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commit/galaxy-central: guerler: Charts: Show/hide optional settings, switch to auto-axis by default
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/abe1482b5508/
Changeset: abe1482b5508
User: guerler
Date: 2014-03-31 23:35:49
Summary: Charts: Show/hide optional settings, switch to auto-axis by default
Affected #: 10 files
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 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 @@
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t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var 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style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var 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id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu 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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:"rkit",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. 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"+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=d3.select(this.$el.find("svg")[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(){this.app.storage.save(),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-gear",tooltip:"Customize 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)},_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.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<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();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<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 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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 ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/charts/_nvd3/config.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/config.js
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/config.js
@@ -23,35 +23,47 @@
title : 'Axis value type',
info : 'Select the value type of the axis.',
type : 'select',
- init : 'f',
+ init : 'auto',
data : [
{
label : '-- Do not show values --',
- value : 'hide'
+ value : 'hide',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ hide : 'x_axis_tick'
},
{
label : 'Float',
- value : 'f'
+ value : 'f',
+ show : 'x_axis_tick'
},
{
label : 'Exponent',
- value : 'e'
+ value : 'e',
+ show : 'x_axis_tick'
},
{
label : 'Integer',
- value : 'd'
+ value : 'd',
+ hide : 'x_axis_tick'
},
{
label : 'Percentage',
- value : 'p'
+ value : 'p',
+ show : 'x_axis_tick'
},
{
label : 'Rounded',
- value : 'r'
+ value : 'r',
+ show : 'x_axis_tick'
},
{
label : 'SI-prefix',
- value : 's'
+ value : 's',
+ show : 'x_axis_tick'
}
]
},
@@ -103,35 +115,47 @@
title : 'Axis value type',
info : 'Select the value type of the axis.',
type : 'select',
- init : 'f',
+ init : 'auto',
data : [
{
label : '-- Do not show values --',
- value : 'hide'
+ value : 'hide',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ hide : 'y_axis_tick'
},
{
label : 'Float',
- value : 'f'
+ value : 'f',
+ show : 'y_axis_tick'
},
{
label : 'Exponent',
- value : 'e'
+ value : 'e',
+ show : 'y_axis_tick'
},
{
label : 'Integer',
- value : 'd'
+ value : 'd',
+ hide : 'y_axis_tick'
},
{
label : 'Percentage',
- value : 'p'
+ value : 'p',
+ show : 'y_axis_tick'
},
{
label : 'Rounded',
- value : 'r'
+ value : 'r',
+ show : 'y_axis_tick'
},
{
label : 'SI-prefix',
- value : 's'
+ value : 's',
+ show : 'y_axis_tick'
}
]
},
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
@@ -18,23 +18,13 @@
this.app.datasets.request(request_dictionary, function(data) {
nv.addGraph(function() {
// x axis
- if (chart.settings.get('x_axis_type') == 'hide') {
- nvd3_model.xAxis.tickFormat(function() { return '' });
- } else {
- var tick = chart.settings.get('x_axis_tick') + chart.settings.get('x_axis_type');
- nvd3_model.xAxis.tickFormat(d3.format(tick));
- }
+ 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
- if (chart.settings.get('y_axis_type') == 'hide') {
- nvd3_model.yAxis.tickFormat(function() { return '' });
- } else {
- var tick = chart.settings.get('y_axis_tick') + chart.settings.get('y_axis_type');
- nvd3_model.yAxis.tickFormat(d3.format(tick));
- }
+ 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'))
@@ -71,6 +61,19 @@
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));
+ }
}
});
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/charts/histogram/config.js
--- a/config/plugins/visualizations/charts/static/charts/histogram/config.js
+++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js
@@ -14,9 +14,6 @@
},
y_axis_label : {
init : 'Density'
- },
- y_axis_tick : {
- init : '.3'
}
}
});
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/charts/piechart/piechart.js
--- a/config/plugins/visualizations/charts/static/charts/piechart/piechart.js
+++ b/config/plugins/visualizations/charts/static/charts/piechart/piechart.js
@@ -44,7 +44,7 @@
nv.utils.windowResize(self.chart_3d.update);
// set chart state
- chart.set('state', 'ok');
+ chart.state('ok', 'Pie chart drawn.');
// unregister process
chart.deferred.done(process_id);
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -43,7 +43,7 @@
// configure tool
data = {
- 'tool_id' : 'rkit',
+ 'tool_id' : 'chartskit',
'inputs' : {
'input' : {
'id' : chart.get('dataset_id'),
@@ -80,6 +80,9 @@
// 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) {
@@ -118,7 +121,7 @@
message = response.message.data.input + '.';
}
// update state
- chart.state('failed', 'This visualization requires the R-kit. Please make sure it is installed. ' + message);
