 2) { + // return path + return path[0] + '/' + path[1]; + } else { + // log status + console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type); + } + return undefined; } });

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 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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No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){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}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return 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class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$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(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/>&nbsp;'+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/>&nbsp;'+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i>&nbsp;'),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/>&nbsp;'+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),l=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.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=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("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(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("GET",config.root+"api/datasets/"+t,{},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("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},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","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$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=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg%22,width:c,height:l%7D);var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/%22,display:%22none%22%7D),r.append(i)),i.empty... in n){var s=$("<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=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg%22,width:i*n,height:r%7D);var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$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.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).%22,buttons:%7BCancel:function()%7Bo.app.moda... n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},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){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+="&nbsp;(all data labels)"),this.table.add(f,"25%"),this.table.add(a.$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)+" 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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.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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 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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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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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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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Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__%22%7D%7D%7D)%7D),define(%22plugin/charts/oth... $.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","plugin/library/ui","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 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/forms/default.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/forms/default.js @@ -0,0 +1,252 @@ +define([], 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' + } + ] + } + } +}; + +}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js +++ /dev/null @@ -1,195 +0,0 @@ -define([], function() { - -return { - title : 'Heatmap', - category : 'Data processing (requires 'charts' tool from Toolshed)', - library : '', - tag : 'div', - use_panels : true, - execute : 'heatmap', - - // columns - columns : { - row_label : { - title : 'Row labels', - is_label : true - }, - col_label : { - title : 'Column labels', - is_label : true - }, - value : { - title : 'Observations' - }, - }, - - // settings - settings: { - /*limit : { - title : 'Limit', - info : 'Which to ranked clusters would you like to visualize', - type : 'select', - init : '20', - data : [ - { - label : '20', - value : '20' - }, - { - label : '30', - value : '30' - }, - { - label : '40', - value : '40' - }, - { - label : '50', - value : '50' - }, - { - label : '60', - value : '60' - }, - { - label : '70', - value : '70' - }, - { - label : '80', - value : '80' - }, - { - label : '90', - value : '90' - }, - { - label : '100', - value : '100' - } - ] - },*/ - color_set : { - title : 'Color scheme', - info : 'Select a color scheme for your heatmap', - type : 'select', - init : 'ocean', - data : [ - { - label : 'Cold-to-Hot', - value : 'hot' - }, - { - label : 'Cool', - value : 'cool' - }, - { - label : 'Copper', - value : 'copper' - }, - { - label : 'Gebco', - value : 'gebco' - }, - { - label : 'Globe', - value : 'globe' - }, - { - label : 'Gray scale', - value : 'gray' - }, - { - label : 'Haxby', - value : 'haxby' - }, - { - label : 'Jet', - value : 'jet' - }, - { - label : 'No-Green', - value : 'no_green' - }, - { - label : 'Ocean', - value : 'ocean' - }, - { - label : 'Polar', - value : 'polar' - }, - { - label : 'Rainbow', - value : 'rainbow' - }, - { - label : 'Red-to-Green', - value : 'redgreen' - }, - { - label : 'Red-to-green (saturated)', - value : 'red2green' - }, - { - label : 'Relief', - value : 'relief' - }, - { - label : 'Seismograph', - value : 'seis' - }, - { - label : 'Sealand', - value : 'sealand' - }, - { - label : 'Split', - value : 'split' - }, - { - label : 'Topo', - value : 'topo' - }, - { - label : 'Wysiwyg', - value : 'wysiwyg' - } - ] - }, - - sorting : { - title : 'Sorting', - info : 'How should the columns be clustered?', - type : 'select', - init : 'hclust', - data : [ - { - label : 'Read from dataset', - value : 'hclust' - }, - { - label : 'Sort column and row labels', - value : 'byboth' - }, - { - label : 'Sort column labels', - value : 'bycolumns' - }, - { - label : 'Sort by rows', - value : 'byrow' - } - ] - } - }, - - // menu definition - menu : function() { - return { - color_set : this.settings.color_set - } - } -}; - -}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js +++ /dev/null @@ -1,52 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { - -// color palettes -var colorSets = { - seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'], - - sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'], - - redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'], - - ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'], - - cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'], - - copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'], - - gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'], - - globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'], - - gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'], - - haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'], - - hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'], - - jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'], - - no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'], - - polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'], - - rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'], - - red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'], - - relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'], - - split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'], - - topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'], - - wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF'] -} - -// return -return { - colorSets: colorSets -} - -}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ /dev/null @@ -1,739 +0,0 @@ -// dependencies -define(['utils/utils'], -function(Utils) { - -// widget -return Backbone.View.extend( -{ - // number of columns and rows - colNumber: 0, - rowNumber: 0, - - // indices - rowIndex: [], - colIndex: [], - - // labels - rowLabel: [], - colLabel: [], - - // cell size - cellSize: 0, - - // font size - fontSize: 0, - - // color buckets - nColors: 0, - - // margins as cells - margin : { - top : 5, - right : 5, - bottom : 5, - left : 5 - }, - - // default settings - optionsDefault: { - title : '', - pace : 1000, - }, - - // initialize - initialize: function(options) { - // link this - var self = this; - - // load options - this.options = Utils.merge(options, this.optionsDefault) - - // check requirements - if (!this.options.data || !this.options.div || !this.options.colors) { - console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.'); - return; - } - - // link data - this.data = this.options.data; - - // set element - this.setElement(this.options.div); - - // - // data indexing - // - - // labels (in alphabetical order) - this.rowLabel = []; - this.colLabel = []; - - // index (order from original dataset) - this.rowIndex = []; - this.colIndex = []; - - // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting) - this.colRank = {}; - this.rowRank = {}; - - // - // identify and parse labels - // - for (var i in this.data) { - var cell = this.data[i]; - - // add label to index list - var col_label = cell.col_label; - if (this.colRank[col_label] === undefined) { - this.colRank[col_label] = true; - this.colLabel.push(col_label); - this.colIndex.push(col_label); - } - var row_label = cell.row_label; - if (this.rowRank[row_label] === undefined) { - this.rowRank[row_label] = true; - this.rowLabel.push(row_label); - this.rowIndex.push(row_label); - } - } - - // - // sort labels and update rank dictionary - // - - // set sizes - this.rowNumber = this.rowLabel.length - this.colNumber = this.colLabel.length - - // sort labels alphabetical - this.rowLabel.sort(); - this.colLabel.sort(); - - // generate sorted key list for rows - for (var i in this.rowLabel) { - var row_label = this.rowLabel[i]; - var row = parseInt(i); - this.rowRank[row_label] = row; - } - - // generate sorted key list for columns - for (var i in this.colLabel) { - var col_label = this.colLabel[i]; - var col = parseInt(i); - this.colRank[col_label] = col; - } - - // - // parse indexing from rank dictionary to cells - // - - // min/max - this.max = undefined; - this.min = undefined - - // add indices to data - for (var i in this.data) { - // get cell data - var cell = this.data[i]; - - // add rank - cell.col = this.colRank[cell.col_label]; - cell.row = this.rowRank[cell.row_label]; - - // identify max/min values - if (this.min == undefined || this.min > cell.value) { - this.min = cell.value; - } - if (this.max == undefined || this.max < cell.value) { - this.max = cell.value; - } - } - - // - // translate original create cluster from order in original data - // - - // generate sorted key list for columns - for (var i in this.colIndex) { - this.colIndex[i] = this.colRank[this.colIndex[i]]; - } - // generate sorted key list for columns - for (var i in this.rowIndex) { - this.rowIndex[i] = this.rowRank[this.rowIndex[i]]; - } - - // middle - this.mid = (this.max + this.min) / 2; - - // - // set colors - // - - // identify buckets - this.nColors = this.options.colors.length; - - // color scale - this.colorScale = d3.scale.quantile() - .domain([this.min, this.mid, this.max]) - .range(this.options.colors); - - // - // add ui elements - // - // create tooltip - this.