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commit/galaxy-central: guerler: Charts: Integrate multipanel charts
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60d37cbc6857/ Changeset: 60d37cbc6857 User: guerler Date: 2014-04-17 01:01:20 Summary: Charts: Integrate multipanel charts Affected #: 7 files diff -r 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof 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this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var 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=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),s=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),a=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:i,Icon:s,ButtonIcon:o,Input:h,Anchor:u,Message:a,Searchbox:f,Title:l,Text:r,Select:t,ButtonMenu:c}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},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:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","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/datasets/"+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:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._create_canvas("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=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()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_create_canvas:function(e){this.canvas&&this.canvas.remove(),this.$el.append($(this._template_canvas(e)));var t=this.$el.find(".canvas");e=="svg"?this.canvas=d3.select(t[0]):this.canvas=t},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r),this._create_canvas(this.chart_settings.element),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas});t.chart_settings.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e)):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_canvas:function(e){return"<"+e+' class="canvas" style="height: 100%;"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("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,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Library"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),this.table.add(h.library,"10%"),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the chartskit available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","nvd3_bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return 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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. 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a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({canvas:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._create_canvas("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_create_canvas:function(e,t){t=t||1;for(var n in this.canvas)this.canvas[n].remove(),this.canvas.slice(n,0);for(var n=0;n<t;n++){var r=$(this._template_canvas(e,parseInt(100/t)));this.$el.append(r),e=="svg"?this.canvas[n]=d3.select(r[0]):this.canvas[n]=r}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._create_canvas(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas});t.chart_settings.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e)):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_canvas:function(e,t){return"<"+e+' class="canvas" style="float: left; display: block; width:'+t+'%; height: 100%;"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("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,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Library"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),this.table.add(h.library,"10%"),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the chartskit available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","nvd3_bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bardiagram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/nvd3_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/nvd3_linewithfocus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/nvd3_piechart/config",[],function(){return{title:"Pie chart",library:"nvd3.js",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_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/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",library:"highcharts.js",element:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bardiagram/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_horizontal/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_linewithfocus/config","plugin/charts/nvd3_piechart/config","plugin/charts/nvd3_scatterplot/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/highcharts_boxplot/config"],function(e,t,n,r,i,s,o,u,a){return Backbone.Model.extend({defaults:{nvd3_bardiagram:e,nvd3_horizontal:n,nvd3_histogram:t,nvd3_line:r,nvd3_linewithfocus:i,nvd3_piechart:s,nvd3_scatterplot:o,nvd3_stackedarea:u,highcharts_boxplot:a}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$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 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js @@ -108,7 +108,7 @@ self.hc_config.series[0].data = data; // draw plot - self.options.canvas.highcharts(self.hc_config); + self.options.canvas[0].highcharts(self.hc_config); // set chart state chart.state('ok', 'Box plot drawn.'); diff -r 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 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 @@ -3,7 +3,7 @@ return { title : '', library : 'nvd3.js', - element : 'svg', + tag : 'svg', columns : { y : { title : 'Values for y-axis' @@ -213,7 +213,7 @@ value : 'false' } ] - }, + } } }; diff -r 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 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 @@ -48,8 +48,8 @@ } // parse data to canvas - self.options.canvas.datum(request_dictionary.groups) - .call(nvd3_model); + self.options.canvas[0].datum(request_dictionary.groups) + .call(nvd3_model); // refresh on window resize nv.utils.windowResize(nvd3_model.update); diff -r 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js @@ -3,7 +3,8 @@ return { title : 'Pie chart', library : 'nvd3.js', - element : 'svg', + tag : 'svg', + use_panels : true, columns : { label : { title : 'Labels', @@ -12,6 +13,101 @@ y : { title : 'Values' } + }, + + settings : { + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'select', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + + donut_ratio : { + title : 'Donut ratio', + info : 'Determine how large the donut hole will be.', + type : 'select', + init : '0.5', + data : [ + { + label : '50%', + value : '0.5' + }, + { + label : '25%', + value : '0.25' + }, + { + label : '10%', + value : '0.10' + }, + { + label : '0%', + value : '0' + } + ] + }, + + label_separator : { + type : 'separator', + title : 'Label settings' + }, + + label_type : { + title : 'Donut label', + info : 'What would you like to show for each slice?', + type : 'select', + init : 'percent', + data : [ + { + label : '-- Nothing --', + value : 'hide', + hide : 'label_outside' + }, + { + label : 'Label column', + value : 'key', + show : 'label_outside' + }, + { + label : 'Value column', + value : 'value', + show : 'label_outside' + }, + { + label : 'Percentage', + value : 'percent', + show : 'label_outside' + } + ], + }, + + label_outside : { + title : 'Show outside', + info : 'Would you like to show labels outside the donut?', + type : 'select', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + } } }; diff -r 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js @@ -18,39 +18,97 @@ this.app.datasets.request(request_dictionary, function() { // loop through data groups - for (var key in request_dictionary.groups) { + for (var group_index in request_dictionary.groups) { // get group - var group = request_dictionary.groups[key]; - - // format chart data - var pie_data = []; - for (var key in group.values) { - var value = group.values[key]; - pie_data.push ({ - y : value.y, - x : value.label - }); - } + var group = request_dictionary.groups[group_index]; + + // draw group + self._draw_group(chart, group, self.options.canvas[group_index]); } - // add graph to screen - nv.addGraph(function() { - self.chart_3d = nv.models.pieChart() - .donut(true) - .showLegend(false); + // set chart state + chart.state('ok', 'Pie chart has been drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + }, + + // draw group + _draw_group: function(chart, group, canvas) { + + // add title + var title = canvas.append('text'); + + // configure title attributes + this._fix_title(chart, canvas, title, group.key); + + // format chart data + var pie_data = []; + for (var key in group.values) { + var value = group.values[key]; + pie_data.push ({ + y : value.y, + x : value.label + }); + } + + // add graph to screen + var self = this; + nv.addGraph(function() { + // legend + var legend_visible = true; + if (chart.settings.get('show_legend') == 'false') { + legend_visible = false; + } + + // legend + var label_outside = true; + if (chart.settings.get('label_outside') == 'false') { + label_outside = false; + } + + // label type + var label_type = chart.settings.get('label_type'); + + // ratio + var donut_ratio = parseFloat(chart.settings.get('donut_ratio')) + + // create chart model + var chart_3d = nv.models.pieChart() + .donut(true) + .labelThreshold(.05) + .showLegend(legend_visible) + .labelType(label_type) + .donutRatio(donut_ratio) + .donutLabelsOutside(label_outside); + + // add data to canvas + canvas.datum(pie_data) + .call(chart_3d); + + // add resize trigger + nv.utils.windowResize(function() { + // update chart + chart_3d.update(); - self.options.canvas.datum(pie_data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - - // set chart state - chart.state('ok', 'Chart has been drawn.'); - - // unregister process - chart.deferred.done(process_id); + // fix title + self._fix_title(chart, canvas, title, group.key); }); }); + }, + + // fix title + _fix_title: function(chart, canvas, title_element, title_text) { + // update title + var width = parseInt(canvas.style('width')); + var height = parseInt(canvas.style('height')); + + // add title + title_element.attr('x', width / 2) + .attr('y', height) + .attr('text-anchor', 'middle') + .text(title_text); } }); diff -r 166660f085a51316976df1ffef426997ed393a24 -r 60d37cbc685789f0419cefdad528863b75b88a18 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 @@ -4,6 +4,10 @@ // widget return Backbone.View.extend({ + + // list of canvas elements + canvas: [], + // initialize initialize: function(app, options) { // link app @@ -81,22 +85,31 @@ }); }, - // create - _create_canvas: function(element) { - // clear canvas - if (this.canvas) { - this.canvas.remove(); + // creates n canvas elements + _create_canvas: function(tag, n) { + // check size of requested canvas elements + n = n || 1; + + // clear previous canvas elements + for (var i in this.canvas) { + this.canvas[i].remove(); + this.canvas.slice(i, 0); } - // create - this.$el.append($(this._template_canvas(element))); - - // find canvas element - var canvas_el = this.$el.find('.canvas'); - if (element == 'svg') { - this.canvas = d3.select(canvas_el[0]); - } else { - this.canvas = canvas_el; + // create requested canvas elements + for (var i = 0; i < n; i++) { + // create element + var canvas_el = $(this._template_canvas(tag, parseInt(100 / n))); + + // add to view + this.$el.append(canvas_el); + + // find canvas element + if (tag == 'svg') { + this.canvas[i] = d3.select(canvas_el[0]); + } else { + this.canvas[i] = canvas_el; + } } }, @@ -114,8 +127,17 @@ // load chart settings this.chart_settings = this.app.types.get(chart_type); - // create canvas element - this._create_canvas(this.chart_settings.element); + // read settings + var use_panels = this.chart_settings.use_panels; + + // determine number of svg/div-elements to create + var n_panels = 1; + if (use_panels) { + n_panels = chart.groups.length; + } + + // create canvas element and add to canvas list + this._create_canvas(this.chart_settings.tag, n_panels); // set chart state chart.state('wait', 'Please wait...'); @@ -247,8 +269,8 @@ }, // template svg/div element - _template_canvas: function(element) { - return '<' + element + ' class="canvas" style="height: 100%;"/>'; + _template_canvas: function(tag, width) { + return '<' + tag + ' class="canvas" style="float: left; display: block; width:' + width + '%; height: 100%;"/>'; } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: data libraries: API improvements; add datasets from history to folder; folder contents sorting; progressive rendering; new error code; new API endpoint; js model comparators; Galaxy.currUser defensive programming;
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/166660f085a5/ Changeset: 166660f085a5 User: martenson Date: 2014-04-16 22:27:13 Summary: data libraries: API improvements; add datasets from history to folder; folder contents sorting; progressive rendering; new error code; new API endpoint; js model comparators; Galaxy.currUser defensive programming; Affected #: 14 files diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -89,6 +89,10 @@ status_code = 403 err_code = error_codes.CONFIG_DOES_NOT_ALLOW +class InsufficientPermissionsException( MessageException ): + status_code = 403 + err_code = error_codes.INSUFFICIENT_PERMISSIONS + class ObjectNotFound( MessageException ): """ Accessed object was not found """ status_code = 404 diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -75,6 +75,11 @@ "message": "The configuration of this Galaxy instance does not allow that operation" }, { + "name": "INSUFFICIENT_PERMISSIONS", + "code": 403005, + "message": "You don't have proper permissions to perform the requested operation" + }, + { "name": "USER_OBJECT_NOT_FOUND", "code": 404001, "message": "No such object found." diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -7,12 +7,12 @@ from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound -from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin import logging log = logging.getLogger( __name__ ) -class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): +class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ): """ Class controls retrieval, creation and updating of folder contents. """ @@ -146,6 +146,55 @@ content_items.append( dataset ) return content_items + @expose_api + def create( self, trans, encoded_folder_id, payload, **kwd ): + """ + create( self, trans, library_id, payload, **kwd ) + * POST /api/folders/{encoded_id}/contents + create a new library file from an HDA + + :param payload: dictionary structure containing: + :type payload: dict + + * folder_id: the parent folder of the new item + * from_hda_id: (optional) the id of an accessible HDA to copy into the library + * ldda_message: (optional) the new message attribute of the LDDA created + * extended_metadata: (optional) dub-dictionary containing any extended + metadata to associate with the item + + :returns: a dictionary containing the id, name, and 'show' url of the new item + :rtype: dict + """ + class_name, encoded_folder_id_16 = self.