+ chart.state('failed', 'This visualization requires the Charts-Kit. Please make sure it is installed. ' + message);
// call error
error && error();
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/library/ui-table-form.js
--- a/config/plugins/visualizations/charts/static/library/ui-table-form.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js
@@ -5,6 +5,9 @@
// widget
var View = Backbone.View.extend(
{
+ // elements
+ list: [],
+
// initialize
initialize: function(options) {
// ui elements
@@ -30,14 +33,28 @@
// reset table
this.table.removeAll();
+ // reset list
+ this.list = [];
+
// load settings elements into table
for (var id in settings) {
this._add(id, settings[id], model);
}
+
+ // trigger change
+ for (var id in this.list) {
+ var onchange = this.list[id].options.onchange;
+ if (onchange) {
+ onchange();
+ }
+ }
},
// add table row
_add: function(id, settings_def, model) {
+ // link this
+ var self = this;
+
// field wrapper
var field = null;
@@ -47,8 +64,9 @@
// text input field
case 'text' :
field = new Ui.Input({
- placeholder: settings_def.placeholder,
- onchange: function() {
+ id : id,
+ placeholder : settings_def.placeholder,
+ onchange : function() {
model.set(id, field.value());
}
});
@@ -56,18 +74,23 @@
// select field
case 'select' :
field = new Ui.Select.View({
- data: settings_def.data,
- onchange: function() {
- model.set(id, field.value());
- }
- });
- break;
- // slider input field
- case 'slider' :
- field = new Ui.Input({
- placeholder: settings_def.placeholder,
- onchange: function() {
- model.set(id, field.value());
+ id : id,
+ data : settings_def.data,
+ onchange : function() {
+ // set new value
+ var selected = field.value();
+ model.set(id, selected);
+
+ // find selected dictionary
+ var dict = _.findWhere(settings_def.data, {value: selected});
+ if (dict) {
+ if (dict.show) {
+ self.$el.find('#' + dict.show).fadeIn('fast');
+ }
+ if (dict.hide) {
+ self.$el.find('#' + dict.hide).fadeOut('fast');
+ }
+ }
}
});
break;
@@ -89,6 +112,9 @@
}
field.value(model.get(id));
+ // add list
+ this.list[id] = field;
+
// combine field and info
var $input = $('<div/>');
$input.append(field.$el);
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/views/viewer.js
--- a/config/plugins/visualizations/charts/static/views/viewer.js
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -27,8 +27,8 @@
title: 'Viewport',
operations: {
edit_button: new Ui.ButtonIcon({
- icon : 'fa-gear',
- tooltip : 'Customize Chart',
+ icon : 'fa-edit',
+ tooltip : 'Customize this chart',
title : 'Customize',
onclick : function() {
// attempt to load chart editor
@@ -36,8 +36,29 @@
self.app.go('editor');
});
}
- })
-
+ }),
+ /*picture_button: new Ui.ButtonIcon({
+ icon : 'fa-camera',
+ tooltip : 'Download SVG-file',
+ title : 'Screenshot',
+ onclick : function() {
+ // attempt to load chart editor
+ self._wait (self.chart, function() {
+ self._screenshot();
+ });
+ }
+ }),
+ settings_button: new Ui.ButtonIcon({
+ icon : 'fa-gear',
+ tooltip : 'Configure this application',
+ title : 'Application',
+ onclick : function() {
+ // attempt to load chart editor
+ self._wait (self.chart, function() {
+ self.app.go('editor');
+ });
+ }
+ })*/
}
});
@@ -74,6 +95,17 @@
this.portlet.title(title);
},
+ // download svg file
+ _screenshot: function() {
+ // Encode the SVG
+ var serializer = new XMLSerializer();
+ var xmlString = serializer.serializeToString(this.viewport_view.svg.node());
+ var imgData = 'data:image/svg+xml;base64,' + btoa(xmlString);
+ //Use the download attribute (or a shim) to provide a link
+ //this.portlet.append('<a href="' + imgData + '" download>Download</a>');
+ window.location.href = 'data:application/x-download/;charset=utf-8,' + encodeURIComponent(xmlString);
+ },
+
// wait for chart to be ready
_wait: function(chart, callback) {
// get chart
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -80,7 +80,8 @@
this.$el.append($(this._template_svg()));
// find svg element
- this.svg = d3.select(this.$el.find('svg')[0]);
+ this.svg_el = this.$el.find('svg');
+ this.svg = d3.select(this.svg_el[0]);
},
// add
@@ -123,10 +124,6 @@
// submit job
self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart),
function() {
- // save
- this.app.storage.save();
-
- // draw
view.draw(process_id, chart, self._defaultRequestDictionary(chart));
},
function() {
diff -r ab8a827af3b3ebf1ed0d830d5c46a9698f8c6714 -r abe1482b550884d58cda3ca1e46200afa6c09ee9 config/plugins/visualizations/charts/templates/charts.mako
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -10,6 +10,7 @@
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><title>${hda.name} | ${visualization_name}</title>
+ ## install shared libraries
${h.js( 'libs/jquery/jquery',
'libs/bootstrap',
'libs/require',
@@ -17,16 +18,16 @@
'libs/backbone/backbone',
'libs/d3')}
- ## css
+ ## shared css
${h.css( 'base' )}
-
+
## install nv.d3 module
${h.javascript_link( app_root + "plugins/nv.d3.js" )}
${h.stylesheet_link( app_root + "plugins/nv.d3.css" )}
-
+
## install boxplot module
##${h.javascript_link( app_root + "plugins/box.js" )}
-
+
## load merged/minified code
${h.javascript_link( app_root + "build-app.js" )}
</head>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ccce23e8d26c/
Changeset: ccce23e8d26c
Branch: galaxy-nekrut
User: natefoo
Date: 2014-03-31 22:42:43
Summary: Close inactive branch.
Affected #: 0 files
https://bitbucket.org/galaxy/galaxy-central/commits/ab8a827af3b3/
Changeset: ab8a827af3b3
User: natefoo
Date: 2014-03-31 22:43:05
Summary: Merge branch close.