$tooltip = $(this._templateTooltip()); - this.$el.append(this.$tooltip); - - // - // finally draw the heatmap - // - this._build(); - - // catch window resize event - $(window).resize(function () { - self._build(); - }); - }, - - _build: function() { - // link this - var self = this; - - // container (full draw area) - this.widthContainer = this.$el.width(); - this.heightContainer = this.$el.height(); - - // get grid dimensions - this.width = this.widthContainer; - this.height = this.heightContainer; - - // calculate cell size - this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)), - (this.width / (this.colNumber + this.margin.left + this.margin.right))); - - // set font size - this.fontSize = Math.min(this.cellSize, 16); - - // set width/height for plugin - this.width = this.cellSize * this.colNumber; - this.height = this.cellSize * this.rowNumber; - - // get dimensions - var margin = this.options.margin; - var width = this.width; - var height = this.height; - - // reset svg - if (this.svg !== undefined) { - this.$el.find('svg').remove(); - } - - // add main group and translate - this.svg = d3.select(this.$el[0]).append('svg') - .append('g') - .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' + - (this.heightContainer - height) / 2 + ')'); - - // reset sorting - this.rowSortOrder = false; - this.colSortOrder = false; - - // build - this.d3RowLabels = this._buildRowLabels(); - this.d3ColLabels = this._buildColLabels(); - this.d3HeatMap = this._buildHeatMap(); - this.d3Legend = this._buildLegend(); - this.d3Title = this._buildTitle(); - }, - - // build title - _buildTitle: function() { - // link this - var self = this; - - // gather data - var height = this.height; - var width = this.width; - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var title = this.options.title; - - // add title - return this.svg.append('g') - .append('text') - .attr('x', width / 2) - .attr('y', height + 3 * cellSize + fontSize + 3) - .attr('text-anchor', 'middle') - .text(title); - }, - - // build legend - _buildLegend: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var height = this.height; - var legendCellWidth = this.width / this.nColors; - - // create range labels - var dataRange = []; - for(var i = 0; i < this.nColors; i++) { - dataRange.push(''); - } - - // prepare indices - var dataRangeMin = 0; - var dataRangeMid = parseInt((dataRange.length - 1) / 2); - var dataRangeMax = dataRange.length - 1; - - // add labels - dataRange[dataRangeMin] = this.min; - dataRange[dataRangeMid] = this.mid; - dataRange[dataRangeMax] = this.max; - - // create legend - var legend = this.svg.selectAll('.legend') - .data(dataRange) - .enter().append('g') - .attr('class', 'legend'); - - // add boxes - legend.append('rect') - .attr('x', function(d, i) { - return legendCellWidth * i; - }) - .attr('y', height + cellSize) - .attr('width', legendCellWidth) - .attr('height', cellSize) - .style('fill', function(d, i) { - return self.options.colors[i]; - }); - - // add text - legend.append('text') - .attr('class', 'mono') - .text(function(d) { - return d; - }) - .attr('width', legendCellWidth) - .attr('x', function(d, i) { - return legendCellWidth * i; - }) - .attr('y', height + cellSize - 3) - .style('font-size', fontSize + 'px'); - - // return - return legend; - }, - - // build column labels - _buildColLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // column labels - var colLabels = this.svg.append('g') - .selectAll('.colLabelg') - .data(colLabel) - .enter() - .append('text') - .text(function (d) { - return d; - }) - .attr('x', 0) - .attr('y', function (d, i) { - return colIndex.indexOf(i) * cellSize; - }) - .style('font-size', fontSize + 'px') - .style('text-anchor', 'left') - .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') - .attr('class', function (d, i) { - return 'colLabel mono c' + i; - }) - .on('mouseover', function(d) { - d3.select(this).classed('text-hover',true); - }) - .on('mouseout' , function(d) { - d3.select(this).classed('text-hover',false); - }) - .on('click', function(d, i) { - self.colSortOrder=!self.colSortOrder; - self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder); - d3.select('#order').property('selectedIndex', 4).node().focus(); - }); - - // return - return colLabels; - }, - - // build row labels - _buildRowLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - - // draw labels - var rowLabels = this.svg.append('g') - .selectAll('.rowLabelg') - .data(rowLabel) - .enter() - .append('text') - .text(function (d) { - return d; - }) - .attr('x', 0) - .attr('y', function (d, i) { - return rowIndex.indexOf(i) * cellSize; - }) - .style('font-size', fontSize + 'px') - .style('text-anchor', 'end') - .