__decode_library_content_id( trans, encoded_folder_id ) + from_hda_id, ldda_message = ( payload.pop( 'from_hda_id', None ), payload.pop( 'ldda_message', '' ) ) + if ldda_message: + ldda_message = util.sanitize_html.sanitize_html( ldda_message, 'utf-8' ) + rval = {} + try: + hda = self.get_dataset( trans, from_hda_id, check_ownership=True, check_accessible=True, check_state=True ) + folder = self.get_library_folder( trans, encoded_folder_id_16, check_accessible=True ) + + if not self.can_current_user_add_to_library_item( trans, folder ): + raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to add a dataset to a folder with id (%s)' % ( encoded_folder_id ) ) + + ldda = self.copy_hda_to_library_folder( trans, hda, folder, ldda_message=ldda_message ) + ldda_dict = ldda.to_dict() + rval = trans.security.encode_dict_ids( ldda_dict ) + + except Exception, exc: + if 'not accessible to the current user' in str( exc ): + raise exceptions.ItemAccessibilityException( 'You do not have access to the requested item' ) + else: + log.exception( exc ) + raise exceptions.InternalServerError( 'An unknown error ocurred. Please try again.' ) + return rval + + def __decode_library_content_id( self, trans, encoded_folder_id ): + if ( len( encoded_folder_id ) == 17 and encoded_folder_id.startswith( 'F' )): + return 'LibraryFolder', encoded_folder_id[1:] + else: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) + @web.expose_api def show( self, trans, id, library_id, **kwd ): """ @@ -154,15 +203,6 @@ raise exceptions.NotImplemented( 'Showing the library folder content is not implemented.' ) @web.expose_api - def create( self, trans, library_id, payload, **kwd ): - """ - POST /api/folders/{encoded_folder_id}/contents - Creates a new folder. This should be superseded by the - LibraryController. - """ - raise exceptions.NotImplemented( 'Creating the library folder content is not implemented.' ) - - @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id}/contents diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -224,26 +224,9 @@ action='download', conditions=dict( method=[ "POST", "GET" ] ) ) - webapp.mapper.connect( 'create_folder', - '/api/folders/:encoded_parent_folder_id', - controller='folders', - action='create', - conditions=dict( method=[ "POST" ] ) ) - webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) - webapp.mapper.resource( 'folder', - 'folders', - path_prefix='/api' ) - - webapp.mapper.resource( 'content', - 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ), - conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'content', 'contents', @@ -257,6 +240,38 @@ path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # ======================= + # ===== FOLDERS API ===== + # ======================= + + webapp.mapper.connect( 'add_history_datasets_to_library', + '/api/folders/:encoded_folder_id/contents', + controller='folder_contents', + action='create', + conditions=dict( method=[ "POST" ] ) ) + + webapp.mapper.connect( 'create_folder', + '/api/folders/:encoded_parent_folder_id', + controller='folders', + action='create', + conditions=dict( method=[ "POST" ] ) ) + + webapp.mapper.resource( 'folder', + 'folders', + path_prefix='/api' ) + + webapp.mapper.resource( 'content', + 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ), + conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.resource( 'job', 'jobs', path_prefix='/api' ) @@ -268,12 +283,7 @@ controller="job_files", name_prefix="job_", path_prefix='/api/jobs/:job_id', - parent_resources=dict( member_name="job", collection_name="jobs") - ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + parent_resources=dict( member_name="job", collection_name="jobs" ) ) _add_item_extended_metadata_controller( webapp, name_prefix="history_dataset_", diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -23,10 +23,13 @@ folderContainer: null, + sort: 'asc', + // event binding events: { - 'click #select-all-checkboxes' : 'selectAll', - 'click .dataset_row' : 'selectClickedRow' + 'click #select-all-checkboxes' : 'selectAll', + 'click .dataset_row' : 'selectClickedRow', + 'click .sort-folder-link' : 'sort_clicked' }, // initialize initialize : function(options){ @@ -34,12 +37,18 @@ this.options = _.defaults(this.options || {}, options); this.queue = jQuery.Deferred(); this.queue.resolve(); - + this.collection = new mod_library_model.Folder(); + this.listenTo(this.collection, 'add', this.addOne); + this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; this.folderContainer.fetch({ - success: function (folderContainer) { - that.render(); + success: function (folder_container) { + that.render(); + + var items = folder_container.get('folder').models; + that.addAll(items); + }, error: function(){ mod_toastr.error('An error occured :('); @@ -54,13 +63,13 @@ // TODO move to server // prepare nice size strings - for (var i = 0; i < this.folderContainer.attributes.folder.models.length; i++) { - var model = this.folderContainer.attributes.folder.models[i]; - if (model.get('type') === 'file'){ - contains_file = true; - model.set('readable_size', this.size_to_string(model.get('file_size'))); - } - } + // for (var i = 0; i < this.collection.models.length; i++) { + // var model = this.collection.models[i]; + // if (model.get('type') === 'file'){ + // contains_file = true; + // model.set('readable_size', this.size_to_string(model.get('file_size'))); + // } + // } // TODO move to server // find the upper id in the full path @@ -73,16 +82,16 @@ } // TODO add template when folder is empty - this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, id: this.options.id, upper_folder_id: upper_folder_id })); + this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); // this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, items: this.folderContainer.attributes.folder.models, id: this.options.id, upper_folder_id: upper_folder_id })); - if (this.folderContainer.attributes.folder.models.length > 0){ + if (this.collection.models.length > 0){ this.renderRows(); } // if (this.folderContainer.attributes.metadata.can_add_library_item === true){ - var metadata = this.folderContainer.attributes.metadata; - metadata.contains_file = contains_file; - Galaxy.libraries.folderToolbarView.configureElements(metadata); + var options = this.folderContainer.attributes.metadata; + options.contains_file = this.options.contains_file; + Galaxy.libraries.folderToolbarView.configureElements(options); // Galaxy.libraries.folderToolbarView.configureElements({ can_add_library_item: this.folderContainer.attributes.metadata.can_add_library_item, contains_file: contains_file }); // } @@ -93,92 +102,128 @@ }, renderRows: function(){ - for (var i = 0; i < this.folderContainer.attributes.folder.models.length; i++) { - var folder_item = this.folderContainer.attributes.folder.models[i]; + for (var i = 0; i < this.collection.models.length; i++) { + var folder_item = this.collection.models[i]; var rowView = new mod_library_folderrow_view.FolderRowView(folder_item); this.$el.find('#folder_list_body').append(rowView.el); } }, - // convert size to nice string - size_to_string : function (size){ - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - // return formatted string - return (Math.round(size) / 10) + unit; + addAll:function(items){ + _.each(items.reverse(), function(item) { + Galaxy.libraries.folderListView.collection.add(item); + }); + }, + + addOne: function(model){ + if (model.get('type') === 'file'){ + this.options.contains_file = true; + model.set('readable_size', this.size_to_string(model.get('file_size'))); + } + var rowView = new mod_library_folderrow_view.FolderRowView(model); + this.$el.find('#folder_list_body').prepend(rowView.el); + }, + + sort_clicked : function(event){ + event.preventDefault(); + if (this.sort === 'asc'){ + this.sortFolder('name','desc'); + this.sort = 'desc'; + } else { + this.sortFolder('name','asc'); + this.sort = 'asc'; + } + this.render(); + }, + + /** Sorts the underlying collection according to the parameters received. + Currently supports only sorting by name. */ + sortFolder: function(sort_by, order){ + if (sort_by === 'name'){ + if (order === 'asc'){ + this.collection.sortByNameAsc(); + } else if (order === 'desc'){ + this.collection.sortByNameDesc(); + } + } + }, + + // convert size to nice string + size_to_string : function (size){ + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; + that = this; + // Iterate each checkbox + $(':checkbox').each(function() { + this.checked = selected; + $row = $(this.parentElement.parentElement); + // Change color of selected/unselected + (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); + }); + // Show the tools in menu + // this.checkTools(); + }, + + // Check checkbox on row itself or row checkbox click + selectClickedRow : function (event) { + var checkbox = ''; + var $row; + var source; + if (event.target.localName === 'input'){ + checkbox = event.target; + $row = $(event.target.parentElement.parentElement); + source = 'input'; + } else if (event.target.localName === 'td') { + checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; + $row = $(event.target.parentElement); + source = 'td'; + } + if (checkbox.checked){ + if (source==='td'){ + checkbox.checked = ''; + this.makeWhiteRow($row); + } else if (source==='input') { + this.makeDarkRow($row); + } + } else { + if (source==='td'){ + checkbox.checked = 'selected'; + this.makeDarkRow($row); + } else if (source==='input') { + this.makeWhiteRow($row); + } + } }, - // select all datasets - selectAll : function (event) { - var selected = event.target.checked; - that = this; - // Iterate each checkbox - $(':checkbox').each(function() { - this.checked = selected; - $row = $(this.parentElement.parentElement); - // Change color of selected/unselected - (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); - }); - // Show the tools in menu - // this.checkTools(); - }, + makeDarkRow: function($row){ + $row.removeClass('light'); + $row.find('a').removeClass('light'); + $row.addClass('dark'); + $row.find('a').addClass('dark'); + $row.find('span').removeClass('fa-file-o'); + $row.find('span').addClass('fa-file'); + }, - // Check checkbox on row itself or row checkbox click - selectClickedRow : function (event) { - var checkbox = ''; - var $row; - var source; - if (event.target.localName === 'input'){ - checkbox = event.target; - $row = $(event.target.parentElement.parentElement); - source = 'input'; - } else if (event.target.localName === 'td') { - checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; - $row = $(event.target.parentElement); - source = 'td'; - } - - if (checkbox.checked){ - if (source==='td'){ - checkbox.checked = ''; - this.makeWhiteRow($row); - } else if (source==='input') { - this.makeDarkRow($row); - } - } else { - if (source==='td'){ - checkbox.checked = 'selected'; - this.makeDarkRow($row); - } else if (source==='input') { - this.makeWhiteRow($row); - } - } - // this.checkTools(); - }, - - makeDarkRow: function($row){ - $row.removeClass('light'); - $row.find('a').removeClass('light'); - $row.addClass('dark'); - $row.find('a').addClass('dark'); - $row.find('span').removeClass('fa-file-o'); - $row.find('span').addClass('fa-file'); - - }, - - makeWhiteRow: function($row){ - $row.removeClass('dark'); - $row.find('a').removeClass('dark'); - $row.addClass('light'); - $row.find('a').addClass('light'); - $row.find('span').addClass('fa-file-o'); - $row.find('span').removeClass('fa-file'); - }, + makeWhiteRow: function($row){ + $row.removeClass('dark'); + $row.find('a').removeClass('dark'); + $row.addClass('light'); + $row.find('a').addClass('light'); + $row.find('span').addClass('fa-file-o'); + $row.find('span').removeClass('fa-file'); + }, // MMMMMMMMMMMMMMMMMM // === TEMPLATES ==== @@ -205,20 +250,20 @@ tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); tmpl_array.push(' <th>data type</th>'); tmpl_array.push(' <th>size</th>'); tmpl_array.push(' <th>time updated (UTC)</th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody id="folder_list_body">'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' </tr>'); + // tmpl_array.push(' <tr>'); + // tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); + // tmpl_array.push(' <td></td>'); + // tmpl_array.push(' <td></td>'); + // tmpl_array.push(' <td></td>'); + // tmpl_array.push(' <td></td>'); + // tmpl_array.push(' <td></td>'); + // tmpl_array.push(' </tr>'); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -1,4 +1,3 @@ -// dependencies define([ "galaxy.masthead", "utils/utils", @@ -36,7 +35,10 @@ render: function(options){ this.options = _.extend(this.options, options); var toolbar_template = this.templateToolBar(); - var is_admin = Galaxy.currUser.isAdmin(); + var is_admin = false; + if (Galaxy.currUser){ + is_admin = Galaxy.currUser.isAdmin(); + } this.$el.html(toolbar_template({id: this.options.id, admin_user: is_admin})); }, @@ -87,9 +89,8 @@ success: function (folder) { self.modal.hide(); mod_toastr.success('Folder created'); - folder.set({'type' : 'folder'}) - Galaxy.libraries.folderListView.folderContainer.attributes.folder.add(folder); - Galaxy.libraries.folderListView.render({id: current_folder_id}); + folder.set({'type' : 'folder'}); + Galaxy.libraries.folderListView.collection.add(folder); }, error: function(){ mod_toastr.error('An error occured :('); @@ -163,8 +164,8 @@ dataset_ids.push(this.parentElement.parentElement.id); } }); - var progress_bar_tmpl = this.templateProgressBar(); - $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl({ history_name : history_name })); + var progress_bar_tmpl = this.templateImportIntoHistoryProgressBar(); + this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ history_name : history_name })); // init the progress bar var progressStep = 100 / dataset_ids.length; @@ -254,15 +255,20 @@ title : 'Add datasets from history to ' + self.options.folder_name, body : template_modal({histories: self.histories.models}), buttons : { - 'Add' : function() {self.addFiles();}, + 'Add' : function() {self.addAllDatasetsFromHistory();}, 'Close' : function() {Galaxy.modal.hide();} } }); - self.fetchAndDisplayHistoryContents(self.histories.models[0].id); - $( "#dataset_add_bulk" ).change(function(event) { - self.fetchAndDisplayHistoryContents(event.target.value); - }); - + + // user should always have a history, even anonymous user + if (self.histories.models.length > 0){ + self.fetchAndDisplayHistoryContents(self.histories.models[0].id); + $( "#dataset_add_bulk" ).change(function(event) { + self.fetchAndDisplayHistoryContents(event.target.value); + }); + } else { + mod_toastr.error('Unable to retrieve histories. Please report this error.'); + } }); }, @@ -282,8 +288,54 @@ }); }, - addFiles: function(){ - alert('adding files'); + // add all selected datasets from history into current folder + addAllDatasetsFromHistory : function (){ + //disable the button to prevent multiple submission + this.modal.disableButton('Add'); + + var history_dataset_ids = []; + this.modal.$el.find('#selected_history_content').find(':checked').each(function(){ + var hid = $(this.parentElement).data('id'); + if (hid) { + history_dataset_ids.push(hid); + } + }); + var folder_name = this.options.folder_name; + var progress_bar_tmpl = this.templateAddingDatasetsProgressBar(); + this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : folder_name })); + + // init the progress bar + this.progressStep = 100 / history_dataset_ids.length; + this.progress = 0; + + // prepare the dataset items to be added + var hdas_to_add = []; + for (var i = history_dataset_ids.length - 1; i >= 0; i--) { + history_dataset_id = history_dataset_ids[i]; + var folder_item = new mod_library_model.Item(); + var self = this; + folder_item.url = '/api/folders/' + this.options.id + '/contents'; + folder_item.set({'from_hda_id':history_dataset_id}); + hdas_to_add.push(folder_item); + } + // call the recursive function to call ajax one after each other (request FIFO queue) + this.chainCallAddingHdas(hdas_to_add); + }, + + chainCallAddingHdas: function(hdas_set){ + var self = this; + this.added_hdas = new mod_library_model.Folder(); + var popped_item = hdas_set.pop(); + if (typeof popped_item === "undefined") { + mod_toastr.success('Selected datasets from history imported'); + this.modal.hide(); + return this.added_hdas; + } + var promise = $.when(popped_item.save({from_hda_id: popped_item.get('from_hda_id')})).done(function(a1){ + Galaxy.libraries.folderListView.collection.add(a1); + self.updateProgress(); + self.chainCallAddingHdas(hdas_set); + }); }, templateToolBar: function(){ @@ -345,7 +397,7 @@ return _.template(tmpl_array.join('')); }, - templateProgressBar : function (){ + templateImportIntoHistoryProgressBar : function (){ var tmpl_array = []; tmpl_array.push('<div class="import_text">'); @@ -361,6 +413,22 @@ return _.template(tmpl_array.join('')); }, + templateAddingDatasetsProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return _.template(tmpl_array.join('')); + }, + templateAddFilesInModal : function (){ var tmpl_array = []; diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -1,4 +1,3 @@ -// dependencies define([ "galaxy.masthead", "mvc/base-mvc", @@ -13,7 +12,6 @@ mod_library_model, mod_library_libraryrow_view) { -// galaxy library view var LibraryListView = Backbone.View.extend({ el: '#libraries_element', @@ -23,6 +21,7 @@ modal: null, + // collection of {Item}s collection: null, // map of library model ids to library views = cache @@ -115,21 +114,10 @@ sortLibraries: function(sort_by, order){ if (sort_by === 'name'){ if (order === 'asc'){ - // this.collection.sort_order = 'asc'; - this.collection.comparator = function(libraryA, libraryB){ - if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) {return 1;} // after - if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) {return -1;} // before - return 0; // equal - }; + this.collection.sortByNameAsc(); } else if (order === 'desc'){ - // this.collection.sort_order = 'desc'; - this.collection.comparator = function(libraryA, libraryB){ - if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) {return -1;} // before - if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) {return 1;} // after - return 0; // equal - }; + this.collection.sortByNameDesc(); } - this.collection.sort(); } }, diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 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 @@ -1,4 +1,3 @@ -// dependencies define([ "galaxy.masthead", "utils/utils", @@ -23,10 +22,16 @@ render: function(){ var toolbar_template = this.templateToolBar(); - var is_admin = Galaxy.currUser.isAdmin(); - var is_anonym = Galaxy.currUser.isAnonymous(); + var is_admin = false; + var is_anonym = false; + if (Galaxy.currUser){ + is_admin = Galaxy.currUser.isAdmin(); + is_anonym = Galaxy.currUser.isAnonymous(); + } else { + is_anonym = true; + } this.