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: data libraries, don't allow showing deleted libraries to non-admins; provide information what actions user is allowed to do on library;
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6f04f0729dc4/
Changeset: 6f04f0729dc4
User: martenson
Date: 2014-03-31 21:36:49
Summary: data libraries, don't allow showing deleted libraries to non-admins; provide information what actions user is allowed to do on library;
Affected #: 5 files
diff -r f7810af7f40c9215f5a3db77053563bf7db0ebde -r 6f04f0729dc4d097a46dd8c98c586faf265a315f lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -33,13 +33,16 @@
query = trans.sa_session.query( trans.app.model.Library )
deleted = kwd.get( 'deleted', 'missing' )
try:
- deleted = util.asbool( deleted )
+ if not trans.user_is_admin(): # non-admins can't see deleted libraries
+ deleted = False
+ else:
+ deleted = util.asbool( deleted )
if deleted:
query = query.filter( trans.app.model.Library.table.c.deleted == True )
else:
query = query.filter( trans.app.model.Library.table.c.deleted == False )
except ValueError:
- # given value wasn't true/false so we don't filter on this parameter at all
+ # given value wasn't true/false but the user is admin so we don't filter on this parameter at all
pass
current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ]
@@ -57,6 +60,16 @@
item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
if trans.app.security_agent.library_is_public( library, contents=False ):
item[ 'public' ] = True
+ current_user_roles = trans.get_current_user_roles()
+ # can_user_add = trans.app.security_agent.can_add_library_item( current_user_roles, library.root_folder )
+ if not trans.user_is_admin():
+ item['can_user_add'] = trans.app.security_agent.can_add_library_item( current_user_roles, library )
+ item['can_user_modify'] = trans.app.security_agent.can_modify_library_item( current_user_roles, library )
+ item['can_user_manage'] = trans.app.security_agent.can_manage_library_item( current_user_roles, library )
+ else:
+ item['can_user_add'] = True
+ item['can_user_modify'] = True
+ item['can_user_manage'] = True
libraries.append( item )
return libraries
diff -r f7810af7f40c9215f5a3db77053563bf7db0ebde -r 6f04f0729dc4d097a46dd8c98c586faf265a315f static/scripts/mvc/library/library-libraryrow-view.js
--- a/static/scripts/mvc/library/library-libraryrow-view.js
+++ b/static/scripts/mvc/library/library-libraryrow-view.js
@@ -22,9 +22,16 @@
this.set_up_visual_features(library);
},
- set_up_visual_features: function(library){
+ set_up_visual_features: function(library, options){
if (library.get('deleted') === true){
this.$el.addClass('active');
+ this.$el.find('.public_lib_ico').hide();
+ this.$el.find('.undelete_library_btn').show();
+ this.$el.find('.upload_library_btn').hide();
+ this.$el.find('.edit_library_btn').hide();
+ this.$el.find('.permission_library_btn').hide();
+ this.$el.find('.cancel_library_btn').hide();
+ this.$el.find('.delete_library_btn').hide();
}
this.$el.show();
},
diff -r f7810af7f40c9215f5a3db77053563bf7db0ebde -r 6f04f0729dc4d097a46dd8c98c586faf265a315f static/scripts/mvc/library/library-librarytoolbar-view.js
--- a/static/scripts/mvc/library/library-librarytoolbar-view.js
+++ b/static/scripts/mvc/library/library-librarytoolbar-view.js
@@ -21,6 +21,11 @@
this.render();
},
+ render: function(){
+ var toolbar_template = this.templateToolBar()
+ this.$el.html(toolbar_template({admin_user: Galaxy.currUser.isAdmin(), anon_user: Galaxy.currUser.isAnonymous()}))
+ },
+
delegate_modal: function(event){
// probably should refactor to have this functionality in this view, not in the library view
libraryListView.show_library_modal(event);
@@ -37,11 +42,6 @@
}
},
- render: function(){
- var toolbar_template = this.templateToolBar()
- this.$el.html(toolbar_template())
- },
-
templateToolBar: function(){
tmpl_array = [];
@@ -49,10 +49,12 @@
// TOOLBAR
tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');
tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
+ tmpl_array.push(' <% if(admin_user === true) { %>');
tmpl_array.push(' <div id="library_toolbar">');
tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');
tmpl_array.push(' </div>');
+ tmpl_array.push(' <% } %>');
tmpl_array.push(' </div>');
tmpl_array.push(' <div id="libraries_element">');
tmpl_array.push(' </div>');
diff -r f7810af7f40c9215f5a3db77053563bf7db0ebde -r 6f04f0729dc4d097a46dd8c98c586faf265a315f static/scripts/packed/mvc/library/library-libraryrow-view.js
--- a/static/scripts/packed/mvc/library/library-libraryrow-view.js
+++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({initialize:function(f){this.render(f)},render:function(g){var f=this.templateRow();this.setElement(f({library:g}));this.set_up_visual_features(g)},set_up_visual_features:function(f){if(f.get("deleted")===true){this.$el.addClass("active")}this.$el.show()},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button"><span class="fa fa-upload"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({initialize:function(f){this.render(f)},render:function(g){var f=this.templateRow();this.setElement(f({library:g}));this.set_up_visual_features(g)},set_up_visual_features:function(f,g){if(f.get("deleted")===true){this.$el.addClass("active");this.$el.find(".public_lib_ico").hide();this.$el.find(".undelete_library_btn").show();this.$el.find(".upload_library_btn").hide();this.$el.find(".edit_library_btn").hide();this.$el.find(".permission_library_btn").hide();this.$el.find(".cancel_library_btn").hide();this.$el.find(".delete_library_btn").hide()}this.$el.show()},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button"><span class="fa fa-upload"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}});
\ No newline at end of file
diff -r f7810af7f40c9215f5a3db77053563bf7db0ebde -r 6f04f0729dc4d097a46dd8c98c586faf265a315f static/scripts/packed/mvc/library/library-librarytoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,d,e,c){var b=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},delegate_modal:function(f){libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.target.checked){libraryListView.preferences.set({with_deleted:true});libraryListView.render()}else{libraryListView.preferences.set({with_deleted:false});libraryListView.render()}},render:function(){var f=this.templateToolBar();this.$el.html(f())},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{ToolbarView:b}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,d,e,c){var b=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();this.$el.html(f({admin_user:Galaxy.currUser.isAdmin(),anon_user:Galaxy.currUser.isAnonymous()}))},delegate_modal:function(f){libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.target.checked){libraryListView.preferences.set({with_deleted:true});libraryListView.render()}else{libraryListView.preferences.set({with_deleted:false});libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{ToolbarView:b}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b6af8a5aefb3/
Changeset: b6af8a5aefb3
User: nsoranzo
Date: 2014-03-28 12:54:53
Summary: Workflow API: show also workflow owner, so a user can check it before importing.
Affected #: 1 file
diff -r 37fa3f5a47f8fc45755ac1ca758a852bb76ea999 -r b6af8a5aefb3c8a6dbd360d48980a2e96bf67ac8 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -76,6 +76,7 @@
item = wf.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id(wf.id)
item['url'] = url_for('workflow', id=encoded_id)
+ item['owner'] = wf.user.username
rval.append(item)
for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by(
user=trans.user ).join( 'stored_workflow' ).filter(
@@ -84,6 +85,7 @@
item = wf_sa.stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
item['url'] = url_for( 'workflow', id=encoded_id )
+ item['owner'] = wf_sa.stored_workflow.user.username
rval.append(item)
return rval
@@ -111,6 +113,7 @@
return "That workflow does not exist."
item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for('workflow', id=workflow_id)
+ item['owner'] = stored_workflow.user.username
latest_workflow = stored_workflow.latest_workflow
inputs = {}
for step in latest_workflow.steps:
https://bitbucket.org/galaxy/galaxy-central/commits/f7810af7f40c/
Changeset: f7810af7f40c
User: dannon
Date: 2014-03-31 19:21:49
Summary: Merged in nsoranzo/galaxy-central (pull request #355)
Workflow API: show also workflow owner, so a user can check it before importing.