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') - .attr('class', function (d, i) { - return 'rowLabel mono r' + i; - } ) - .on('mouseover', function(d) { - d3.select(this).classed('text-hover',true); - }) - .on('mouseout' , function(d) { - d3.select(this).classed('text-hover',false); - }) - .on('click', function(d, i) { - self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder); - d3.select('#order').property('selectedIndex', 4).node().focus(); - }); - - // return - return rowLabels; - }, - - // build heat map - _buildHeatMap: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // heat map - var heatmap = this.svg.append('g').attr('class','g3') - .selectAll('.cellg') - .data(self.data, function(d) { - return d.row + ':' + d.col; - }) - .enter() - .append('rect') - .attr('x', function(d) { - return colIndex.indexOf(d.col) * cellSize; - }) - .attr('y', function(d) { - return rowIndex.indexOf(d.row) * cellSize; - }) - .attr('class', function(d){ - return 'cell cell-border cr' + d.row + ' cc' + d.col; - }) - .attr('width', cellSize) - .attr('height', cellSize) - .style('fill', function(d) { - return self.colorScale(d.value); - }) - .on('mouseover', function(d){ - // highlight text - d3.select(this).classed('cell-hover',true); - d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);}); - d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);}); - - // update the tooltip position and value - d3.select('#heatmap-tooltip') - .style('left', (d3.event.pageX+10) + 'px') - .style('top', (d3.event.pageY-10) + 'px') - .select('#value') - .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value); - // show the tooltip - d3.select('#heatmap-tooltip').classed('hidden', false); - }) - .on('mouseout', function(){ - d3.select(this).classed('cell-hover',false); - d3.selectAll('.rowLabel').classed('text-highlight',false); - d3.selectAll('.colLabel').classed('text-highlight',false); - d3.select('#heatmap-tooltip').classed('hidden', true); - }); - - // return - return heatmap; - }, - - // change ordering of cells - _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) { - // get cell size - var cellSize = this.cellSize; - - // define transition / prepare element - var t = this.svg.transition().duration(this.options.pace); - - // create cells - var cells=[]; - for (var i = 0; i < n; i++) { - cells[i] = { - value: this.min - 1 - } - cells[i][rowORcol] = i; - } - - // collect cells - t.selectAll('.c' + rORc + index).filter(function(ce) { - cells[ce[rowORcol]].value = ce.value; - }); - - // sort cells - cells.sort(function(a, b) { - if (sortOrder) { - return b.value - a.value; - } else { - return a.value - b.value; - } - }); - - // get sorted key list - var sorted = []; - for (var i in cells) { - sorted.push(cells[i][rowORcol]); - } - - // rows or columns - if(rORc == 'r') { - // sort cells - t.selectAll('.cell') - .attr('x', function(d) { - return sorted.indexOf(d.col) * cellSize; - }); - - // sort labels - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } else { - // sort cells - t.selectAll('.cell') - .attr('y', function(d) { - return sorted.indexOf(d.row) * cellSize; - }); - - // sort labels - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } - }, - - // sort function - _sortByOrder: function (value) { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // set duration / select element - var t = this.svg.transition().duration(this.options.pace); - if(value=='hclust'){ - t.selectAll('.cell') - .attr('x', function(d) { - return colIndex.indexOf(d.col) * cellSize; - }) - .attr('y', function(d) { - return rowIndex.indexOf(d.row) * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function(d, i) { - return rowIndex.indexOf(i) * cellSize; - }); - - t.selectAll('.colLabel') - .attr('y', function(d, i) { - return colIndex.indexOf(i) * cellSize; - }); - - } else if (value=='byboth') { - t.selectAll('.cell') - .attr('x', function(d) { - return d.col * cellSize; - }) - .attr('y', function(d) { - return d.row * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } else if (value=='byrow') { - t.selectAll('.cell') - .attr('y', function(d) { - return d.row * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } else if (value=='bycol'){ - t.selectAll('.cell') - .attr('x', function(d) { - return d.col * cellSize; - }); - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } - }, - - // selection of cells - _addSelectionTool: function() { - // - // selection - // - var sa=d3.select('.g3') - .on('mousedown', function() { - if( !d3.event.altKey) { - d3.selectAll('.cell-selected').classed('cell-selected', false); - d3.selectAll('.rowLabel').classed('text-selected', false); - d3.selectAll('.colLabel').classed('text-selected', false); - } - var p = d3.mouse(this); - sa.append('rect') - .attr({ - rx : 0, - ry : 0, - class : 'selection', - x : p[0], - y : p[1], - width : 1, - height : 1 - }) - }) - .on('mousemove', function() { - var s = sa.select('rect.selection'); - - if(!s.empty()) { - var p = d3.mouse(this), - d = { - x : parseInt(s.attr('x'), 10), - y : parseInt(s.attr('y'), 10), - width : parseInt(s.attr('width'), 10), - height : parseInt(s.attr('height'), 10) - }, - move = { - x : p[0] - d.x, - y : p[1] - d.y - }; - - if(move.x < 1 || (move.x*2<d.width)) { - d.x = p[0]; - d.width -= move.x; - } else { - d.width = move.x; - } - - if(move.y < 1 || (move.y*2<d.height)) { - d.y = p[1]; - d.height -= move.y; - } else { - d.height = move.y; - } - s.attr(d); - - // deselect all temporary selected state objects - d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false); - d3.selectAll('.text-selection.text-selected').classed('text-selected',false); - d3.selectAll('.cell').filter(function(cell_d, i) { - if(!d3.select(this).classed('cell-selected') && - // inner circle inside selection frame - (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && - (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) - { - d3.select(this) - .classed('cell-selection', true) - .classed('cell-selected', true); - - d3.select('.r' + cell_d.row) - .classed('text-selection',true) - .classed('text-selected',true); - - d3.select('.c' + cell_d.col) - .classed('text-selection',true) - .classed('text-selected',true); - } - }); - } - }) - .on('mouseup', function() { - // remove selection frame - sa.selectAll('rect.selection').remove(); - - // remove temporary selection marker class - d3.selectAll('.cell-selection').classed('cell-selection', false); - d3.selectAll('.text-selection').classed('text-selection', false); - }) - .on('mouseout', function() { - if(d3.event.relatedTarget.tagName=='html') { - // remove selection frame - sa.selectAll('rect.selection').remove(); - - // remove temporary selection marker class - d3.selectAll('.cell-selection').classed('cell-selection', false); - d3.selectAll('.rowLabel').classed('text-selected',false); - d3.selectAll('.colLabel').classed('text-selected',false); - } - }); - }, - - // template - _templateSelect: function() { - return '<select id="order">' + - '<option value="hclust">Cluster</option>' + - '<option value="byboth">Sort by row and column</option>' + - '<option value="byrow">Sort by row label</option>' + - '<option value="bycol">Sort by column label</option>' + - '</select>'; - }, - - // template - _templateTooltip: function() { - return '<div id="heatmap-tooltip" class="hidden">' + - '<p><span id="value"></p>' - '</div>'; - } -}); -}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/heatmap/logo.png Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js +++ /dev/null @@ -1,86 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], -function(Utils, HeatmapPlugin, HeatmapParameters) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // link this - var self = this; - - // loop through data groups - var index = 0; - for (var group_index in request_dictionary.groups) { - - // configure request - var tmp_dict = { - id : request_dictionary.id, - groups : [{ - key : request_dictionary.groups[group_index].key, - columns : { - row_label: { - index : index++, - is_label : true - }, - col_label: { - index : index++, - is_label : true - }, - value: { - index : index++ - } - } - }] - }; - - // target div - var group_div = self.options.canvas[group_index]; - - // draw group - this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) { - if (group_index == request_dictionary.groups.length - 1) { - // set chart state - chart.state('ok', 'Heat map drawn.'); - - // unregister process - chart.deferred.done(process_id); - } - }); - } - }, - - // draw group - _draw_group: function(group_index, div, chart, request_dictionary, callback) { - // link this - var self = this; - - // request data - this.app.datasets.request(request_dictionary, function() { - - // get group - var group = request_dictionary.groups[0]; - - // draw plot - var heatmap = new HeatmapPlugin({ - 'title' : group.key, - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : div - }); - - // callback on completion - callback (group_index); - }); - } -}); - -}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js +++ /dev/null @@ -1,40 +0,0 @@ -define([], function() { - -return { - title : 'Box plot', - category : 'Data processing (requires 'charts' tool from Toolshed)', - library : 'highcharts.js', - tag : 'div', - execute : 'boxplot', - columns : { - y : { - title : 'Observations' - } - }, - settings : { - separator_label : { - title : 'X axis', - type : 'separator' - }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - } - } -}; - -}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js +++ /dev/null @@ -1,122 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // highcharts configuration - hc_config : { - chart: { - type: 'boxplot' - }, - - title: { - text: '' - }, - - legend: { - enabled: false - }, - - credits: { - enabled: false - }, - - plotOptions: { - series: { - animation: false - } - }, - - xAxis: { - categories: [], - title: { - text: '' - } - }, - - yAxis: { - title: { - text: '' - } - }, - - series: [{ - name: 'Details:', - data: [], - tooltip: { - headerFormat: '<em>{point.key}</em><br/>' - } - }] - }, - - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // configure request - var index = 0; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - x: { - index: index++ - } - } - } - - // set axis labels - this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label'); - this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label'); - - // request data - var self = this; - this.app.datasets.request(request_dictionary, function() { - - // reset data/categories - var data = []; - var