[galaxy-commits] commit/galaxy-central: natefoo: Open next-stable branch.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/089d1264d719/ Changeset: 089d1264d719 Branch: next-stable User: natefoo Date: 2014-04-03 18:02:24 Summary: Open next-stable branch. Affected #: 772 files diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 .hgignore --- a/.hgignore +++ b/.hgignore @@ -77,6 +77,7 @@ tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt tool-data/*.loc tool-data/genome/* diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 .hgtags --- a/.hgtags +++ b/.hgtags @@ -5,3 +5,4 @@ 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 +5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 README.txt --- a/README.txt +++ b/README.txt @@ -26,6 +26,6 @@ on adding tools can be found on the Galaxy website (linked above). Not all dependencies are included for the tools provided in the sample -tool_conf.xml. A full list of external dependencies is available at: +tool_conf.xml. A full list of external dependencies is available at: -http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/additional_template_paths.xml --- /dev/null +++ b/config/plugins/visualizations/additional_template_paths.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- these relative paths can contain common templates importable by all visualization plugins --> +<paths> + <path>common/templates</path> +</paths> diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/Gruntfile.js --- /dev/null +++ b/config/plugins/visualizations/charts/Gruntfile.js @@ -0,0 +1,24 @@ +// NOTE: use 'sudo npm install .', then 'grunt' to use this file +module.exports = function(grunt) { + grunt.initConfig({ + pkg: grunt.file.readJSON('package.json'), + requirejs: { + compile: { + options: { + baseUrl : "../../../../static/scripts/", + paths : { + "plugin": "../../config/plugins/visualizations/charts/static" + }, + shim : { + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" } + }, + name : "plugin/app", + out : "static/build-app.js", + } + } + } + }); + grunt.loadNpmTasks('grunt-contrib-requirejs'); + grunt.registerTask( 'default', [ 'requirejs' ]); +}; diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/config/charts.xml --- a/config/plugins/visualizations/charts/config/charts.xml +++ b/config/plugins/visualizations/charts/config/charts.xml @@ -7,15 +7,9 @@ <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test><to_param param_attr="id">dataset_id</to_param></data_source> - <data_source> - <model_class>Visualization</model_class> - <test test_attr="type">charts</test> - <to_param param_attr="id">visualization_id</to_param> - </data_source></data_sources><params><param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> - <param type="visualization" var_name_in_template="visualization">visualization_id</param></params><template>charts.mako</template></visualization> diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/package.json --- /dev/null +++ b/config/plugins/visualizations/charts/package.json @@ -0,0 +1,18 @@ +{ + "name": "galaxy-charts", + "version": "0.0.0", + "description": "Charts visualization plugin for the Galaxy informatics framework", + "main": " ", + "keywords": [ + "galaxy", + "visualization", + "d3" + ], + "author": "Aysam Guerler", + "license": "BSD", + "devDependencies": { + "grunt": "~0.4.1", + "grunt-cli": "~0.1.9", + "grunt-contrib-requirejs": "~0.4.3" + } +} diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,10 +1,12 @@ // dependencies -define(['library/portlet', 'library/ui', 'library/utils', - 'views/charts', 'views/viewport', 'views/chart', 'views/group', - 'models/config', 'models/datasets', 'models/chart', 'models/charts', 'models/group', 'models/types'], - function( Portlet, Ui, Utils, - ChartsView, ViewportView, ChartView, GroupView, - Config, Datasets, Chart, Charts, Group, Types +define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', + 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', + 'plugin/views/viewer', 'plugin/views/editor', + 'plugin/models/config', 'plugin/models/chart', + 'plugin/charts/types'], + function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, + ViewerView, EditorView, + Config, Chart, Types ) { // widget @@ -13,66 +15,75 @@ // initialize initialize: function(options) { + // deactivate all debugs outputs + //window.console.debug = function() {}; + // link options this.options = options; - // link galaxy - this.modal = parent.Galaxy.modal; + // link galaxy modal or create one + if (Galaxy && Galaxy.modal) { + this.modal = Galaxy.modal; + } else { + this.modal = new Modal.View(); + } - // create configuration model + // + // models + // this.config = new Config(); - - // create chart models this.types = new Types(); this.chart = new Chart(); - this.charts = new Charts(); - this.group = new Group(); - // create dataset handler + // + // libraries + // + this.jobs = new Jobs(this); this.datasets = new Datasets(this); + this.storage = new Storage(this); - // create views - this.charts_view = new ChartsView(this); - this.group_view = new GroupView(this); - this.chart_view = new ChartView(this); - this.viewport_view = new ViewportView(this); - - // append view port to charts viewer - this.charts_view.append(this.viewport_view.