$el.html(toolbar_template({admin_user: is_admin, anon_user: is_anonym})); - if (Galaxy.currUser.isAdmin() === true){ + if (is_admin){ this.$el.find('#include_deleted_chk')[0].checked = Galaxy.libraries.preferences.get('with_deleted'); } }, diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -1,13 +1,13 @@ -// dependencies define([], function() { - // LIBRARY +// ============================================================================ +// LIBRARY RELATED MODELS + var Library = Backbone.Model.extend({ urlRoot: '/api/libraries/', - /** based on show_deleted - * would this lib show in the list of lib's? - * @param {Boolean} show_deleted are we showing deleted libraries? + /** based on show_deleted would this lib show in the list of lib's? + * @param {Boolean} show_deleted are we including deleted libraries? */ isVisible : function(show_deleted){ var isVisible = true; @@ -18,12 +18,6 @@ } }); - // FOLDER AS MODEL - var FolderAsModel = Backbone.Model.extend({ - urlRoot: '/api/folders' - }); - - // LIBRARIES var Libraries = Backbone.Collection.extend({ url: '/api/libraries', @@ -38,31 +32,119 @@ }, /** Get every 'shown' library in this collection based on deleted filter - * @param {Boolean} show_deleted are we showing deleted libraries? + * @param {Boolean} show_deleted are we including deleted libraries? * @returns array of library models */ getVisible : function(show_deleted, filters){ filters = filters || []; - // always filter by show deleted first var filteredLibraries = new Libraries( this.filter( function( item ){ return item.isVisible(show_deleted); })); return filteredLibraries; + }, + + /** Sort collection by library name (ascending) and return the sorted + * collection + */ + sortByNameAsc: function(){ + this.comparator = function(libraryA, libraryB){ + if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) { + return 1; // after + } + if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) { + return -1; // before + } + return 0; // equal + }; + this.sort(); + return this; + }, + + /** Sort collection by library name (descending) and return the sorted + * collection + */ + sortByNameDesc: function(){ + this.comparator = function(libraryA, libraryB){ + if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) { + return -1; // before + } + if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) { + return 1; // after + } + return 0; // equal + }; + this.sort(); + return this; } + }); - // ITEM +// ============================================================================ +// FOLDER RELATED MODELS + var Item = Backbone.Model.extend({ urlRoot : '/api/libraries/datasets' }); - // FOLDER AS COLLECTION - var Folder = Backbone.Collection.extend({ - model: Item + var FolderAsModel = Backbone.Model.extend({ + urlRoot: '/api/folders' }); - // CONTAINER for folder contents (folders, items and metadata). + var Folder = Backbone.Collection.extend({ + model: Item, + + /** Sort collection by item name (ascending) and return the sorted + * collection. Folders go before datasets. + */ + sortByNameAsc: function(){ + this.comparator = function(itemA, itemB){ + if (itemA.get('type') === itemB.get('type')){ + if (itemA.get('name').toLowerCase() > itemB.get('name').toLowerCase()) { + return 1; // after + } + if (itemB.get('name').toLowerCase() > itemA.get('name').toLowerCase()) { + return -1; // before + } + return 0; // equal + } else { + if (itemA.get('type') === 'folder'){ + return -1; // folder is always before dataset + } else { + return 1; + } + } + }; + this.sort(); + return this; + }, + + /** Sort collection by item name (descending) and return the sorted + * collection. Folders go before datasets. + */ + sortByNameDesc: function(){ + this.comparator = function(itemA, itemB){ + if (itemA.get('type') === itemB.get('type')){ + if (itemA.get('name').toLowerCase() > itemB.get('name').toLowerCase()) { + return -1; // after + } + if (itemB.get('name').toLowerCase() > itemA.get('name').toLowerCase()) { + return 1; // before + } + return 0; // equal + } else { + if (itemA.get('type') === 'folder'){ + return -1; // folder is always before dataset + } else { + return 1; + } + } + }; + this.sort(); + return this; + } + }); + var FolderContainer = Backbone.Model.extend({ defaults : { folder : new Folder(), @@ -77,12 +159,15 @@ } }); - // HISTORY ITEM + +// ============================================================================ +// HISTORY RELATED MODELS +// TODO UNITE + var HistoryItem = Backbone.Model.extend({ urlRoot : '/api/histories/' }); - // HISTORY CONTENTS var HistoryContents = Backbone.Collection.extend({ urlRoot : '/api/histories/', initialize: function(options){ @@ -94,18 +179,15 @@ model : HistoryItem }); - // HISTORY var GalaxyHistory = Backbone.Model.extend({ urlRoot : '/api/histories/' }); - // HISTORIES var GalaxyHistories = Backbone.Collection.extend({ url : '/api/histories', model : GalaxyHistory }); -// return return { Library: Library, FolderAsModel : FolderAsModel, diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",progress:0,progressStep:1,modal:null,folderContainer:null,events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow"},initialize:function(g){var h=this;this.options=_.defaults(this.options||{},g);this.queue=jQuery.Deferred();this.queue.resolve();this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(i){h.render()},error:function(){f.error("An error occured :(")}})},render:function(h){this.options=_.defaults(this.options||{},h);var l=this.templateFolder();var m=false;for(var k=0;k<this.folderContainer.attributes.folder.models.length;k++){var g=this.folderContainer.attributes.folder.models[k];if(g.get("type")==="file"){m=true;g.set("readable_size",this.size_to_string(g.get("file_size")))}}var n=this.folderContainer.attributes.metadata.full_path;var o;if(n.length===1){o=0}else{o=n[n.length-2][0]}this.$el.html(l({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:o}));if(this.folderContainer.attributes.folder.models.length>0){this.renderRows()}var j=this.folderContainer.attributes.metadata;j.contains_file=m;Galaxy.libraries.folderToolbarView.configureElements(j);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(){for(var j=0;j<this.folderContainer.attributes.folder.models.length;j++){var h=this.folderContainer.attributes.folder.models[j];var g=new a.FolderRowView(h);this.$el.find("#folder_list_body").append(g.el)}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);(g)?that.makeDarkRow($row):that.makeWhiteRow($row)})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(" <th>name</th>");g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(" <tr>");g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){var h=this;this.options=_.defaults(this.options||{},g);this.queue=jQuery.Deferred();this.queue.resolve();this.collection=new d.Folder();this.listenTo(this.collection,"add",this.addOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(i){h.render();var j=i.get("folder").models;h.addAll(j)},error:function(){f.error("An error occured :(")}})},render:function(g){this.options=_.defaults(this.options||{},g);var h=this.templateFolder();var i=false;var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));if(this.collection.models.length>0){this.renderRows()}var g=this.folderContainer.attributes.metadata;g.contains_file=this.options.contains_file;Galaxy.libraries.folderToolbarView.configureElements(g);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(){for(var j=0;j<this.collection.models.length;j++){var h=this.collection.models[j];var g=new a.FolderRowView(h);this.$el.find("#folder_list_body").append(g.el)}},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)})},addOne:function(h){if(h.get("type")==="file"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#folder_list_body").prepend(g.el)},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){this.collection.sortByNameAsc()}else{if(g==="desc"){this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);(g)?that.makeDarkRow($row):that.makeWhiteRow($row)})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-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({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal"},defaults:{can_add_library_item:false,contains_file:false},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=Galaxy.currUser.isAdmin();this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var h=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;var g=this;h.save(f,{success:function(i){g.modal.hide();e.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.folderContainer.attributes.folder.add(i);Galaxy.libraries.folderListView.render({id:current_folder_id})},error:function(){e.error("An error occured :(")}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(){}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var h=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateProgressBar();$(this.modal.elMain).find(".modal-body").html(n({history_name:m}));var j=100/o.length;this.initProgress(j);var f=[];for(var g=o.length-1;g>=0;g--){library_dataset_id=o[g];var k=new c.HistoryItem();var l=this;k.url=k.urlRoot+h+"/contents";k.content=library_dataset_id;k.source="library";f.push(k)}this.chainCall(f)},chainCall:function(g){var f=this;var h=g.pop();if(typeof h==="undefined"){e.success("All datasets imported");this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source})).done(function(j){f.updateProgress();f.chainCall(g)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addFiles()},Close:function(){Galaxy.modal.hide()}}});f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();e.success("history contents fetched");f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("history contents fetch failed")}})},addFiles:function(){alert("adding files")},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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_folder_toolbar" >');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView: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({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal"},defaults:{can_add_library_item:false,contains_file:false},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var h=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;var g=this;h.save(f,{success:function(i){g.modal.hide();e.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(){e.error("An error occured :(")}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(){}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var h=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var j=100/o.length;this.initProgress(j);var f=[];for(var g=o.length-1;g>=0;g--){library_dataset_id=o[g];var k=new c.HistoryItem();var l=this;k.url=k.urlRoot+h+"/contents";k.content=library_dataset_id;k.source="library";f.push(k)}this.chainCall(f)},chainCall:function(g){var f=this;var h=g.pop();if(typeof h==="undefined"){e.success("All datasets imported");this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source})).done(function(j){f.updateProgress();f.chainCall(g)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("Unable to retrieve histories. Please report this error.")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();e.success("history contents fetched");f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("history contents fetch failed")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var m=this.options.folder_name;var l=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(l({folder_name:m}));this.progressStep=100/f.length;this.progress=0;var k=[];for(var j=f.length-1;j>=0;j--){history_dataset_id=f[j];var h=new c.Item();var g=this;h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.chainCallAddingHdas(k)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){e.success("Selected datasets from history imported");this.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")})).done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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_folder_toolbar" >');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(j){h.render()},error:function(k,j){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.sortLibraries("name","desc");Galaxy.libraries.preferences.set({sort_order:"desc"})}else{this.sortLibraries("name","asc");Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(i,h){if(i==="name"){if(h==="asc"){this.collection.comparator=function(k,j){if(k.get("name").toLowerCase()>j.get("name").toLowerCase()){return 1}if(j.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}return 0}}else{if(h==="desc"){this.collection.comparator=function(k,j){if(k.get("name").toLowerCase()>j.get("name").toLowerCase()){return -1}if(j.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(j){h.render()},error:function(k,j){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.sortLibraries("name","desc");Galaxy.libraries.preferences.set({sort_order:"desc"})}else{this.sortLibraries("name","asc");Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(i,h){if(i==="name"){if(h==="asc"){this.collection.sortByNameAsc()}else{if(h==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 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,c,d,b){var e=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 h=this.templateToolBar();var g=Galaxy.currUser.isAdmin();var f=Galaxy.currUser.isAnonymous();this.$el.html(h({admin_user:g,anon_user:f}));if(Galaxy.currUser.isAdmin()===true){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');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{LibraryToolbarView:e}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,c,d,b){var e=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 h=this.templateToolBar();var g=false;var f=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}else{f=true}this.$el.html(h({admin_user:g,anon_user:f}));if(g){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');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{LibraryToolbarView:e}}); \ No newline at end of file diff -r ed5f15df397e839a285b77797fcfc0ebcdef90ab -r 166660f085a51316976df1ffef426997ed393a24 static/scripts/packed/mvc/library/library-model.js --- a/static/scripts/packed/mvc/library/library-model.js +++ b/static/scripts/packed/mvc/library/library-model.js @@ -1,1 +1,1 @@ -define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(l){var k=true;if((!show_delete)&&(this.get("deleted"))){k=false}return k}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(k){k=k||{}},getVisible:function(l,m){m=m||[];var k=new i(this.filter(function(n){return n.isVisible(l)}));return k}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:g});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(k){this.get("folder").reset(k.folder_contents);return k}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(k){this.id=k.