categories = []; - - // loop through data groups - for (var key in request_dictionary.groups) { - // get group - var group = request_dictionary.groups[key]; - - // add category - categories.push(group.key); - - // format chart data - var point = []; - for (var key in group.values) { - point.push(group.values[key].x); - } - - // add to data - data.push (point); - } - - // categories - self.hc_config.xAxis.categories = categories; - - // update data - self.hc_config.series[0].data = data; - - // draw plot - self.options.canvas[0].highcharts(self.hc_config); - - // set chart state - chart.state('ok', 'Box plot drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } -}); - -}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js @@ -0,0 +1,20 @@ +define(['plugin/charts/jqplot/common/config'], function(plot_config) { + +return $.extend(true, {}, plot_config, { + title : 'Regular', + category : 'Bar diagrams', + columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, + y : { + title : 'Values for y-axis', + is_numeric : true + } + } +}); + +}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png has changed

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -0,0 +1,26 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { + +// widget +return Backbone.Model.extend({ + initialize: function(app, options) { + options.makeConfig = function(groups, plot_config){ + $.extend(true, plot_config, { + seriesDefaults: { + renderer : $.jqplot.BarRenderer + }, + axes: { + xaxis: { + min : -1 + }, + yaxis: { + pad : 1.2 + } + } + }); + }; + new Plot(app, options); + } +}); + +}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js @@ -0,0 +1,23 @@ +define(['plugin/charts/jqplot/common/config'], function(plot_config) { + +return $.extend(true, {}, plot_config, { + 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 : true + } + }, + settings : { + show_legend : { + init : 'false' + } + } +}); + +}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png has changed

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -0,0 +1,127 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper', 'plugin/charts/tools'], function(Plot, Tools) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + // get request dictionary + var request_dictionary = options.request_dictionary; + var chart = options.chart; + + // modify request + var index = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = null; + group.columns = { + x: { + index: index++ + } + } + } + + // create plot + var plot = new Plot(app, { + process_id : options.process_id, + chart : options.chart, + request_dictionary : options.request_dictionary, + canvas_list : options.canvas_list, + makeConfig : function(groups, plot_config){ + var boundary = Tools.getDomains(groups, 'x'); + $.extend(true, plot_config, { + seriesDefaults: { + renderer: $.jqplot.OHLCRenderer, + rendererOptions : { + candleStick : true, + fillUpBody : true, + fillDownBody : true + } + }, + axes : { + xaxis: { + min: -1, + max: groups.length + 0.01 + }, + yaxis: { + min: boundary.x.min, + max: boundary.x.max + } + } + }); + }, + makeCategories: function(groups) { + // define custom category labels + var x_labels = []; + for (var group_index in groups) { + x_labels.push(groups[group_index].key); + } + + // use default mapping + Tools.mapCategories (groups, x_labels); + + // return labels array for x axis + return { + array: { + x : x_labels + } + } + }, + makeSeriesLabels : function (groups, plot_config) { + return [{ + label: 'Boxplot values' + }]; + }, + makeSeries: function (groups) { + /*/ example data + var catOHLC = [ + [0, 138.7, 139.68, 135.18, 135.4], + [1, 143.46, 144.66, 139.79, 140.02], + [2, 140.67, 143.56, 132.88, 142.44], + [3, 136.01, 139.5, 134.53, 139.48] + ]; + return [catOHLC];*/ + + // plot data + var plot_data = []; + + // check group length + if (groups.length == 0 || groups[0].values.length < 5) { + chart.state('failed', 'Boxplot data could not be found.'); + return [plot_data]; + } + + // loop through data groups + var indeces = [2, 4, 0, 1]; + for (var group_index in groups) { + // get group + var group = groups[group_index]; + + // format chart data + var point = []; + point.push(parseInt(group_index)); + for (var key in indeces) { + point.push(group.values[indeces[key]].x); + } + + // add to data + plot_data.push (point); + } + + // HACK: the boxplot renderer has an issue with single elements + var point = []; + point[0] = plot_data.length; + for (var key in indeces) { + point.push(0); + } + plot_data.push (point); + + // return + return [plot_data]; + } + }); + } +}); + +}); \ No newline at end of file

diff -r 9874065b40c630122d198bc2c53443d50ddb9cca -r e6813f244a2ad99cec27bba6492c89008459b338 config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -0,0 +1,51 @@ +define(['plugin/charts/forms/default'], function(config_default) { + +return $.extend(true, {}, config_default, { + title : '', + category : '', + library : 'jqPlot', + tag : 'div', + zoomable : true, + keywords : 'medium', + query_limit : 10000, + 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' + } + ] + } + } +}); + +}); \ No newline at end of file

This diff is so big that we needed to truncate the remainder.

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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