$el); - - // create portlet - if (!this.options.config.widget) { - this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'}); - } else { - this.portlet = $('<div></div>'); - } + // + // views + // + this.viewer_view = new ViewerView(this); + this.editor_view = new EditorView(this); // append views - this.portlet.append(this.charts_view.$el); - this.portlet.append(this.group_view.$el); - this.portlet.append(this.chart_view.$el); - - // set element - if (!this.options.config.widget) { - this.setElement(this.portlet.$el); + this.$el.append(this.viewer_view.$el); + this.$el.append(this.editor_view.$el); + + // pick start screen + if (!this.storage.load()) { + // show editor + this.go('editor'); } else { - this.setElement(this.portlet); + // show viewport + this.go('viewer'); + + // draw chart + var self = this; + this.chart.deferred.execute(function() { + self.chart.trigger('redraw'); + }); } - - // hide views - this.group_view.$el.hide(); - this.charts_view.$el.hide(); - - // events - var self = this; - this.config.on('change:current_view', function() { - self._showCurrent(); - }); }, - // current view - _showCurrent: function() { + // loads a view and makes sure that all others are hidden + go: function(view_id) { + // hide all tooltips + $('.tooltip').hide(); + // pick view + switch (view_id) { + case 'editor' : + this.editor_view.show(); + this.viewer_view.hide(); + break; + case 'viewer' : + this.editor_view.hide(); + this.viewer_view.show(); + break; + } }, // execute command diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/build-app.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -0,0 +1,6 @@ +// Underscore.js 1.4.4 +// http://underscorejs.org +// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. +// 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e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),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)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:a,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","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},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-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},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._fetch(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)}})}},_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="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_svg();var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg_el=this.$el.find("svg"),this.svg=d3.select(this.svg_el[0])},_draw:function(e){var t=this;this._create_svg(),e.state("wait","Please wait...");var n=e.deferred.register(),r=e.get("type"),i=this.app.types.get(r);if(!i.execute||i.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var s=new r(t.app,{svg:t.svg});i.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){s.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):s.draw(n,e,t._defaultRequestDictionary(e)):s.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.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=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),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:"Customize",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=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<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.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/_nvd3/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/_nvd3/config.js @@ -0,0 +1,218 @@ +define([], function() { + +return { + title : '', + columns : { + y : { + title : 'Values for y-axis' + } + }, + settings : { + separator_label : { + title : 'X axis', + type : 'separator' + }, + x_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'X-axis', + placeholder : 'Axis label' + }, + x_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + hide : 'x_axis_tick' + }, + { + label : 'Auto', + value : 'auto', + hide : 'x_axis_tick' + }, + { + label : 'Float', + value : 'f', + show : 'x_axis_tick' + }, + { + label : 'Exponent', + value : 'e', + show : 'x_axis_tick' + }, + { + label : 'Integer', + value : 'd', + hide : 'x_axis_tick' + }, + { + label : 'Percentage', + value : 'p', + show : 'x_axis_tick' + }, + { + label : 'Rounded', + value : 'r', + show : 'x_axis_tick' + }, + { + label : 'SI-prefix', + value : 's', + show : 'x_axis_tick' + } + ] + }, + x_axis_tick : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '.1', + data : [ + { + label : '0.00001', + value : '.5' + }, + { + label : '0.0001', + value : '.4' + }, + { + label : '0.001', + value : '.3' + }, + { + label : '0.01', + value : '.2' + }, + { + label : '0.1', + value : '.1' + }, + { + label : '1', + value : '1' + } + ] + + }, + separator_tick : { + title : 'Y axis', + type : 'separator' + }, + y_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'Y-axis', + placeholder : 'Axis label' + }, + y_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + hide : 'y_axis_tick' + }, + { + label : 'Auto', + value : 'auto', + hide : 'y_axis_tick' + }, + { + label : 'Float', + value : 'f', + show : 'y_axis_tick' + }, + { + label : 'Exponent', + value : 'e', + show : 'y_axis_tick' + }, + { + label : 'Integer', + value : 'd', + hide : 'y_axis_tick' + }, + { + label : 'Percentage', + value : 'p', + show : 'y_axis_tick' + }, + { + label : 'Rounded', + value : 'r', + show : 'y_axis_tick' + }, + { + label : 'SI-prefix', + value : 's', + show : 'y_axis_tick' + } + ] + }, + y_axis_tick : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '.1', + data : [ + { + label : '0.00001', + value : '.5' + }, + { + label : '0.0001', + value : '.4' + }, + { + label : '0.001', + value : '.3' + }, + { + label : '0.01', + value : '.2' + }, + { + label : '0.1', + value : '.1' + }, + { + label : '1', + value : '1' + } + ] + + }, + separator_legend : { + title : 'Others', + type : 'separator' + }, + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'select', + init : 'true', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + } +}; + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js @@ -0,0 +1,80 @@ +// dependencies +define([], function() { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, nvd3_model, chart, request_dictionary, callback) + { + // request data + var self = this; + this.app.datasets.request(request_dictionary, function(data) { + nv.addGraph(function() { + // x axis + self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); + + // x axis label + nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label')); + + // y axis + self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); + + // y axis label + nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label')) + .axisLabelDistance(30); + + // controls + if (chart.groups.length == 1) { + nvd3_model.options({ showControls: false }); + } + + // legend + var legend_visible = true; + if (chart.settings.get('show_legend') == 'false') { + legend_visible = false; + } + nvd3_model.showLegend(legend_visible); + + // custom callback + if (callback) { + callback(nvd3_model); + } + + // parse data to svg + self.options.svg.datum(data) + .call(nvd3_model); + + // refresh on window resize + nv.utils.windowResize(nvd3_model.update); + + // set chart state + chart.state('ok', 'Chart has been drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + }); + }, + + // make axis + _axis: function(axis, type, tick) { + switch (type) { + case 'hide': + axis.tickFormat(function() { return '' }); + break; + case 'auto': + break; + default: + axis.tickFormat(d3.format(tick + type)); + } + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/bardiagram.js --- a/config/plugins/visualizations/charts/static/charts/bardiagram.js +++ /dev/null @@ -1,33 +0,0 @@ -// dependencies -define([], function() { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.d3_chart = nv.models.multiBarChart(); - - self.d3_chart.xAxis.tickFormat(d3.format('.2f')) - self.d3_chart.yAxis.tickFormat(d3.format('.1f')) - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/bardiagram/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/bardiagram/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Bar diagram', +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/histogram/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js @@ -0,0 +1,21 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Histogram', + execute : true, + columns : { + y : { + title : 'Observations' + } + }, + settings : { + x_axis_label : { + init : 'Breaks' + }, + y_axis_label : { + init : 'Density' + } + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/histogram/histogram.