Affected #: 1 file
diff -r 4d593e0fafe501f233cfe8c67ad608bd12a37ff6 -r f7810af7f40c9215f5a3db77053563bf7db0ebde lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -76,6 +76,7 @@
item = wf.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id(wf.id)
item['url'] = url_for('workflow', id=encoded_id)
+ item['owner'] = wf.user.username
rval.append(item)
for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by(
user=trans.user ).join( 'stored_workflow' ).filter(
@@ -84,6 +85,7 @@
item = wf_sa.stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
item['url'] = url_for( 'workflow', id=encoded_id )
+ item['owner'] = wf_sa.stored_workflow.user.username
rval.append(item)
return rval
@@ -111,6 +113,7 @@
return "That workflow does not exist."
item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for('workflow', id=workflow_id)
+ item['owner'] = stored_workflow.user.username
latest_workflow = stored_workflow.latest_workflow
inputs = {}
for step in latest_workflow.steps:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: added is_admin to the javascript user object for UI rendering purposes;
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4d593e0fafe5/
Changeset: 4d593e0fafe5
User: martenson
Date: 2014-03-31 18:55:06
Summary: added is_admin to the javascript user object for UI rendering purposes;
modified is_admin_user in masthead config to be consistent with standard is_admin check
Affected #: 4 files
diff -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a -r 4d593e0fafe501f233cfe8c67ad608bd12a37ff6 lib/galaxy/webapps/galaxy/api/users.py
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -81,6 +81,7 @@
#TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??)
#TODO: works with other users (from admin)??
item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
+ item['is_admin'] = trans.user_is_admin()
return item
@web.expose_api
diff -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a -r 4d593e0fafe501f233cfe8c67ad608bd12a37ff6 static/scripts/mvc/user/user-model.js
--- a/static/scripts/mvc/user/user-model.js
+++ b/static/scripts/mvc/user/user-model.js
@@ -30,7 +30,8 @@
email : "",
total_disk_usage : 0,
nice_total_disk_usage : "",
- quota_percent : null
+ quota_percent : null,
+ is_admin : false
},
/** Set up and bind events
@@ -47,6 +48,10 @@
return ( !this.get( 'email' ) );
},
+ isAdmin : function(){
+ return ( this.get( 'is_admin' ) );
+ },
+
/** Load a user with the API using an id.
* If getting an anonymous user or no access to a user id, pass the User.CURRENT_ID_STR
* (e.g. 'current') and the API will return the current transaction's user data.
diff -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a -r 4d593e0fafe501f233cfe8c67ad608bd12a37ff6 static/scripts/packed/mvc/user/user-model.js
--- a/static/scripts/packed/mvc/user/user-model.js
+++ b/static/scripts/packed/mvc/user/user-model.js
@@ -1,1 +1,1 @@
-define(["mvc/base-mvc"],function(a){var c=Backbone.Model.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(d){this.log("User.initialize:",d);this.on("loaded",function(e,f){this.log(this+" has loaded:",e,f)});this.on("change",function(e,f){this.log(this+" has changed:",e,f.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(g,e){g=g||c.CURRENT_ID_STR;e=e||{};var d=this,f=e.success;e.success=function(i,h){d.trigger("loaded",i,h);if(f){f(i,h)}};if(g===c.CURRENT_ID_STR){e.url=this.urlRoot+"/"+c.CURRENT_ID_STR}return Backbone.Model.prototype.fetch.call(this,e)},clearSessionStorage:function(){for(var d in sessionStorage){if(d.indexOf("history:")===0){sessionStorage.removeItem(d)}else{if(d==="history-panel"){sessionStorage.removeItem(d)}}}},toString:function(){var d=[this.get("username")];if(this.get("id")){d.unshift(this.get("id"));d.push(this.get("email"))}return"User("+d.join(":")+")"}});c.CURRENT_ID_STR="current";c.getCurrentUserFromApi=function(e){var d=new c();d.loadFromApi(c.CURRENT_ID_STR,e);return d};var b=Backbone.Collection.extend(a.LoggableMixin).extend({model:c,urlRoot:galaxy_config.root+"api/users"});return{User:c}});
\ No newline at end of file
+define(["mvc/base-mvc"],function(a){var c=Backbone.Model.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:false},initialize:function(d){this.log("User.initialize:",d);this.on("loaded",function(e,f){this.log(this+" has loaded:",e,f)});this.on("change",function(e,f){this.log(this+" has changed:",e,f.changes)})},isAnonymous:function(){return(!this.get("email"))},isAdmin:function(){return(this.get("is_admin"))},loadFromApi:function(g,e){g=g||c.CURRENT_ID_STR;e=e||{};var d=this,f=e.success;e.success=function(i,h){d.trigger("loaded",i,h);if(f){f(i,h)}};if(g===c.CURRENT_ID_STR){e.url=this.urlRoot+"/"+c.CURRENT_ID_STR}return Backbone.Model.prototype.fetch.call(this,e)},clearSessionStorage:function(){for(var d in sessionStorage){if(d.indexOf("history:")===0){sessionStorage.removeItem(d)}else{if(d==="history-panel"){sessionStorage.removeItem(d)}}}},toString:function(){var d=[this.get("username")];if(this.get("id")){d.unshift(this.get("id"));d.push(this.get("email"))}return"User("+d.join(":")+")"}});c.CURRENT_ID_STR="current";c.getCurrentUserFromApi=function(e){var d=new c();d.loadFromApi(c.CURRENT_ID_STR,e);return d};var b=Backbone.Collection.extend(a.LoggableMixin).extend({model:c,urlRoot:galaxy_config.root+"api/users"});return{User:c}});
\ No newline at end of file
diff -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a -r 4d593e0fafe501f233cfe8c67ad608bd12a37ff6 templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -9,6 +9,7 @@
user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans )
users_api_controller = trans.webapp.api_controllers[ 'users' ]
user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user )
+ user_dict[ 'is_admin' ] = trans.user_is_admin()
else:
usage = 0
percent = None
@@ -50,7 +51,7 @@
'terms_url' : app.config.get("terms_url", ""),
'allow_user_creation' : app.config.allow_user_creation,
'logo_url' : h.url_for(app.config.get( 'logo_url', '/')),
- 'is_admin_user' : trans.user and app.config.is_admin_user(trans.user),
+ 'is_admin_user' : trans.user_is_admin(),
'active_view' : active_view,
'ftp_upload_dir' : app.config.get("ftp_upload_dir", None),
'ftp_upload_site' : app.config.get("ftp_upload_site", None),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix base-mvc SessionStorageModel to require an id; Show alert on disabled sessionStorage
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8217bcfd4c3c/
Changeset: 8217bcfd4c3c
User: carlfeberhard
Date: 2014-03-31 18:08:21
Summary: Fix base-mvc SessionStorageModel to require an id; Show alert on disabled sessionStorage