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file +define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(l){var k=true;if((!show_delete)&&(this.get("deleted"))){k=false}return k}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(k){k=k||{}},getVisible:function(l,m){m=m||[];var k=new i(this.filter(function(n){return n.isVisible(l)}));return k},sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(k){this.get("folder").reset(k.folder_contents);return k}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(k){this.id=k.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: davebgx: Fix certain failing functional tests.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ed5f15df397e/ Changeset: ed5f15df397e User: davebgx Date: 2014-04-16 22:13:11 Summary: Fix certain failing functional tests. Affected #: 3 files diff -r aafe686858916d0191a29c9bd7252525769cea21 -r ed5f15df397e839a285b77797fcfc0ebcdef90ab test-data/users/test1(a)bx.psu.edu/1.fasta --- /dev/null +++ b/test-data/users/test1(a)bx.psu.edu/1.fasta @@ -0,0 +1,2 @@ +>hg17 +gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAGGGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAGGACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAcccccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC----------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTACCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCCGAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAGCAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGCCGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGGCATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTCCTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATCCCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAGCTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGATTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCAGGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATTGGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGACATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCCTGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAGTAGAGGTGGGGGGAAACAAGTGTCAGGAAGA--------------------------------------------CTCAAA---------ATCTTC--------------------------------------------------------------CAGAGAAATTGT-----GCAGGGTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATGAGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAACTTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTATAGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACACTCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACAGTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAGG----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAGAGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GTGCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGGTGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGATTGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAATGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGGCAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCCCAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCCTCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAATATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGACAGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGTCTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAGGAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGCACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCATCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCCTTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGCTTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTGACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTGTTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATTTCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGGG-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---GGGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCCAGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGATGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCACATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCATTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCAAAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTTACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagatatttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttctgagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaattgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaaggcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaaccccatctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagctacttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgagccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacacacacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-tatctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCTGTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTGGTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTGTGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTGAATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGAAAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCCTGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCTCACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTCTGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAATGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCCACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAGGAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGTAGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgtgtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCCTACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTCTACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttggcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagttcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTTTGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGTTGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAACTTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGAGTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCAAATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT-------CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTGGG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAAGAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCATCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTTGTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAGGGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAACTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGCAGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTATATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatcttttttggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtgatcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcccaagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta--ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggctcaagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacacccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTTCTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GCCAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AGGGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC---CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCTCCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC--------TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAATGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACAGCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACAGCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGACTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGGACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAGTTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TGCTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGATTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCCACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctctcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatctcctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gcattggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcagccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaaaactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATAGCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACCCAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaatgcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatacaaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaaggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcctatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccagctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgagccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaagaaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggaggatgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaacactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaataaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGCACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAATCAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATCCCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTGGCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATTATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtggtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGAATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTTCTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTAATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtttggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtctctcacacacacccagcacaagtccaag-------------------------accagcatggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagttgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccatatctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacgacaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttagtcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatggccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaagatattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgtgtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GATTCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATAGGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAGCTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTGGTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATTTGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGGGGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTGGAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCACTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTAACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGGAAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAAATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGGA---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc--------------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctgagccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAACATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCCTACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAATATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATTGGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtctttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccatatttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgccttccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcccattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgttgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcagtaagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAGTGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATGGGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACACCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagatagatatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatgcagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AGCATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAGCTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCTAAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGATGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTGGTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCTGTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCACTGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctgaatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTCTGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG--------------------------------------------------------TTCTAATTCTAAACCACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggctgggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcattcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaataataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggctgagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgccaccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaataaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttaggaggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggcaagacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGATTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCGATTAGCTGAGC----------CACATGCAGGCACAG------------------------CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCCTCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCTTG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------CTCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tgtagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccctttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtcttttctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaattaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaagttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA diff -r aafe686858916d0191a29c9bd7252525769cea21 -r ed5f15df397e839a285b77797fcfc0ebcdef90ab test-data/users/test3(a)bx.psu.edu/run1/2.fasta --- /dev/null +++ b/test-data/users/test3(a)bx.psu.edu/run1/2.fasta @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt +tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac +cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg +aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg +gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt +tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac +ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt +ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt +tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa +aacaattcta atggtcaaaa a diff -r aafe686858916d0191a29c9bd7252525769cea21 -r ed5f15df397e839a285b77797fcfc0ebcdef90ab test/functional/test_library_features.py --- a/test/functional/test_library_features.py +++ b/test/functional/test_library_features.py @@ -2,8 +2,8 @@ from base.test_db_util import * -# TODO: Functional tests start failing at 070, fix or eliminate rest of tests. class TestLibraryFeatures( TwillTestCase ): + def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -34,6 +34,7 @@ assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' global admin_user_private_role admin_user_private_role = get_private_role( admin_user ) + def test_005_create_libraries( self ): """Testing creating libraries used in this script, then renaming one of them""" # Logged in as admin_user @@ -72,6 +73,7 @@ new_description='library1 description', new_synopsis='library1 synopsis' ) refresh( library1 ) + def test_030_add_folder_to_library1( self ): """Testing adding a folder to a library1""" # logged in as admin_user @@ -89,6 +91,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ folder1.name, folder1.description ] ) + def test_035_add_subfolder_to_folder( self ): """Testing adding a folder to a folder""" # logged in as admin_user @@ -105,6 +108,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ subfolder1.name, subfolder1.description ] ) + def test_040_add_2nd_folder_to_library1( self ): """Testing adding a 2nd folder to a library1""" # logged in as admin_user @@ -121,6 +125,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ folder2.name, folder2.description ] ) + def test_045_add_public_dataset_to_folder2( self ): """Testing adding a public dataset to folder2""" # Logged in as admin_user @@ -140,6 +145,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) + def test_050_add_2nd_public_dataset_to_folder2( self ): """Testing adding a 2nd public dataset folder2""" # Logged in as admin_user @@ -159,6 +165,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ ldda3.name, ldda3.message, 'bed' ] ) + def test_055_copy_dataset_from_history_to_subfolder( self ): """Testing copying a dataset from the current history to a subfolder""" # logged in as admin_user @@ -179,6 +186,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ ldda4.name, ldda4.message, 'bed' ] ) + def test_060_editing_dataset_attribute_info( self ): """Testing editing a library dataset's attribute information""" # logged in as admin_user @@ -193,6 +201,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_displayed=[ new_ldda_name, ldda4.message ] ) + def test_065_uploading_new_dataset_version( self ): """Testing uploading a new version of a library dataset""" # logged in as admin_user @@ -227,6 +236,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_not_displayed=[ ldda4.name, ldda4.message ] ) + def test_070_upload_directory_of_files_from_libraries_view( self ): """Testing uploading a directory of files to a root folder from the Data Libraries view""" # logged in as admin_user @@ -269,6 +279,7 @@ server_dir='run1', ldda_message=ldda_message, strings_displayed=[ 'Upload a directory of files', '<option>None</option>' ] ) + def test_075_download_archive_of_library_files( self ): """Testing downloading an archive of files from library1""" # logged in as regular_user3 @@ -292,6 +303,7 @@ format=format ) self.check_archive_contents( archive, ( ldda1, ldda2 ) ) os.remove( archive ) + def test_080_check_libraries_for_uploaded_directories_of_files( self ): """Testing the results of uploading directories of files to library1""" # We'll make sure the directories of files were uploaded in test_070... above. @@ -306,6 +318,7 @@ self.browse_library( 'library', self.security.encode_id( library1.id ), strings_displayed=[ 'fasta', ldda_message, '2.fasta' ] ) + def test_085_mark_ldda2_deleted( self ): """Testing marking ldda2 as deleted""" # Logged in as admin_user @@ -317,6 +330,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_not_displayed=[ ldda2.name, ldda2.message ] ) + def test_090_display_and_hide_deleted_ldda2( self ): """Testing displaying and hiding a deleted ldda2""" # Logged in as admin_user @@ -327,6 +341,7 @@ self.browse_library( 'library_admin', self.security.encode_id( library1.id ), strings_not_displayed=[ ldda2.name, ldda2.message ] ) + def test_095_mark_folder2_deleted( self ): """Testing marking folder2 as deleted""" # Logged in as admin_user @@ -338,6 +353,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), strings_not_displayed=[ folder2.name ] ) + def test_100_mark_folder_undeleted( self ): """Testing marking a library folder as undeleted""" # Logged in as admin_user @@ -352,6 +368,7 @@ library_id=self.security.encode_id( library1.id ), strings_displayed=[ folder2.name ], strings_not_displayed=[ ldda2.name ] ) + def test_105_mark_library_deleted( self ): """Testing marking a library as deleted""" # Logged in as admin_user @@ -368,6 +385,7 @@ item_type='library' ) self.browse_libraries_admin( strings_not_displayed=[ library1.name ] ) self.browse_libraries_admin( deleted=True, strings_displayed=[ library1.name ] ) + def test_110_mark_library_undeleted( self ): """Testing marking a library as undeleted""" # Logged in as admin_user @@ -381,6 +399,7 @@ library_id=self.security.encode_id( library1.id ), strings_displayed=[ library1.name ], strings_not_displayed=[ folder2.name ] ) + def test_115_purge_library( self ): """Testing purging a library""" # Logged in as admin_user @@ -394,6 +413,7 @@ refresh( library1 ) if not ( library1.deleted and library1.purged ): raise AssertionError( 'The library id %s named "%s" has not been marked as deleted and purged.' % ( str( library1.id ), library1.name ) ) + def check_folder( library_folder ): for folder in library_folder.folders: refresh( folder ) @@ -421,6 +441,7 @@ raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \ ( str( library_dataset.id ), library_dataset.name ) ) check_folder( library1.root_folder ) + def test_120_populate_public_library2( self ): """Testing library datasets within a library""" # Logged in as admin_user @@ -500,6 +521,7 @@ global ldda7 ldda7 = get_latest_ldda_by_name( filename ) assert ldda7 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda7 from the database' + def test_125_move_dataset_within_library2( self ): """Testing moving a dataset within library2""" # Logged in as admin_user @@ -513,6 +535,7 @@ strings_displayed=[ 'Move data library items', '3.bed' ], strings_displayed_after_submit=[ '1 dataset moved to folder (Three) within data library (library2)' ] ) + def test_130_move_folder_to_another_library( self ): """Testing moving a folder to another library""" # Logged in as admin_user @@ -536,6 +559,7 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library3.id ), strings_displayed=[ folder5.name, folder5.description, ldda7.name ] ) + def test_135_upload_unsorted_bam_to_library_using_file_path_with_link_to_file( self ): """Test uploading 3unsorted.bam, using filesystem_paths option in combination with link_to_files""" filename = '3unsorted.bam' @@ -555,6 +579,7 @@ folder_id=self.security.encode_id( library2.root_folder.id ), ldda_id=self.security.encode_id( ldda8.id ), strings_displayed=[ 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be' ] ) + def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c05752549163/ Changeset: c05752549163 Branch: stable User: dan Date: 2014-04-16 19:28:22 Summary: Fix for bug reporting in Chrome (webkit), due to it not properly handling forms with disabled submit buttons. Affected #: 1 file diff -r aab39d3344e2fbe83c209f33d7e69fea2350709d -r c05752549163e2b3b6aeddbab8019af06443c461 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -39,7 +39,8 @@ hiddenInput.name = button.name; hiddenInput.value = button.value; form.appendChild( hiddenInput ); - return true; + form.submit(); + return false; } return false; } https://bitbucket.org/galaxy/galaxy-central/commits/aafe68685891/ Changeset: aafe68685891 User: dan Date: 2014-04-16 19:31:00 Summary: merge stable Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for bug reporting in Chrome (webkit), due to it not properly handling forms with disabled submit buttons.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d8ab92940fb/ Changeset: 2d8ab92940fb User: dan Date: 2014-04-16 19:28:22 Summary: Fix for bug reporting in Chrome (webkit), due to it not properly handling forms with disabled submit buttons. Affected #: 1 file diff -r bd1abde45a4132a9d8297a76731245062be14440 -r 2d8ab92940fb7f7ee42b8a7478fd9f4406d401d3 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -39,7 +39,8 @@ hiddenInput.name = button.name; hiddenInput.value = button.value; form.appendChild( hiddenInput ); - return true; + form.submit(); + return false; } return false; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aab39d3344e2/ Changeset: aab39d3344e2 Branch: stable User: dan Date: 2014-04-16 16:50:23 Summary: Manually graft IGB updates to stable, since the old display applications now no longer work properly. Affected #: 8 files diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -26,6 +26,7 @@ </datatype><datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"><converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /></datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> @@ -98,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -1,58 +1,14 @@ <display id="igb_bam" version="0.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bam_file.dbkey}&feature_…</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - </link> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${bam_file.dbkey}&feature_url…</url> + <param type="data" name="bam_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bam_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" strip_https="True" /> + <param type="data" name="bam_file" url="${niceName}.bam" strip_https="True" /> + </link> - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/" /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument> - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${thenicename}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -1,58 +1,14 @@ <display id="igb_bb" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bigbed_file.dbkey}&loadr…</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${bigbed_file.dbkey}&loadresi…</url><param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigbed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigbed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/" /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument> - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> + <param type="data" name="bigbed_file" url="${niceName}.bigbed" strip_https="True" /></link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -1,73 +1,17 @@ <display id="igb_bed" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bed_file.dbkey}&${positi…</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bed_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bed_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bed_file" url="${niceName}.bed" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${bed_file.dbkey}&loadresidue… </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/" /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument> - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bed_file.dbkey}&${position}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link> + </link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bedgraph.xml --- /dev/null +++ b/display_applications/igb/bedgraph.xml @@ -0,0 +1,17 @@ +<display id="igb_bedgraph" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bedgraph_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bedgraph_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadre… + </param> + </link> +</display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -1,14 +1,14 @@ <display id="igb_bigwig" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bigwig_file.dbkey}&loadr…</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${bigwig_file.dbkey}&loadresi…</url><param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigwig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> + <param type="data" name="bigwig_file" url="${niceName}.bigwig" strip_https="True" /></link> - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigwig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/" /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument> - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -1,14 +1,14 @@ <display id="igb_wig" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${wig_file.dbkey}&${positi…</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${wig_file.dbkey}&${position}…</url><param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$wig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" /> + <param type="data" name="wig_file" url="${niceName}.wig" strip_https="True" /><param type="template" name="position" strip="True" > #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) #if $chrom is not None: @@ -18,57 +18,5 @@ #end if </param></link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$wig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/" /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument> - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${thenicename}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link></display> https://bitbucket.org/galaxy/galaxy-central/commits/bd1abde45a41/ Changeset: bd1abde45a41 User: dan Date: 2014-04-16 16:51:00 Summary: merge stable Affected #: 8 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: If 'populating' state from tool API request - stop processing tree on conditional test param error.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c6fce1fd9e7/ Changeset: 7c6fce1fd9e7 User: jmchilton Date: 2014-04-16 16:11:31 Summary: If 'populating' state from tool API request - stop processing tree on conditional test param error. Attempting to populate the state below the conditional parameter can result in uncaught exceptions in some cases. See Peter's post here - http://dev.list.galaxyproject.org/Unclear-API-and-Twill-test-failure-for-un… for example. Affected #: 1 file diff -r cd73af9c02e7f94d76239c010da12fcf1f91d1d4 -r 7c6fce1fd9e7f7adb4811cd92a56cdff05ea748d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2133,28 +2133,31 @@ context, source ) - current_case = input.get_current_case( value, trans ) - # Current case has changed, throw away old state - group_state = state[input.name] = {} - # TODO: we should try to preserve values if we can - self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context, history=history ) - group_errors = self.populate_state( trans, - input.cases[current_case].inputs, - group_state, - incoming, - history, - source, - prefix=group_prefix, - context=context, - ) if test_param_error: - group_errors[ input.test_param.name ] = test_param_error - if group_errors: - errors[ input.name ] = group_errors - # Store the current case in a special value - group_state['__current_case__'] = current_case - # Store the value of the test element - group_state[ input.test_param.name ] = value + errors[ input.name ] = [ test_param_error ] + # Store the value of the test element + group_state[ input.test_param.name ] = value + else: + current_case = input.get_current_case( value, trans ) + # Current case has changed, throw away old state + group_state = state[input.name] = {} + # TODO: we should try to preserve values if we can + self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context, history=history ) + group_errors = self.populate_state( trans, + input.cases[current_case].inputs, + group_state, + incoming, + history, + source, + prefix=group_prefix, + context=context, + ) + if group_errors: + errors[ input.name ] = group_errors + # Store the current case in a special value + group_state['__current_case__'] = current_case + # Store the value of the test element + group_state[ input.test_param.name ] = value elif isinstance( input, UploadDataset ): group_state = state[input.name] group_errors = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Remove stray debug output.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd73af9c02e7/ Changeset: cd73af9c02e7 User: davebgx Date: 2014-04-16 15:23:09 Summary: Remove stray debug output. Affected #: 1 file diff -r f3c5d9a5ed95956442dbd39e9ce97367cdc0d93b -r cd73af9c02e7f94d76239c010da12fcf1f91d1d4 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -637,7 +637,6 @@ # for the compute server. def metadata_path_on_compute(path): compute_path = path - log.info(compute_tmp_dir) if compute_tmp_dir and tmp_dir and in_directory(path, tmp_dir): path_relative = os.path.relpath(path, tmp_dir) compute_path = os.path.join(compute_tmp_dir, path_relative) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Modify test framework to account for recent UI changes.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3c5d9a5ed95/ Changeset: f3c5d9a5ed95 User: davebgx Date: 2014-04-16 15:18:56 Summary: Modify test framework to account for recent UI changes. Affected #: 2 files diff -r 6f698dec58950f0f56421a13474df0359c0777d7 -r f3c5d9a5ed95956442dbd39e9ce97367cdc0d93b test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -385,12 +385,6 @@ return value == hda[ key ] return False - def clear_history( self ): - """Empties a history of all datasets""" - self.visit_page( "clear_history" ) - self.check_history_for_string( 'Your history is empty' ) - self.home() - def delete_history( self, id ): """Deletes one or more histories""" history_list = self.get_histories_as_data_list() @@ -466,7 +460,8 @@ self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) ) else: self.visit_url( "%s/history_new" % self.url ) - self.check_history_for_string('Your history is empty') + self.check_page_for_string( 'New history created' ) + assert self.is_history_empty(), 'Creating new history did not result in an empty history.' self.home() def rename_history( self, id, old_name, new_name ): diff -r 6f698dec58950f0f56421a13474df0359c0777d7 -r f3c5d9a5ed95956442dbd39e9ce97367cdc0d93b test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -98,7 +98,7 @@ if not historyB.deleted: raise AssertionError( "Problem deleting history id %d" % historyB.id ) # Since we deleted the current history, make sure the history frame was refreshed - self.check_history_for_string( 'Your history is empty.' ) + assert self.is_history_empty(), 'Deleting active history did not result in a new empty history being created.' # We'll now test deleting a list of histories # After deleting the current history, a new one should have been created global history1 @@ -121,7 +121,7 @@ ids = '%s,%s' % ( self.security.encode_id( history1.id ), self.security.encode_id( history2.id ) ) self.delete_history( ids ) # Since we deleted the current history, make sure the history frame was refreshed - self.check_history_for_string( 'Your history is empty.' ) + assert self.is_history_empty(), 'Deleting active history did not result in a new empty history being created.' try: self.view_stored_active_histories( strings_displayed=[ history1.name ] ) raise AssertionError( "History %s is displayed in the active history list after it was deleted" % history1.name ) @@ -790,7 +790,7 @@ self.check_page_for_string( 'hg15' ) self.assertEqual( len( self.get_history_as_data_list() ), 1 ) # Delete the history item - self.delete_history_item( str( latest_hda.id ), strings_displayed=[ "Your history is empty" ] ) + self.delete_history_item( str( latest_hda.id ), strings_displayed=[] ) self.assertEqual( len( self.get_history_as_data_list() ), 0 ) # Try deleting an invalid hid try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Client App: factor out config serializer, move defensive programming