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/histogram/histogram.js @@ -0,0 +1,31 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // configure request + var index = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = { + x: index++, + y: index++ + } + } + + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/horizontal.js --- a/config/plugins/visualizations/charts/static/charts/horizontal.js +++ /dev/null @@ -1,33 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.d3_chart = nv.models.multiBarHorizontalChart(); - - self.d3_chart.xAxis.tickFormat(function() { return ''; }); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/horizontal/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/horizontal/config.js @@ -0,0 +1,12 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Bar diagram (horizontal)', + settings : { + x_axis_type : { + init : 'hide' + } + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/line.js --- a/config/plugins/visualizations/charts/static/charts/line.js +++ /dev/null @@ -1,39 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.lineChart(); - - self.chart_3d.xAxis - .tickFormat(d3.format(',f')); - - self.chart_3d.yAxis - .tickFormat(d3.format(',.2f')); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - - return self.chart_3d; - }); - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/line/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/line/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Line chart', +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/line/line.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/line/line.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/linewithfocus.js --- a/config/plugins/visualizations/charts/static/charts/linewithfocus.js +++ /dev/null @@ -1,37 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.lineWithFocusChart(); - - self.chart_3d.xAxis - .tickFormat(d3.format(',f')); - - self.chart_3d.yAxis - .tickFormat(d3.format(',.2f')); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - }); - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/linewithfocus/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Line with focus', +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/piechart.js --- a/config/plugins/visualizations/charts/static/charts/piechart.js +++ /dev/null @@ -1,51 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // loop through data groups - for (var key in data) { - // get group - var group = data[key]; - - // format chart data - var pie_data = []; - for (var key in group.values) { - var value = group.values[key]; - pie_data.push ({ - key : value.x, - y : value.y - }); - } - - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.pieChart() - .donut(true) - .showLegend(false); - - d3.select(self.options.svg_id) - .datum(pie_data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - - return self.chart_3d; - }); - } - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/piechart/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/piechart/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Pie chart', +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/piechart/piechart.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/piechart/piechart.js @@ -0,0 +1,57 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // request data + var self = this; + this.app.datasets.request(request_dictionary, function(data) { + + // loop through data groups + for (var key in request_dictionary.groups) { + // get group + var group = request_dictionary.groups[key]; + + // format chart data + var pie_data = []; + for (var key in group.values) { + var value = group.values[key]; + pie_data.push ({ + key : value.x, + y : value.y + }); + } + + // add graph to screen + nv.addGraph(function() { + self.chart_3d = nv.models.pieChart() + .donut(true) + .showLegend(false); + + self.options.svg.datum(pie_data) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + + // set chart state + chart.state('ok', 'Pie chart drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + } + }); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/scatterplot.js --- a/config/plugins/visualizations/charts/static/charts/scatterplot.js +++ /dev/null @@ -1,37 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.d3_chart = nv.models.scatterChart() - .showDistX(true) - .showDistY(true) - .color(d3.scale.category10().range()); - - self.d3_chart.xAxis.tickFormat(d3.format('.02f')) - self.d3_chart.yAxis.tickFormat(d3.format('.02f')) - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/scatterplot/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/scatterplot/config.js @@ -0,0 +1,12 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Scatter plot', + columns : { + x : { + title : 'Values for x-axis' + } + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js @@ -0,0 +1,25 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) { + nvd3_model.showDistX(true) + .showDistY(true) + .color(d3.scale.category10().range()); + }); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/stackedarea.js --- a/config/plugins/visualizations/charts/static/charts/stackedarea.js +++ /dev/null @@ -1,59 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - // check data - var valid = true; - var length = 0; - for (var key in data) { - // evalute length - if (length == 0) { - length = data[key].values.length; - } else { - if (length != data[key].values.length) { - valid = false; - break; - } - } - } - if (!valid) { - return; - } - - // make plot - self.d3_chart = nv.models.stackedAreaChart() - .x(function(d) { - return d.x - }) - .y(function(d) { - return d.y - }) - .clipEdge(true); - - self.d3_chart.xAxis.tickFormat(function() { return ''; }); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/stackedarea/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/stackedarea/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Stacked area' +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js @@ -0,0 +1,26 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) { + // make plot + nvd3_model.x(function(d) { return d.x }) + .y(function(d) { return d.y }) + .clipEdge(true); + }); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/charts/types.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/types.js @@ -0,0 +1,39 @@ +// dependencies +define(['plugin/charts/bardiagram/config', + //'plugin/charts/boxplot/config', + 'plugin/charts/histogram/config', + 'plugin/charts/horizontal/config', + 'plugin/charts/line/config', + 'plugin/charts/linewithfocus/config', + 'plugin/charts/piechart/config', + 'plugin/charts/scatterplot/config', + 'plugin/charts/stackedarea/config', + ], function(bardiagram, + //boxplot, + histogram, + horizontal, + line, + linewithfocus, + piechart, + scatterplot, + stackedarea + ) { + +// widget +return Backbone.Model.extend( +{ + // types + defaults: { + 'bardiagram' : bardiagram, + //'boxplot' : boxplot, + 'horizontal' : horizontal, + 'histogram' : histogram, + 'line' : line, + 'linewithfocus' : linewithfocus, + 'piechart' : piechart, + 'scatterplot' : scatterplot, + 'stackedarea' : stackedarea + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/library/datasets.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/datasets.js @@ -0,0 +1,149 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.Collection.extend( +{ + // list of datasets + list: {}, + + // initialize + initialize: function(app, options) + { + // link app + this.app = app; + + // configure options + this.options = Utils.merge(options, this.optionsDefault); + }, + + // wait + request: function(options, success, error) { + // link this + var self = this; + + // check if column data is requested + if (options.groups) { + this._fetch(options, success); + } else { + // check if dataset is available from cache + var dataset = this.list[options.id]; + if (dataset) { + success(dataset); + return; + } + + // request dataset + Utils.request('GET', config.root + 'api/datasets/' + options.id, {}, function(dataset) { + switch (dataset.state) { + case 'error': + if (error) { + error(dataset); + } + break; + default: + self.list[options.id] = dataset; + success(dataset); + } + }); + } + }, + + // fetch data columns into dataset object + _fetch: function(options, callback) { + // set offset + var offset = options.start ? options.start : 0; + + // set limit + var limit = Math.abs(options.end - options.start); + var query_limit = this.app.config.get('query_limit'); + if (!limit || limit > query_limit) { + limit = query_limit; + } + + // get column indices + var index_string = ''; + var index_map = {}; + var index_count = 0; + for (var i in options.groups) { + var group = options.groups[i]; + for (var key in group.columns) { + var column = group.columns[key]; + + // add to index string + index_string += column + ','; + + // add to dictionary + index_map[column] = index_count; + + // increase counter + index_count++; + } + } + if (index_count == 0) { + callback({}); + return; + } + index_string = index_string.substring(0, index_string.length - 1); + + // initialize result dictionary + var result = options.groups.slice(0); + for (var i in result) { + result[i].values = []; + } + + // make request + var self = this; + Utils.request('GET', config.root + 'api/datasets/' + options.id, { + data_type : 'raw_data', + provider : 'dataset-column', + limit : limit, + offset : offset, + indeces : index_string + }, function(response) { + + // loop through rows + for (var i in