Affected #: 3 files
diff -r a2d33a3caaa4ed28d774324e5add3c1eaed9397c -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a static/scripts/mvc/base-mvc.js
--- a/static/scripts/mvc/base-mvc.js
+++ b/static/scripts/mvc/base-mvc.js
@@ -53,8 +53,11 @@
*/
var SessionStorageModel = Backbone.Model.extend({
initialize : function( initialAttrs ){
- // create unique id if none provided
- initialAttrs.id = ( !_.isString( initialAttrs.id ) )?( _.uniqueId() ):( initialAttrs.id );
+ // check for sessionStorage and error if no id is provided
+ this._checkEnabledSessionStorage();
+ if( !initialAttrs.id ){
+ throw new Error( 'SessionStorageModel requires an id in the initial attributes' );
+ }
this.id = initialAttrs.id;
// load existing from storage (if any), clear any attrs set by bbone before init is called,
@@ -69,6 +72,15 @@
});
},
+ _checkEnabledSessionStorage : function(){
+ try {
+ return sessionStorage.length;
+ } catch( err ){
+ alert( 'Please enable cookies in your browser for this Galaxy site' );
+ return false;
+ }
+ },
+
/** override of bbone sync to save to sessionStorage rather than REST
* bbone options (success, errror, etc.) should still apply
*/
diff -r a2d33a3caaa4ed28d774324e5add3c1eaed9397c -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a static/scripts/packed/mvc/base-mvc.js
--- a/static/scripts/packed/mvc/base-mvc.js
+++ b/static/scripts/packed/mvc/base-mvc.js
@@ -1,1 +1,1 @@
-define([],function(){var c={logger:null,log:function(){if(this.logger){var d=this.logger.log;if(typeof this.logger.log==="object"){d=Function.prototype.bind.call(this.logger.log,this.logger)}return d.apply(this.logger,arguments)}return undefined}};var a=Backbone.Model.extend({initialize:function(e){e.id=(!_.isString(e.id))?(_.uniqueId()):(e.id);this.id=e.id;var d=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,d,e),{silent:true});this.on("change",function(){this.save()})},sync:function(g,e,d){if(!d.silent){e.trigger("request",e,{},d)}var f;switch(g){case"create":f=this._create(e);break;case"read":f=this._read(e);break;case"update":f=this._update(e);break;case"delete":f=this._delete(e);break}if(f!==undefined||f!==null){if(d.success){d.success()}}else{if(d.error){d.error()}}return f},_create:function(d){var e=d.toJSON(),f=sessionStorage.setItem(d.id,JSON.stringify(e));return(f===null)?(f):(e)},_read:function(d){return JSON.parse(sessionStorage.getItem(d.id))},_update:function(d){return d._create(d)},_delete:function(d){return sessionStorage.removeItem(d.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){a.prototype=_.omit(a.prototype,"url","urlRoot")}());var b={hiddenUntilActivated:function(d,f){f=f||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,f||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(d){var e=this;d.on("click",function(g){e.toggle(e.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};return{LoggableMixin:c,SessionStorageModel:a,HiddenUntilActivatedViewMixin:b}});
\ No newline at end of file
+define([],function(){var c={logger:null,log:function(){if(this.logger){var d=this.logger.log;if(typeof this.logger.log==="object"){d=Function.prototype.bind.call(this.logger.log,this.logger)}return d.apply(this.logger,arguments)}return undefined}};var a=Backbone.Model.extend({initialize:function(e){this._checkEnabledSessionStorage();if(!e.id){throw new Error("SessionStorageModel requires an id in the initial attributes")}this.id=e.id;var d=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,d,e),{silent:true});this.on("change",function(){this.save()})},_checkEnabledSessionStorage:function(){try{return sessionStorage.length}catch(d){alert("Please enable cookies in your browser for this Galaxy site");return false}},sync:function(g,e,d){if(!d.silent){e.trigger("request",e,{},d)}var f;switch(g){case"create":f=this._create(e);break;case"read":f=this._read(e);break;case"update":f=this._update(e);break;case"delete":f=this._delete(e);break}if(f!==undefined||f!==null){if(d.success){d.success()}}else{if(d.error){d.error()}}return f},_create:function(d){var e=d.toJSON(),f=sessionStorage.setItem(d.id,JSON.stringify(e));return(f===null)?(f):(e)},_read:function(d){return JSON.parse(sessionStorage.getItem(d.id))},_update:function(d){return d._create(d)},_delete:function(d){return sessionStorage.removeItem(d.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){a.prototype=_.omit(a.prototype,"url","urlRoot")}());var b={hiddenUntilActivated:function(d,f){f=f||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,f||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(d){var e=this;d.on("click",function(g){e.toggle(e.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};return{LoggableMixin:c,SessionStorageModel:a,HiddenUntilActivatedViewMixin:b}});
\ No newline at end of file
diff -r a2d33a3caaa4ed28d774324e5add3c1eaed9397c -r 8217bcfd4c3c8986c4a62f93f6b17dc8b3fed55a templates/webapps/galaxy/history/history_panel.mako
--- a/templates/webapps/galaxy/history/history_panel.mako
+++ b/templates/webapps/galaxy/history/history_panel.mako
@@ -123,7 +123,7 @@
])}
<script type="text/javascript">
-var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false,
+var //debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false,
// use deferred to allow multiple callbacks (.done())
onhistoryready = jQuery.Deferred();
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix to add spacing in hda-edit deleted/hidden info boxes between added sentences
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a2d33a3caaa4/
Changeset: a2d33a3caaa4
User: carlfeberhard
Date: 2014-03-31 17:21:14
Summary: Fix to add spacing in hda-edit deleted/hidden info boxes between added sentences
Affected #: 2 files
diff -r 8752e2c14b711ad6b6bd5e0162a65a198402b480 -r a2d33a3caaa4ed28d774324e5add3c1eaed9397c static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -282,11 +282,11 @@
//TODO: this won't localize easily
$newRender.find( '.dataset-deleted-msg' ).append(
- _l( 'Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it' +
+ _l( ' Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it' +
' or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk' ));
$newRender.find( '.dataset-hidden-msg' ).append(
- _l( 'Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it' ));
+ _l( ' Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it' ));
return $newRender;
},
diff -r 8752e2c14b711ad6b6bd5e0162a65a198402b480 -r a2d33a3caaa4ed28d774324e5add3c1eaed9397c static/scripts/packed/mvc/dataset/hda-edit.js
--- a/static/scripts/packed/mvc/dataset/hda-edit.js