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f698dec5895/ Changeset: 6f698dec5895 User: carlfeberhard Date: 2014-04-15 22:06:26 Summary: Client App: factor out config serializer, move defensive programming Affected #: 1 file diff -r 1da9460ee1d0d5f3f89a767e41c40b5188af988c -r 6f698dec58950f0f56421a13474df0359c0777d7 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -3,27 +3,10 @@ <%def name="bootstrap()"> ## Bootstap dictionaries for GalaxyApp object's JSON, create GalaxyApp, ## and steal existing attributes from plain objects already created - <% - config_dict = {} - user_dict = {} - try: - if 'configuration' in trans.webapp.api_controllers: - config_dict = ( trans.webapp.api_controllers[ 'configuration' ] - .get_config_dict( trans.app.config, trans.user_is_admin() ) ) - - if 'users' in trans.webapp.api_controllers: - user_dict = self.get_user_dict() - - except Exception, exc: - pass - - # genomes - # datatypes - %><script type="text/javascript"> require([ 'galaxy-app-base' ], function( app ){ galaxy = new app.GalaxyApp({ - config : ${ h.to_json_string( config_dict ) }, + config : ${ get_config_json() }, userJSON : ${ get_user_json() }, root : '${h.url_for( "/" )}', //TODO: get these options from the server @@ -48,34 +31,64 @@ </script></%def> + +## ---------------------------------------------------------------------------- +<%def name="get_config_dict()"> + ## Return a dictionary of universe_wsgi.ini settings + <% + config_dict = {} + try: + if 'configuration' in trans.webapp.api_controllers: + config_dict = ( trans.webapp.api_controllers[ 'configuration' ] + .get_config_dict( trans.app.config, trans.user_is_admin() ) ) + except Exception, exc: + pass + + return config_dict + %> +</%def> + +<%def name="get_config_json()"> + ## Conv. fn to write as JSON +${ h.to_json_string( get_config_dict() )} +</%def> + + ## ---------------------------------------------------------------------------- <%def name="get_user_dict()"> ## Return a dictionary of user or anonymous user data including: ## email, id, disk space used, quota percent, and tags used <% - if trans.user: - user_dict = trans.user.to_dict( view='element', - value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) - user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) + user_dict = {} + try: + if trans.user: + user_dict = trans.user.to_dict( view='element', + value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) + user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) - # tags used - users_api_controller = trans.webapp.api_controllers[ 'users' ] - user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) - return user_dict + # tags used + users_api_controller = trans.webapp.api_controllers[ 'users' ] + user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) + return user_dict - usage = 0 - percent = None - try: - usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) - percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) - except AssertionError, assertion: - # no history for quota_agent.get_usage assertion + usage = 0 + percent = None + try: + usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) + percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) + except AssertionError, assertion: + # no history for quota_agent.get_usage assertion + pass + return { + 'total_disk_usage' : int( usage ), + 'nice_total_disk_usage' : util.nice_size( usage ), + 'quota_percent' : percent + } + + except Exception, exc: pass - return { - 'total_disk_usage' : int( usage ), - 'nice_total_disk_usage' : util.nice_size( usage ), - 'quota_percent' : percent - } + + return user_dict %></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix to dcc0c19 when user controller isn't present, gen. defensive programming
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1da9460ee1d0/ Changeset: 1da9460ee1d0 User: carlfeberhard Date: 2014-04-15 21:40:48 Summary: Fix to dcc0c19 when user controller isn't present, gen. defensive programming Affected #: 1 file diff -r 5e079414e9f9ca489229816553e5133f5b3d5c0e -r 1da9460ee1d0d5f3f89a767e41c40b5188af988c templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -5,11 +5,17 @@ ## and steal existing attributes from plain objects already created <% config_dict = {} - if 'configuration' in trans.webapp.api_controllers: - config_dict = ( trans.webapp.api_controllers[ 'configuration' ] - .get_config_dict( trans.app.config, trans.user_is_admin() ) ) + user_dict = {} + try: + if 'configuration' in trans.webapp.api_controllers: + config_dict = ( trans.webapp.api_controllers[ 'configuration' ] + .get_config_dict( trans.app.config, trans.user_is_admin() ) ) - user_dict = self.get_user_dict() + if 'users' in trans.webapp.api_controllers: + user_dict = self.get_user_dict() + + except Exception, exc: + pass # genomes # datatypes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix to dcc0c19 when configuration controller isn't present
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e079414e9f9/ Changeset: 5e079414e9f9 User: carlfeberhard Date: 2014-04-15 21:27:18 Summary: Fix to dcc0c19 when configuration controller isn't present Affected #: 1 file diff -r b8c2e002769773350c8bc729f099110cc26d9d01 -r 5e079414e9f9ca489229816553e5133f5b3d5c0e templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -4,13 +4,12 @@ ## Bootstap dictionaries for GalaxyApp object's JSON, create GalaxyApp, ## and steal existing attributes from plain objects already created <% - config_dict = ( trans.webapp.api_controllers[ 'configuration' ] - .get_config_dict( trans.app.config, trans.user_is_admin() ) ) - #import pprint - #pprint.pprint( config_dict ) + config_dict = {} + if 'configuration' in trans.webapp.api_controllers: + config_dict = ( trans.webapp.api_controllers[ 'configuration' ] + .get_config_dict( trans.app.config, trans.user_is_admin() ) ) user_dict = self.get_user_dict() - #pprint.pprint( user_dict ) # genomes # datatypes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Temporary fix to galaxy.panels.mako to ensure AMD order
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8c2e0027697/ Changeset: b8c2e0027697 User: carlfeberhard Date: 2014-04-15 21:06:40 Summary: Temporary fix to galaxy.panels.mako to ensure AMD order Affected #: 5 files diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 static/scripts/galaxy-app-base.js --- a/static/scripts/galaxy-app-base.js +++ b/static/scripts/galaxy-app-base.js @@ -46,6 +46,11 @@ self._initUser( options.userJSON || {} ); self.debug( 'GalaxyApp.user: ', self.user ); + //TODO: temp + if( typeof options.onload === 'function' ){ + options.onload(); + } + return self; }; @@ -69,6 +74,8 @@ var self = this; self.debug( '_initUser:', userJSON ); self.user = new userModel.User( userJSON ); + //TODO: temp + self.currUser = self.user; return self; }; diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 static/scripts/packed/galaxy-app-base.js --- a/static/scripts/packed/galaxy-app-base.js +++ b/static/scripts/packed/galaxy-app-base.js @@ -1,1 +1,1 @@ -define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,c,f,d){function g(m){var l=this;return l._init(m||{})}f(g,"GalaxyApp");g.defaultOptions={root:"/"};g.prototype._init=function j(m){var l=this;l._processOptions(m);l.debug("GalaxyApp.options: ",l.options);l._initLogger(m.loggerOptions||{});l.debug("GalaxyApp.logger: ",l.logger);l._initLocale();l.debug("GalaxyApp.localize: ",l.localize);l.config=m.config||{};l.debug("GalaxyApp.config: ",l.config);l._initUser(m.userJSON||{});l.debug("GalaxyApp.user: ",l.user);return l};g.prototype._processOptions=function e(n){var m=this,o=g.defaultOptions;m.debug("_processOptions: ",n);m.options={};for(var l in o){if(o.hasOwnProperty(l)){m.options[l]=(n.hasOwnProperty(l))?(n[l]):(o[l])}}return m};g.prototype._initUser=function i(m){var l=this;l.debug("_initUser:",m);l.user=new a.User(m);return l};g.prototype._initLogger=function k(m){var l=this;l.debug("_initLogger:",m);l.logger=new c.MetricsLogger(m);return l};g.prototype._initLocale=function h(m){var l=this;l.debug("_initLocale:",m);l.localize=d;window._l=l.localize;return l};g.prototype.toString=function b(){var l=this.user.get("email")||"(anonymous)";return"GalaxyApp("+l+")"};return{GalaxyApp:g}}); \ No newline at end of file +define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,c,f,d){function g(m){var l=this;return l._init(m||{})}f(g,"GalaxyApp");g.defaultOptions={root:"/"};g.prototype._init=function j(m){var l=this;l._processOptions(m);l.debug("GalaxyApp.options: ",l.options);l._initLogger(m.loggerOptions||{});l.debug("GalaxyApp.logger: ",l.logger);l._initLocale();l.debug("GalaxyApp.localize: ",l.localize);l.config=m.config||{};l.debug("GalaxyApp.config: ",l.config);l._initUser(m.userJSON||{});l.debug("GalaxyApp.user: ",l.user);if(typeof m.onload==="function"){m.onload()}return l};g.prototype._processOptions=function e(n){var m=this,o=g.defaultOptions;m.debug("_processOptions: ",n);m.options={};for(var l in o){if(o.hasOwnProperty(l)){m.options[l]=(n.hasOwnProperty(l))?(n[l]):(o[l])}}return m};g.prototype._initUser=function i(m){var l=this;l.debug("_initUser:",m);l.user=new a.User(m);l.currUser=l.user;return l};g.prototype._initLogger=function k(m){var l=this;l.debug("_initLogger:",m);l.logger=new c.MetricsLogger(m);return l};g.prototype._initLocale=function h(m){var l=this;l.debug("_initLocale:",m);l.localize=d;window._l=l.localize;return l};g.prototype.toString=function b(){var l=this.user.get("email")||"(anonymous)";return"GalaxyApp("+l+")"};return{GalaxyApp:g}}); \ No newline at end of file diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -22,6 +22,7 @@ userJSON : ${ get_user_json() }, root : '${h.url_for( "/" )}', //TODO: get these options from the server + onload : window.Galaxy? window.Galaxy.onload: null, loggerOptions : { } }); diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -85,33 +85,36 @@ 'mvc/user/user-model', 'mvc/user/user-quotameter' ], function( mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload, user, quotameter ){ + if( !Galaxy.currUser ){ + // this doesn't need to wait for the page being readied + Galaxy.currUser = new user.User(${ h.to_json_string( get_user_json(), indent=2 ) }); + } + $(function() { - ## check if masthead is available - if (Galaxy.masthead) + // check if masthead is available + if (Galaxy.masthead){ return; + } - ## get configuration + // get configuration var masthead_config = ${ h.to_json_string( masthead_config ) }; - ## load global galaxy objects + // load global galaxy objects Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); Galaxy.modal = new mod_modal.View(); Galaxy.frame = new mod_frame.GalaxyFrame(); - ## construct default menu options + // construct default menu options Galaxy.menu = new mod_menu.GalaxyMenu({ masthead: Galaxy.masthead, config: masthead_config }); - ## add upload plugin + // add upload plugin Galaxy.upload = new GalaxyUpload(masthead_config); - if( !Galaxy.currUser ){ - Galaxy.currUser = new user.User(${ h.to_json_string( get_user_json(), indent=2 ) }); - } - ## set up the quota meter (And fetch the current user data from trans) - ## add quota meter to masthead + // set up the quota meter (And fetch the current user data from trans) + // add quota meter to masthead Galaxy.quotaMeter = new quotameter.UserQuotaMeter({ model : Galaxy.currUser, el : Galaxy.masthead.$('.quota-meter-container') diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -1,4 +1,5 @@ <%namespace name="masthead" file="/webapps/galaxy/galaxy.masthead.mako"/> +<%namespace name="galaxy_client" file="../../galaxy_client_app.mako" /><!DOCTYPE HTML> @@ -93,6 +94,7 @@ %endif </style> + ## default script wrapper <script type="text/javascript"> ## configure require @@ -104,27 +106,25 @@ "libs/backbone/backbone": { exports: "Backbone" }, } }); - - ## get configuration + + // load any app configured var galaxy_config = ${ h.to_json_string( self.galaxy_config ) }; - - ## on page load - $(function() - { - ## check if script is defined + Galaxy.onload = function(){ var jscript = galaxy_config.app.jscript; - if (jscript) - { - ## load galaxy app - require([jscript], function(js_lib) - { - ## load galaxy module application - var module = new js_lib.GalaxyApp(); + if( jscript ){ + $( function(){ + require([ jscript ], function( js_lib ){ + ## load galaxy module application + var module = new js_lib.GalaxyApp(); + }); }); - } else + } else { console.log("'galaxy_config.app.jscript' missing."); - }); + } + } </script> + ${ galaxy_client.bootstrap() } + </%def> ## default late-load javascripts @@ -229,4 +229,4 @@ ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout ${self.late_javascripts()} -</html> \ No newline at end of file +</html> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Allow copying Histories directly from the list of Saved Histories.
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a03ea4880a71/ Changeset: a03ea4880a71 User: dan Date: 2014-04-15 20:24:14 Summary: Allow copying Histories directly from the list of Saved Histories. Affected #: 1 file diff -r f7983ecf5ea7c15e5c4235f079e86943576fbdba -r a03ea4880a7117156cead39eecb658ca1da301b3 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -91,6 +91,7 @@ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ), grids.GridOperation( "View", allow_multiple=False ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False, inbound=True ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ), grids.GridOperation( "Delete Permanently", condition=( lambda item: not item.purged ), confirm="History contents will be removed from disk, this cannot be undone. Continue?", async_compatible=True ), @@ -237,6 +238,8 @@ show_deleted=history.deleted, use_panels=False ) ) #return self.view( trans, id=kwargs['id'], show_deleted=history.deleted, use_panels=False ) + if operation == 'copy' and kwargs.get( 'id', None ): + return self.copy( trans, id=kwargs.get( 'id', None ) ) history_ids = galaxy.util.listify( kwargs.get( 'id', [] ) ) # Display no message by default status, message = None, None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Provide run and edit links for workflows after extraction from history.