response.data) { + // get row + var row = response.data[i]; + + // collect all data into the defined groups + for (var j in options.groups) { + // get group + var group = options.groups[j]; + + // initialize value + var value = { + x : parseInt(i) + offset + }; + + // fill value + for (var key in group.columns) { + // get column + var column = group.columns[key]; + + // identify column + var index = index_map[column]; + + // read value from row + var v = row[index]; + if(isNaN(v) || !v) { + v = 0; + } + + // add value to dictionary + value[key] = v; + } + + // add to result + result[j].values.push(value); + } + } + + // callback + callback(result); + }); + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/library/deferred.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -0,0 +1,85 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// deferred process handler +return Backbone.Model.extend( +{ + // queue + queue: [], + + // list of currently registered processes + process: {}, + + // process counter + counter: 0, + + // initialize + initialize: function() + { + // loop through queue and check states + this.on('refresh', function() { + if (this.counter == 0) { + for (var index in this.queue) { + // execute callback + this.queue[index](); + + // remove callback + this.queue.splice(index, 1); + } + } + }); + }, + + // executes callback once all processes are unregistered + execute: function(callback) { + // add wrapper to queue + this.queue.push(callback); + + // trigger change + this.trigger('refresh'); + }, + + // register process + register: function() { + // create unique id + var id = Utils.uuid(); + + // add process to queue + this.process[id] = true; + + // increase process counter + this.counter++; + + // log + console.debug('Deferred:register() - Registering ' + id); + + // return unique id + return id; + }, + + // unregister process + done: function(id) { + // delete tag + delete this.process[id]; + + // decrease process counter + this.counter--; + + // log + console.debug('Deferred:done() - Unregistering ' + id); + + // trigger change + this.trigger('refresh'); + }, + + // ready + ready: function() { + if (this.counter == 0) { + return true; + } else { + return false; + } + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/library/jobs.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -0,0 +1,152 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.Model.extend( +{ + // initialize + initialize: function(app, options) { + // link app + this.app = app; + + // link options + this.options = Utils.merge(options, this.optionsDefault); + }, + + // clean + cleanup: function(chart) { + // cleanup previous dataset file + var previous = chart.get('dataset_id_job'); + if (previous != '') { + var self = this; + Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() { + // update galaxy history + self._refreshHdas(); + }); + + // reset id + chart.set('dataset_id_job', ''); + } + }, + + // create job + submit: function(chart, settings_string, columns_string, success, error) { + // link this + var self = this; + + // backup chart details + var chart_id = chart.id; + var chart_type = chart.get('type'); + + // get chart settings + var chart_settings = this.app.types.get(chart_type); + + // configure tool + data = { + 'tool_id' : 'chartskit', + 'inputs' : { + 'input' : { + 'id' : chart.get('dataset_id'), + 'src' : 'hda' + }, + 'module' : chart_type, + 'columns' : columns_string, + 'settings' : settings_string + } + } + + // set chart state + chart.state('wait', 'Sending job request...'); + + // post job + Utils.request('POST', config.root + 'api/tools', data, + // success handler + function(response) { + if (!response.outputs || response.outputs.length == 0) { + chart.state('failed', 'Job submission failed. No response.'); + + // call error + error && error(); + } else { + // update galaxy history + self._refreshHdas(); + + // get dataset + var job = response.outputs[0]; + + // check dataset + chart.state('wait', 'Job has been queued...'); + + // backup resulting dataset id + chart.set('dataset_id_job', job.id); + + // save + this.app.storage.save(); + + // wait for job completion + self._loop(job.id, function(job) { + switch (job.state) { + case 'ok': + // update state + chart.state('wait', 'Job completed successfully...'); + + // execute success + success(job); + + // stop loop + return true; + case 'error': + // update state + chart.state('failed', 'Job has failed. Please check the history for details.'); + + // call error + error && error(); + + // stop loop + return true; + case 'running': + // wait + chart.state('wait', 'Job is running...'); + + // continue loop + return