+++ b/static/scripts/packed/mvc/dataset/hda-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations"],function(f,b,a,e){var g=b.HDABaseView.extend({initialize:function(h){b.HDABaseView.prototype.initialize.call(this,h);this.hasUser=h.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=h.tagsEditorShown||false;this.annotationEditorShown=h.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var j=this.model.get("purged"),h=this.model.get("deleted"),i={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(h||j){i.disabled=true;if(j){i.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(h){i.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=_l("This dataset must finish uploading before it can be edited")}}i.faIcon="fa-pencil";return faIconButton(i)},_render_deleteButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this,i={title:_l("Delete"),classes:"dataset-delete",onclick:function(){h.$el.find(".icon-btn.dataset-delete").trigger("mouseout");h.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),disabled:true}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==f.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var h=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(h))){return null}if(_.isObject(h[0])){return this._render_visualizationsFrameworkButton(h)}if(!this.urls.visualization){return null}var j=this.model.get("dbkey"),n=this.urls.visualization,k={},o={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(j){o.dbkey=j}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function l(p){if(p==="trackster"){return c(n,o,j)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:n+"/"+p+"?"+$.param(o)})}}function m(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(h.length===1){i.attr("data-original-title",_l("Visualize in ")+_l(m(h[0])));i.click(l(h[0]))}else{_.each(h,function(p){k[_l(m(p))]=l(p)});make_popupmenu(i,k)}return i},_render_visualizationsFrameworkButton:function(h){if(!(this.model.hasData())||!(h&&!_.isEmpty(h))){return null}var j=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(h.length===1){var i=h[0];j.attr("data-original-title",_l("Visualize in ")+i.html);j.attr("href",i.href)}else{var k=[];_.each(h,function(l){l.func=function(m){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:l.href});m.preventDefault();return false}return true};k.push(l);return false});PopupMenu.create(j,k)}return j},_buildNewRender:function(){var h=b.HDABaseView.prototype._buildNewRender.call(this);h.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));h.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return h},_render_body_failed_metadata:function(){var i=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),h=$("<span/>").text(". "+_l("You may be able to")+" ").append(i),j=b.HDABaseView.prototype._render_body_failed_metadata.call(this);j.find(".warningmessagesmall strong").append(h);return j},_render_body_error:function(){var h=b.HDABaseView.prototype._render_body_error.call(this);h.find(".dataset-actions .left").prepend(this._render_errButton());return h},_render_body_ok:function(){var h=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return h}this.makeDbkeyEditLink(h);if(this.hasUser){h.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(h);this._renderAnnotation(h)}return h},_renderTags:function(h){var i=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:h.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true},onhide:function(){i.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(h){var i=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:h.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true},onhide:function(){i.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var h=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);i.find(".dataset-dbkey .value").replaceWith(h)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(h){this.model.undelete();return false},"click .dataset-unhide":function(h){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(h){this.model.purge();return false},toString:function(){var h=(this.model)?(this.model+""):("(no model)");return"HDAView("+h+")"}});function c(h,j,i){return function(){var k={};if(i){k["f-dbkey"]=i}$.ajax({url:h+"/list_tracks?"+$.param(k),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(l){var m=window.parent;m.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){m.Galaxy.modal.hide()},"View in saved visualization":function(){m.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:l,buttons:{Cancel:function(){m.Galaxy.modal.hide()},"Add to visualization":function(){$(m.document).find("input[name=id]:checked").each(function(){m.Galaxy.modal.hide();var n=$(this).val();j.id=n;m.Galaxy.frame.add({title:"Trackster",type:"url",content:h+"/trackster?"+$.param(j)})})}}})},"View in new visualization":function(){m.Galaxy.modal.hide();var n=h+"/trackster?"+$.param(j);m.Galaxy.frame.add({title:"Trackster",type:"url",content:n})}}})}});return false}}return{HDAEditView:g}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations"],function(f,b,a,e){var g=b.HDABaseView.extend({initialize:function(h){b.HDABaseView.prototype.initialize.call(this,h);this.hasUser=h.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=h.tagsEditorShown||false;this.annotationEditorShown=h.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var j=this.model.get("purged"),h=this.model.get("deleted"),i={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(h||j){i.disabled=true;if(j){i.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(h){i.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=_l("This dataset must finish uploading before it can be edited")}}i.faIcon="fa-pencil";return faIconButton(i)},_render_deleteButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this,i={title:_l("Delete"),classes:"dataset-delete",onclick:function(){h.$el.find(".icon-btn.dataset-delete").trigger("mouseout");h.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),disabled:true}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==f.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var h=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(h))){return null}if(_.isObject(h[0])){return this._render_visualizationsFrameworkButton(h)}if(!this.urls.visualization){return null}var j=this.model.get("dbkey"),n=this.urls.visualization,k={},o={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(j){o.dbkey=j}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function l(p){if(p==="trackster"){return c(n,o,j)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:n+"/"+p+"?"