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7983ecf5ea7/ Changeset: f7983ecf5ea7 User: dan Date: 2014-04-15 20:01:21 Summary: Provide run and edit links for workflows after extraction from history. Affected #: 1 file diff -r 3a154b52090316dee61f42993eaa5a1fa40116d3 -r f7983ecf5ea7c15e5c4235f079e86943576fbdba lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1201,7 +1201,7 @@ history=history ) else: - extract_workflow( + stored_workflow = extract_workflow( trans, user=user, job_ids=job_ids, @@ -1209,9 +1209,10 @@ workflow_name=workflow_name ) # Index page with message - return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) - ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" - ## % ( workflow_name, web.url_for(controller='workflow', action='editor', id=trans.security.encode_id(stored.id) ) ) ) + workflow_id = trans.security.encode_id( stored_workflow.id ) + return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % + ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ), + url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose def run( self, trans, id, history_id=None, multiple_input_mode="product", hide_fixed_params=False, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5813b1de27ae/ Changeset: 5813b1de27ae User: natefoo Date: 2014-04-15 19:32:01 Summary: Update build platforms for dist-scrambling. Affected #: 1 file diff -r 9ea6c8749ab13e8a4e0d917bf3b49d09b43f55e1 -r 5813b1de27ae8bfb0f31db3215162d563ad2becb dist-eggs.ini --- a/dist-eggs.ini +++ b/dist-eggs.ini @@ -8,22 +8,20 @@ ; [hosts] -py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6 -py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6 -py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.7 -py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7 -py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6 -py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 -py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.7 -py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 -py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 -py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 -py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6 +py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-i686-ucs2/bin/python2.6 +py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-i686-ucs4/bin/python2.6 +py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-x86_64-ucs2/bin/python2.6 +py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-x86_64-ucs4/bin/python2.6 +py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-i686-ucs2/bin/python2.7 +py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-i686-ucs4/bin/python2.7 +py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs2/bin/python2.7 +py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs4/bin/python2.7 +py2.6-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.6 py2.7-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.7 ; ; these hosts are used to build eggs with no C extensions -py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 -py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 +py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-x86_64-ucs4/bin/python2.6 +py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs4/bin/python2.7 [groups] py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 @@ -35,8 +33,8 @@ linux-i686 = py2.6-linux-i686 py2.7-linux-i686 linux-x86_64 = py2.6-linux-x86_64 py2.7-linux-x86_64 linux = linux-i686 linux-x86_64 -py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 -py2.7-macosx = py2.7-macosx-10.3-fat-ucs2 py2.7-macosx-10.6-intel-ucs2 +py2.6-macosx = py2.6-macosx-10.6-intel-ucs2 +py2.7-macosx = py2.7-macosx-10.6-intel-ucs2 macosx = py2.6-macosx py2.7-macosx py2.6-all = py2.6-linux py2.6-macosx py2.7-all = py2.7-linux py2.7-macosx https://bitbucket.org/galaxy/galaxy-central/commits/3a154b520903/ Changeset: 3a154b520903 User: natefoo Date: 2014-04-15 19:32:31 Summary: Update bx-python to 0.7.2 Affected #: 1 file diff -r 5813b1de27ae8bfb0f31db3215162d563ad2becb -r 3a154b52090316dee61f42993eaa5a1fa40116d3 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -12,7 +12,7 @@ no_auto = pbs_python [eggs:platform] -bx_python = 0.7.1 +bx_python = 0.7.2 Cheetah = 2.2.2 MarkupSafe = 0.12 mercurial = 2.2.3 @@ -78,7 +78,6 @@ psycopg2 = _9.2.4_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _7b95ff194725 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 pysam = _kanwei_b10f6e722e9a Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove old platforms and versions from platform string manipulation. Egg compatibility enhancements for OS X. Galaxy's prepackaged OS X eggs should now work on any Python interpreter on Intel versions of OS X 10.6 and newer.
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9ea6c8749ab1/ Changeset: 9ea6c8749ab1 User: natefoo Date: 2014-04-15 19:27:36 Summary: Remove old platforms and versions from platform string manipulation. Egg compatibility enhancements for OS X. Galaxy's prepackaged OS X eggs should now work on any Python interpreter on Intel versions of OS X 10.6 and newer. Affected #: 1 file diff -r dcc0c19147ead86c6e357c739e0513addfe02cb2 -r 9ea6c8749ab13e8a4e0d917bf3b49d09b43f55e1 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py +++ b/lib/galaxy/__init__.py @@ -4,24 +4,36 @@ __import__( "pkg_resources" ).declare_namespace( __name__ ) -import os, sys, re -from distutils.sysconfig import get_config_var, get_config_vars +import re +import os +import sys +import platform import pkg_resources # patch get_platform() for better ABI recognition def _get_build_platform(): plat = pkg_resources._get_build_platform() - if sys.version_info[:2] == ( 2, 5 ) and \ - ( ( os.uname()[-1] in ( 'x86_64', 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ - ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ) ): - plat = 'macosx-10.3-fat' - if sys.platform == "sunos5" and not (plat.endswith('_32') or plat.endswith('_64')): - if sys.maxint > 2**31: - plat += '_64' - else: - plat += '_32' - if sys.platform == "linux2" and sys.maxint < 2**31 and plat.endswith( '-x86_64' ): + if sys.platform == 'darwin': + # Assert OS X version is new enough + current_minor_ver = int( platform.mac_ver()[0].split( '.' )[1] ) + assert current_minor_ver >= 6, 'Galaxy is not compatible with Mac OS X < 10.6 (your version is %s)' % platform.mac_ver()[0] + # Python build target may be even older, but this will prevent it from + # fetching our 10.6+ eggs, so fix if necessary (newer versions will be + # fine) + plat_split = plat.split( '-' ) + build_minor_ver = int( plat_split[1].split( '.' )[1] ) + if build_minor_ver < 6: + plat_split[1] = '10.6' + # Our intel (dual arch) eggs will work fine on single-arch builds + if plat_split[-1] in ( 'i386', 'x86_64' ): + plat_split[-1] = 'intel' + # Ditto universal (if you're not on PPC) + if plat_split[-1] == 'universal' and platform.processor() != 'powerpc': + plat_split[-1] = 'intel' + plat = '-'.join( plat_split ) + elif sys.platform == "linux2" and sys.maxint < 2**31 and plat.endswith( '-x86_64' ): + # 32 bit Python on 64 bit Linux plat = plat.replace( '-x86_64', '-i686' ) if not (plat.endswith('-ucs2') or plat.endswith('-ucs4')): if sys.maxunicode > 2**16: @@ -36,34 +48,6 @@ pkg_resources.get_build_platform = _get_build_platform pkg_resources.get_platform = _get_build_platform -# patch compatible_platforms() to allow for Solaris binary compatibility -solarisVersionString = re.compile(r"solaris-(\d)\.(\d+)-(.*)") -def _compatible_platforms(provided,required): - # this is a bit kludgey since we need to know a bit about what happened in - # the original method - if provided is None or required is None or provided==required: - return True # easy case - reqMac = pkg_resources.macosVersionString.match(required) - if reqMac: - return pkg_resources._compatible_platforms(provided,required) - reqSol = solarisVersionString.match(required) - if reqSol: - provSol = solarisVersionString.match(provided) - if not provSol: - return False - if provSol.group(1) != reqSol.group(1) or \ - provSol.group(3) != reqSol.group(3): - return False - if int(provSol.group(2)) > int(reqSol.group(2)): - return False - return True - return False -try: - assert pkg_resources._compatible_platforms -except: - pkg_resources._compatible_platforms = pkg_resources.compatible_platforms - pkg_resources.compatible_platforms = _compatible_platforms - # patch to insert eggs at the beginning of sys.path instead of at the end def _insert_on(self, path, loc = None): """Insert self.location in path before its nearest parent directory""" @@ -108,4 +92,4 @@ pass logging.NullHandler = NullHandler -import galaxy.eggs \ No newline at end of file +import galaxy.eggs Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI: add GalaxyApp to base_panels.mako; add requirejs i18n plugin and nls/zh, nls/ja locale files, wire into _l client localizer, remove previous localization cruft; remove reliance on history_panel.mako
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

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1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Apr '14

15 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c2a0ca50e640/ Changeset: c2a0ca50e640 User: dan Date: 2014-04-15 17:59:14 Summary: UI, make HDAs in NEW state have delete, info and rerun buttons, as well as disabled view and edit buttons. Move new state to NOT READY STATES. Affected #: 3 files diff -r 3b3365a391944f848b403412f226ee9e5499c0d5 -r c2a0ca50e6400bff4b9dc549db3fe14305e4473a static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -165,7 +165,6 @@ // (do show if in error, running) if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.DISCARDED ) - || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) || ( !this.model.get( 'accessible' ) ) ){ return null; } @@ -185,6 +184,11 @@ displayBtnData.disabled = true; displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' ); + // disable if still new + } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ){ + displayBtnData.disabled = true; + displayBtnData.title = _l( 'This dataset is not yet viewable' ); + } else { displayBtnData.title = _l( 'View data' ); @@ -312,7 +316,8 @@ */ _render_body_new : function(){ return this._render_stateBodyHelper( - '<div>' + _l( 'This is a new dataset and not all of its data are available yet' ) + '</div>' + '<div>' + _l( 'This is a new dataset and not all of its data are available yet' ) + '</div>', + this.defaultPrimaryActionButtonRenderers ); }, /** Render inaccessible, not-owned by curr user. */ diff -r 3b3365a391944f848b403412f226ee9e5499c0d5 -r c2a0ca50e6400bff4b9dc549db3fe14305e4473a static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -64,8 +64,7 @@ _render_editButton : function(){ // don't show edit while uploading, in-accessible // DO show if in error (ala previous history panel) - if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.DISCARDED ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.DISCARDED ) || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ return null; @@ -93,6 +92,11 @@ } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ){ editBtnData.disabled = true; editBtnData.title = _l( 'This dataset must finish uploading before it can be edited' ); + + // disable if new + } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ){ + editBtnData.disabled = true; + editBtnData.title = _l( 'This dataset is not yet editable' ); } editBtnData.faIcon = 'fa-pencil'; return faIconButton( editBtnData ); @@ -103,8 +107,7 @@ */ _render_deleteButton : function(){ // don't show delete if... - if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ return null; } diff -r 3b3365a391944f848b403412f226ee9e5499c0d5 -r c2a0ca50e6400bff4b9dc549db3fe14305e4473a static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -377,7 +377,6 @@ /** states that are in a final state (the underlying job is complete) */ HistoryDatasetAssociation.READY_STATES = [ - HistoryDatasetAssociation.STATES.NEW, HistoryDatasetAssociation.STATES.OK, HistoryDatasetAssociation.STATES.EMPTY, HistoryDatasetAssociation.STATES.PAUSED, @@ -392,7 +391,8 @@ HistoryDatasetAssociation.STATES.UPLOAD, HistoryDatasetAssociation.STATES.QUEUED, HistoryDatasetAssociation.STATES.RUNNING, - HistoryDatasetAssociation.STATES.SETTING_METADATA + HistoryDatasetAssociation.STATES.SETTING_METADATA, + HistoryDatasetAssociation.STATES.NEW ]; //============================================================================== https://bitbucket.org/galaxy/galaxy-central/commits/8346ec4baa39/ Changeset: 8346ec4baa39 User: dan Date: 2014-04-15 18:00:02 Summary: Update packed scripts Affected #: 3 files diff -r c2a0ca50e6400bff4b9dc549db3fe14305e4473a -r 8346ec4baa3992f4dc0161f0fc79a0ba893c0a63 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(h){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display});h.preventDefault()}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW){g.disabled=true;g.title=_l("This dataset is not yet viewable")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(h){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display});h.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}}); \ No newline at end of file diff -r c2a0ca50e6400bff4b9dc549db3fe14305e4473a -r 8346ec4baa3992f4dc0161f0fc79a0ba893c0a63 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?"+$.param(j);m.Galaxy.frame.add({title:"Trackster",type:"url",content:n})}}})}});return false}}return{HDAEditView:g}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations"],function(f,b,a,e){var g=b.HDABaseView.extend({initialize:function(h){b.HDABaseView.prototype.initialize.call(this,h);this.hasUser=h.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=h.tagsEditorShown||false;this.annotationEditorShown=h.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var j=this.model.get("purged"),h=this.model.get("deleted"),i={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(h||j){i.disabled=true;if(j){i.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(h){i.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=_l("This dataset must finish uploading before it can be edited")}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW){i.disabled=true;i.title=_l("This dataset is not yet editable")}}}i.faIcon="fa-pencil";return faIconButton(i)},_render_deleteButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this,i={title:_l("Delete"),classes:"dataset-delete",onclick:function(){h.