false; + } + }); + } + }, + // error handler + function(response) { + var message = ''; + if (response && response.message && response.message.data && response.message.data.input) { + message = response.message.data.input + '.'; + } + // update state + chart.state('failed', 'This visualization requires the Charts-Kit. Please make sure it is installed. ' + message); + + // call error + error && error(); + + } + ); + }, + + // request job details + _loop: function(id, callback) { + var self = this; + Utils.request('GET', config.root + 'api/jobs/' + id, {}, function(job) { + if (!callback(job)) { + setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout')); + } + }); + }, + + // refresh history panel + _refreshHdas: function() { + // update galaxy history + if (Galaxy && Galaxy.currHistoryPanel) { + Galaxy.currHistoryPanel.refreshHdas(); + } + } +}); + +}); \ No newline at end of file diff -r 3fccf761066931c39aa087bf7e132ed2ed65cb05 -r 089d1264d719891de3306684ee26fa0543577d55 config/plugins/visualizations/charts/static/library/portlet.js --- a/config/plugins/visualizations/charts/static/library/portlet.js +++ /dev/null @@ -1,171 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// return -return Backbone.View.extend( -{ - // visibility - visible: false, - - // defaults options - optionsDefault: { - label : '', - icon : 'fa-tasks', - buttons : null, - body : null, - height : null, - operations : null, - placement : 'bottom', - overflow : 'auto' - }, - - // content - $content : null, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this.template(this.options)); - - // link content - this.$content = this.$el.find('#content'); - - // set content height - if (this.options.height) { - this.$el.find('#body').css('height', this.options.height); - this.$el.find('#content').css('overflow', this.options.overflow); - } - - // append buttons - this.$buttons = $(this.el).find('#buttons'); - if (this.options.buttons) { - // link functions - var self = this; - $.each(this.options.buttons, function(name, item) { - item.$el.prop('id', name); - self.$buttons.append(item.$el); - }); - } else { - this.$buttons.remove(); - } - - // append operations - this.$operations = $(this.el).find('#operations'); - if (this.options.operations) { - // link functions - var self = this; - $.each(this.options.operations, function(name, item) { - item.$el.prop('id', name); - self.$operations.append(item.$el); - }); - } - - // add body - if(this.options.body) { - this.append(this.options.body); - } - }, - - // append - append: function($el) { - this.$content.append(Utils.wrap($el)); - }, - - // content - content: function() { - return this.$content; - }, - - // hide modal - show: function(){ - // fade in - this.$el.fadeIn('fast'); - - // set flag - this.visible = true; - }, - - // hide modal - hide: function(){ - // fade out - this.$el.fadeOut('fast'); - - // set flag - this.visible = false; - }, - - // enable buttons - enableButton: function(id) { - this.$buttons.find('#' + id).prop('disabled', false); - }, - - // disable buttons - disableButton: function(id) { - this.$buttons.find('#' + id).prop('disabled', true); - }, - - // enable operation - hideOperation: function(id) { - this.$operations.find('#' + id).hide(); - }, - - // disable operation - showOperation: function(id) { - this.$operations.find('#' + id).show(); - }, - - // set operation - setOperation: function(id, callback) { - var $el = this.$operations.find('#' + id); - $el.off('click'); - $el.on('click', callback); - }, - - // label - label: function(new_label) { - var $el = this.$el.find('#label'); - if (new_label) { - $el.html(new_label); - } - return $el.html(); - }, - - // fill regular modal template - template: function(options) { - var tmpl = '<div class="toolForm">'; - - if (options.label || options.icon) { - tmpl += '<div id="title" class="toolFormTitle" style="overflow:hidden;">' + - '<div id="operations" style="float: right;"></div>' + - '<div style="overflow: hidden">'; - - if (options.icon) - tmpl += '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; - - tmpl += '<div id="label" style="padding-top: 2px; float: left;">' + options.label + '</div>'; - - tmpl += '</div>' + - '</div>'; - } - tmpl += '<div id="body" class="toolFormBody">'; - - if (options.placement == 'top') { - tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; - } - - tmpl += '<div id="content" class="content" style="height: inherit; padding: 10px;"></div>'; - - if (options.placement == 'bottom') { - tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; - } - - tmpl += '</div>' + - '</div>'; - return tmpl; - } -}); - -}); This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.