+$.param(o)})}}function m(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(h.length===1){i.attr("data-original-title",_l("Visualize in ")+_l(m(h[0])));i.click(l(h[0]))}else{_.each(h,function(p){k[_l(m(p))]=l(p)});make_popupmenu(i,k)}return i},_render_visualizationsFrameworkButton:function(h){if(!(this.model.hasData())||!(h&&!_.isEmpty(h))){return null}var j=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(h.length===1){var i=h[0];j.attr("data-original-title",_l("Visualize in ")+i.html);j.attr("href",i.href)}else{var k=[];_.each(h,function(l){l.func=function(m){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:l.href});m.preventDefault();return false}return true};k.push(l);return false});PopupMenu.create(j,k)}return j},_buildNewRender:function(){var h=b.HDABaseView.prototype._buildNewRender.call(this);h.find(".dataset-deleted-msg").append(_l(' Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));h.find(".dataset-hidden-msg").append(_l(' Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return h},_render_body_failed_metadata:function(){var i=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),h=$("<span/>").text(". "+_l("You may be able to")+" ").append(i),j=b.HDABaseView.prototype._render_body_failed_metadata.call(this);j.find(".warningmessagesmall strong").append(h);return j},_render_body_error:function(){var h=b.HDABaseView.prototype._render_body_error.call(this);h.find(".dataset-actions .left").prepend(this._render_errButton());return h},_render_body_ok:function(){var h=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return h}this.makeDbkeyEditLink(h);if(this.hasUser){h.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(h);this._renderAnnotation(h)}return h},_renderTags:function(h){var i=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:h.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true},onhide:function(){i.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(h){var i=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:h.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true},onhide:function(){i.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var h=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);i.find(".dataset-dbkey .value").replaceWith(h)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(h){this.model.undelete();return false},"click .dataset-unhide":function(h){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(h){this.model.purge();return false},toString:function(){var h=(this.model)?(this.model+""):("(no model)");return"HDAView("+h+")"}});function c(h,j,i){return function(){var k={};if(i){k["f-dbkey"]=i}$.ajax({url:h+"/list_tracks?"+$.param(k),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(l){var m=window.parent;m.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){m.Galaxy.modal.hide()},"View in saved visualization":function(){m.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:l,buttons:{Cancel:function(){m.Galaxy.modal.hide()},"Add to visualization":function(){$(m.document).find("input[name=id]:checked").each(function(){m.Galaxy.modal.hide();var n=$(this).val();j.id=n;m.Galaxy.frame.add({title:"Trackster",type:"url",content:h+"/trackster?"+$.param(j)})})}}})},"View in new visualization":function(){m.Galaxy.modal.hide();var n=h+"/trackster?"+$.param(j);m.Galaxy.frame.add({title:"Trackster",type:"url",content:n})}}})}});return false}}return{HDAEditView:g}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Eliminate unused method in the tool shed's repository controller.
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8752e2c14b71/
Changeset: 8752e2c14b71
User: greg
Date: 2014-03-31 14:00:19
Summary: Eliminate unused method in the tool shed's repository controller.
Affected #: 1 file
diff -r 3f349df2bb9cade82ea55ab4b3ed7f9ad473cdf5 -r 8752e2c14b711ad6b6bd5e0162a65a198402b480 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1907,36 +1907,6 @@
readme_files_dict=readme_files_dict,
repo_info_dict=repo_info_dict )
- @web.json
- def get_versions_of_tool( self, trans, name, owner, changeset_revision, encoded_guid ):
- #def get_versions_of_tool( self, trans, repository_id, repository_metadata, guid ):
- """
- Return the tool version lineage chain in descending order for the received guid contained
- in the repsitory_metadata.tool_versions column associated with the received changeset_revision
- whose associated repository is associated with the received name and owner.
- """
- guid = encoding_util.tool_shed_decode( encoded_guid )
- repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
- version_lineage = []
- if repository:
- repository_id = trans.security.encode_id( repository.id )
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
- repository_id,
- changeset_revision )
- if not repository_metadata:
- repo_dir = repository.repo_path( trans.app )
- repo = hg.repository( suc.get_configured_ui(), repo_dir )
- updated_changeset_revision = suc.get_next_downloadable_changeset_revision( repository,
- repo,
- changeset_revision )
- if updated_changeset_revision:
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
- repository_id,
- updated_changeset_revision )
- if repository_metadata:
- version_lineage = tool_util.get_version_lineage_for_tool( trans, repository_id, repository_metadata, guid )
- return version_lineage
-
@web.expose
def help( self, trans, **kwd ):
message = kwd.get( 'message', '' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Improvements for populating the tool panel when installing a repository containing a version of a tool alreadly loaded in the tool panel.
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3f349df2bb9c/
Changeset: 3f349df2bb9c
User: greg
Date: 2014-03-31 13:37:45
Summary: Improvements for populating the tool panel when installing a repository containing a version of a tool alreadly loaded in the tool panel.
Affected #: 1 file
diff -r b397f2fe3e7c6350de924c2557a83bebd6301f8d -r 3f349df2bb9cade82ea55ab4b3ed7f9ad473cdf5 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -63,8 +63,6 @@
from galaxy.web.form_builder import SelectField
from galaxy.model.item_attrs import Dictifiable
from galaxy.model import Workflow
-from tool_shed.util import common_util
-from tool_shed.util import encoding_util
from tool_shed.util import shed_util_common as suc
from .loader import load_tool, template_macro_params
from .wrappers import (
@@ -283,41 +281,15 @@
panel_dict[ key ] = tool
log.debug( "Loaded tool id: %s, version: %s into tool panel.." % ( tool.id, tool.version ) )
else:
- # We are in the process of installing the tool. The version lineage chain will not yet be
- # built on the Galaxy side, so we have to get it from the Tool Shed.
- tool_shed_url = suc.get_url_from_tool_shed( self.app, str( tool.tool_shed ) )
- # get_versions_of_tool( self, trans, name, owner, changeset_revision, encoded_guid )
- params = '?name=%s&owner=%s&changeset_revision=%s&encoded_guid=%s' % \
- ( str( tool.repository_name ),
- str( tool.repository_owner ),
- str( tool.installed_changeset_revision ),
- encoding_util.tool_shed_encode( tool.guid ) )
- url = suc.url_join( tool_shed_url, 'repository/get_versions_of_tool%s' % params )
- try:
- # For backward compatibility - some versions of the Tool Shed will not have the
- # get_versions_of_tool() method.
- raw_text = common_util.tool_shed_get( self.app, tool_shed_url, url )
- tool_lineage_ids = json.loads( raw_text )
- except Exception, e:
- log.exception( "Error with url\n%s\n%s" % ( str( url ), str( e ) ) )
- tool_lineage_ids = []
+ # We are in the process of installing the tool.
+ tool_version = self.__get_tool_version( tool_id )
+ tool_lineage_ids = tool_version.get_version_ids( self.app, reverse=True )
for lineage_id in tool_lineage_ids:
if lineage_id in self.tools_by_id:
loaded_version_key = 'tool_%s' % lineage_id
if loaded_version_key in panel_dict:
if not already_loaded:
already_loaded = True
- # Even though a version of the tool is loaded in the tool panel, we need to find out if it
- # is the most recent version.
- key = 'tool_%s' % tool.guid
- index = panel_dict.keys().index( loaded_version_key )
- if loaded_version_key > key:
- index = panel_dict.keys().index( loaded_version_key )
- del panel_dict[ loaded_version_key ]
- panel_dict.insert( index, key, tool )
- log.debug( "Loaded tool id: %s, version: %s into tool panel..." % ( tool.id, tool.version ) )
- inserted = True
- break
if not already_loaded:
# If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel.
panel_dict[ key ] = tool
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: When multiple versions of the same tool are loaded into the Galaxy tool panel, make sure the newest version of the tool is displayed by default in the tool version select list on the tool form when it is initially loaded.
by commits-noreply@bitbucket.org 31 Mar '14
by commits-noreply@bitbucket.org 31 Mar '14
31 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b397f2fe3e7c/
Changeset: b397f2fe3e7c
User: greg
Date: 2014-03-31 04:48:17
Summary: When multiple versions of the same tool are loaded into the Galaxy tool panel, make sure the newest version of the tool is displayed by default in the tool version select list on the tool form when it is initially loaded.
Affected #: 2 files
diff -r 8aabd0a1acf8439553970fcbd5661f2ec8b34884 -r b397f2fe3e7c6350de924c2557a83bebd6301f8d lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -265,7 +265,7 @@
inserted = True
if not inserted:
# Check the tool's installed versions.
- for lineage_id in tool.tool_version_ids:
+ for lineage_id in tool.lineage_ids:
lineage_id_key = 'tool_%s' % lineage_id
for index, integrated_panel_key in enumerate( self.integrated_tool_panel.keys() ):
if lineage_id_key == integrated_panel_key:
@@ -504,14 +504,15 @@
def get_tool_components( self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ):
"""
- Retrieve all loaded versions of a tool from the toolbox and return a select list enabling selection of a different version, the list of the tool's
- loaded versions, and the specified tool.
+ Retrieve all loaded versions of a tool from the toolbox and return a select list enabling
+ selection of a different version, the list of the tool's loaded versions, and the specified tool.
"""
toolbox = self
tool_version_select_field = None
tools = []
tool = None
- # Backwards compatibility for datasource tools that have default tool_id configured, but which are now using only GALAXY_URL.
+ # Backwards compatibility for datasource tools that have default tool_id configured, but which
+ # are now using only GALAXY_URL.
tool_ids = listify( tool_id )
for tool_id in tool_ids:
if get_loaded_tools_by_lineage:
@@ -534,11 +535,11 @@
refresh_on_change_values.append( tool.id )
select_field = SelectField( name='tool_id', refresh_on_change=True, refresh_on_change_values=refresh_on_change_values )
for option_tup in options:
- selected = set_selected and option_tup[1] == tool_id
+ selected = set_selected and option_tup[ 1 ] == tool_id
if selected:
- select_field.add_option( 'version %s' % option_tup[0], option_tup[1], selected=True )
+ select_field.add_option( 'version %s' % option_tup[ 0 ], option_tup[ 1 ], selected=True )
else:
- select_field.add_option( 'version %s' % option_tup[0], option_tup[1] )
+ select_field.add_option( 'version %s' % option_tup[ 0 ], option_tup[ 1 ] )
return select_field
def load_tool_tag_set( self, elem, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None ):
diff -r 8aabd0a1acf8439553970fcbd5661f2ec8b34884 -r b397f2fe3e7c6350de924c2557a83bebd6301f8d lib/galaxy/webapps/galaxy/controllers/tool_runner.py
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -50,14 +50,19 @@
return self.get_toolbox().get_tool_components( tool_id, tool_version, get_loaded_tools_by_lineage, set_selected )
@web.expose
- def index(self, trans, tool_id=None, from_noframe=None, **kwd):
+ def index( self, trans, tool_id=None, from_noframe=None, **kwd ):
# No tool id passed, redirect to main page
if tool_id is None:
return trans.response.send_redirect( url_for( controller="root", action="welcome" ) )
+ # When the tool form is initially loaded, the received kwd will not include a 'refresh'
+ # entry (which only is included when another option is selected in the tool_version_select_field),
+ # so the default selected option should be the most recent version of the tool. The following
+ # check will mae sure this occurs.
+ refreshed_on_change = kwd.get( 'refresh', False )
tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
- set_selected=True )
+ set_selected=refreshed_on_change )
# No tool matching the tool id, display an error (shouldn't happen)
if not tool:
log.error( "index called with tool id '%s' but no such tool exists", tool_id )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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