$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 diff -r c2a0ca50e6400bff4b9dc549db3fe14305e4473a -r 8346ec4baa3992f4dc0161f0fc79a0ba893c0a63 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc"],function(b){var e=Backbone.Model.extend(b.LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var j=this.get("id");if(!j){return{}}var i={purge:galaxy_config.root+"datasets/"+j+"/purge_async",display:galaxy_config.root+"datasets/"+j+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+j+"/edit",download:galaxy_config.root+"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+j,rerun:galaxy_config.root+"tool_runner/rerun?id="+j,show_params:galaxy_config.root+"datasets/"+j+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+j,set:galaxy_config.root+"dataset/annotate_async?id="+j},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};return i},initialize:function(i){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",e.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(j,i){this.log(this+" has changed state:",j,i);if(this.inReadyState()){this.trigger("state:ready",j,i,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(j,k){var i=true;if((!j)&&(this.get("deleted")||this.get("purged"))){i=false}if((!k)&&(!this.get("visible"))){i=false}return i},hidden:function(){return !this.get("visible")},inReadyState:function(){var i=_.contains(e.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||i)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function d(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function c(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function h(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},purge:function g(i){if(this.get("purged")){return jQuery.when()}i=i||{};i.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var j=this,k=jQuery.ajax(i);k.done(function(n,l,m){j.set({deleted:true,purged:true})});k.fail(function(p,l,o){var m=_l("Unable to purge dataset");var n=("Removal of datasets by users is not allowed in this Galaxy instance");if(p.responseJSON&&p.responseJSON.error){m=p.responseJSON.error}else{if(p.responseText.indexOf(n)!==-1){m=n}}p.responseText=m;j.trigger("error",j,p,i,_l(m),{error:m})});return k},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(k,i){var j=this.get(k);if(!i||(j===undefined||j===null)){return false}if(_.isArray(j)){return this._searchArrayAttribute(j,i)}return(j.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)},_searchArrayAttribute:function(j,i){i=i.toLowerCase();return _.any(j,function(k){return(k.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)})},search:function(i){var j=this;return _.filter(this.searchAttributes,function(k){return j.searchAttribute(k,i)})},matches:function(j){var l="=",i=j.split(l);if(i.length>=2){var k=i[0];k=this.searchAliases[k]||k;return this.searchAttribute(k,i[1])}return !!this.search(j).length},matchesAll:function(j){var i=this;j=j.match(/(".*"|\w*=".*"|\S*)/g).filter(function(k){return !!k});return _.all(j,function(k){k=k.replace(/"/g,"");return i.matches(k)})},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HDA("+i+")"}});e.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};e.READY_STATES=[e.STATES.NEW,e.STATES.OK,e.STATES.EMPTY,e.STATES.PAUSED,e.STATES.FAILED_METADATA,e.STATES.NOT_VIEWABLE,e.STATES.DISCARDED,e.STATES.ERROR];e.NOT_READY_STATES=[e.STATES.UPLOAD,e.STATES.QUEUED,e.STATES.RUNNING,e.STATES.SETTING_METADATA];var f=Backbone.Collection.extend(b.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(j,i){i=i||{};this.historyId=i.historyId},ids:function(){return this.map(function(i){return i.id})},notReady:function(){return this.filter(function(i){return !i.inReadyState()})},running:function(){var i=[];this.each(function(j){if(!j.inReadyState()){i.push(j.get("id"))}});return i},getByHid:function(i){return _.first(this.filter(function(j){return j.get("hid")===i}))},getVisible:function(i,l,k){k=k||[];var j=new f(this.filter(function(m){return m.isVisible(i,l)}));_.each(k,function(m){if(!_.isFunction(m)){return}j=new f(j.filter(m))});return j},haveDetails:function(){return this.all(function(i){return i.hasDetails()})},fetchAllDetails:function(j){j=j||{};var i={details:"all"};j.data=(j.data)?(_.extend(j.data,i)):(i);return this.fetch(j)},ajaxQueue:function(l,k){var j=jQuery.Deferred(),i=this.length,n=[];if(!i){j.resolve([]);return j}var m=this.chain().reverse().map(function(p,o){return function(){var q=l.call(p,k);q.done(function(r){j.notify({curr:o,total:i,response:r,model:p})});q.always(function(r){n.push(r);if(m.length){m.shift()()}else{j.resolve(n)}})}}).value();m.shift()();return j},matches:function(i){return this.filter(function(j){return j.matches(i)})},set:function(k,i){var j=this;k=_.map(k,function(m){var n=j.get(m.id);if(!n){return m}var l=n.toJSON();_.extend(l,m);return l});Backbone.Collection.prototype.set.call(this,k,i)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:e,HDACollection:f}}); \ No newline at end of file +define(["mvc/base-mvc"],function(b){var e=Backbone.Model.extend(b.LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var j=this.get("id");if(!j){return{}}var i={purge:galaxy_config.root+"datasets/"+j+"/purge_async",display:galaxy_config.root+"datasets/"+j+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+j+"/edit",download:galaxy_config.root+"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+j,rerun:galaxy_config.root+"tool_runner/rerun?id="+j,show_params:galaxy_config.root+"datasets/"+j+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+j,set:galaxy_config.root+"dataset/annotate_async?id="+j},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};return i},initialize:function(i){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",e.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(j,i){this.log(this+" has changed state:",j,i);if(this.inReadyState()){this.trigger("state:ready",j,i,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(j,k){var i=true;if((!j)&&(this.get("deleted")||this.get("purged"))){i=false}if((!k)&&(!this.get("visible"))){i=false}return i},hidden:function(){return !this.get("visible")},inReadyState:function(){var i=_.contains(e.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||i)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function d(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function c(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function h(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},purge:function g(i){if(this.get("purged")){return jQuery.when()}i=i||{};i.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var j=this,k=jQuery.ajax(i);k.done(function(n,l,m){j.set({deleted:true,purged:true})});k.fail(function(p,l,o){var m=_l("Unable to purge dataset");var n=("Removal of datasets by users is not allowed in this Galaxy instance");if(p.responseJSON&&p.responseJSON.error){m=p.responseJSON.error}else{if(p.responseText.indexOf(n)!==-1){m=n}}p.responseText=m;j.trigger("error",j,p,i,_l(m),{error:m})});return k},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(k,i){var j=this.get(k);if(!i||(j===undefined||j===null)){return false}if(_.isArray(j)){return this._searchArrayAttribute(j,i)}return(j.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)},_searchArrayAttribute:function(j,i){i=i.toLowerCase();return _.any(j,function(k){return(k.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)})},search:function(i){var j=this;return _.filter(this.searchAttributes,function(k){return j.searchAttribute(k,i)})},matches:function(j){var l="=",i=j.split(l);if(i.length>=2){var k=i[0];k=this.searchAliases[k]||k;return this.searchAttribute(k,i[1])}return !!this.search(j).length},matchesAll:function(j){var i=this;j=j.match(/(".*"|\w*=".*"|\S*)/g).filter(function(k){return !!k});return _.all(j,function(k){k=k.replace(/"/g,"");return i.matches(k)})},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HDA("+i+")"}});e.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};e.READY_STATES=[e.STATES.OK,e.STATES.EMPTY,e.STATES.PAUSED,e.STATES.FAILED_METADATA,e.STATES.NOT_VIEWABLE,e.STATES.DISCARDED,e.STATES.ERROR];e.NOT_READY_STATES=[e.STATES.UPLOAD,e.STATES.QUEUED,e.STATES.RUNNING,e.STATES.SETTING_METADATA,e.STATES.NEW];var f=Backbone.Collection.extend(b.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(j,i){i=i||{};this.historyId=i.historyId},ids:function(){return this.map(function(i){return i.id})},notReady:function(){return this.filter(function(i){return !i.inReadyState()})},running:function(){var i=[];this.each(function(j){if(!j.inReadyState()){i.push(j.get("id"))}});return i},getByHid:function(i){return _.first(this.filter(function(j){return j.get("hid")===i}))},getVisible:function(i,l,k){k=k||[];var j=new f(this.filter(function(m){return m.isVisible(i,l)}));_.each(k,function(m){if(!_.isFunction(m)){return}j=new f(j.filter(m))});return j},haveDetails:function(){return this.all(function(i){return i.hasDetails()})},fetchAllDetails:function(j){j=j||{};var i={details:"all"};j.data=(j.data)?(_.extend(j.data,i)):(i);return this.fetch(j)},ajaxQueue:function(l,k){var j=jQuery.Deferred(),i=this.length,n=[];if(!i){j.resolve([]);return j}var m=this.chain().reverse().map(function(p,o){return function(){var q=l.call(p,k);q.done(function(r){j.notify({curr:o,total:i,response:r,model:p})});q.always(function(r){n.push(r);if(m.length){m.shift()()}else{j.resolve(n)}})}}).value();m.shift()();return j},matches:function(i){return this.filter(function(j){return j.matches(i)})},set:function(k,i){var j=this;k=_.map(k,function(m){var n=j.get(m.id);if(!n){return m}var l=n.toJSON();_.extend(l,m);return l});Backbone.Collection.prototype.set.call(this,k,i)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:e,HDACollection:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c4e3b85aa3b/ Changeset: 8c4e3b85aa3b Branch: next-stable User: natefoo Date: 2014-04-15 01:26:24 Summary: Close next-stable branch. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/9e53251b0b7e/ Changeset: 9e53251b0b7e Branch: stable User: natefoo Date: 2014-04-15 01:27:21 Summary: Update stable branch from next-stable for release. Affected #: 749 files diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc .hgignore --- a/.hgignore +++ b/.hgignore @@ -77,6 +77,7 @@ tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt tool-data/*.loc tool-data/genome/* diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc README.txt --- a/README.txt +++ b/README.txt @@ -26,6 +26,6 @@ on adding tools can be found on the Galaxy website (linked above). Not all dependencies are included for the tools provided in the sample -tool_conf.xml. A full list of external dependencies is available at: +tool_conf.xml. A full list of external dependencies is available at: -http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/additional_template_paths.xml --- /dev/null +++ b/config/plugins/visualizations/additional_template_paths.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<paths> + <path>common/templates</path> +</paths> diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/Gruntfile.js --- /dev/null +++ b/config/plugins/visualizations/charts/Gruntfile.js @@ -0,0 +1,24 @@ +// NOTE: use 'sudo npm install .', then 'grunt' to use this file +module.exports = function(grunt) { + grunt.initConfig({ + pkg: grunt.file.readJSON('package.json'), + requirejs: { + compile: { + options: { + baseUrl : "../../../../static/scripts/", + paths : { + "plugin": "../../config/plugins/visualizations/charts/static" + }, + shim : { + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" } + }, + name : "plugin/app", + out : "static/build-app.js", + } + } + } + }); + grunt.loadNpmTasks('grunt-contrib-requirejs'); + grunt.registerTask( 'default', [ 'requirejs' ]); +}; diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/config/charts.xml --- a/config/plugins/visualizations/charts/config/charts.xml +++ b/config/plugins/visualizations/charts/config/charts.xml @@ -7,15 +7,9 @@ <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test><to_param param_attr="id">dataset_id</to_param></data_source> - <data_source> - <model_class>Visualization</model_class> - <test test_attr="type">charts</test> - <to_param param_attr="id">visualization_id</to_param> - </data_source></data_sources><params><param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> - <param type="visualization" var_name_in_template="visualization">visualization_id</param></params><template>charts.mako</template></visualization> diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/package.json --- /dev/null +++ b/config/plugins/visualizations/charts/package.json @@ -0,0 +1,18 @@ +{ + "name": "galaxy-charts", + "version": "0.0.0", + "description": "Charts visualization plugin for the Galaxy informatics framework", + "main": " ", + "keywords": [ + "galaxy", + "visualization", + "d3" + ], + "author": "Aysam Guerler", + "license": "BSD", + "devDependencies": { + "grunt": "~0.4.1", + "grunt-cli": "~0.1.9", + "grunt-contrib-requirejs": "~0.4.3" + } +} diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,10 +1,12 @@ // dependencies -define(['library/portlet', 'library/ui', 'library/utils', - 'views/charts', 'views/viewport', 'views/chart', 'views/group', - 'models/config', 'models/datasets', 'models/chart', 'models/charts', 'models/group', 'models/types'], - function( Portlet, Ui, Utils, - ChartsView, ViewportView, ChartView, GroupView, - Config, Datasets, Chart, Charts, Group, Types +define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', + 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', + 'plugin/views/viewer', 'plugin/views/editor', + 'plugin/models/config', 'plugin/models/chart', + 'plugin/charts/types'], + function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, + ViewerView, EditorView, + Config, Chart, Types ) { // widget @@ -13,66 +15,75 @@ // initialize initialize: function(options) { + // deactivate all debugs outputs + //window.console.debug = function() {}; + // link options this.options = options; - // link galaxy - this.modal = parent.Galaxy.modal; + // link galaxy modal or create one + if (Galaxy && Galaxy.modal) { + this.modal = Galaxy.modal; + } else { + this.modal = new Modal.View(); + } - // create configuration model + // + // models + // this.config = new Config(); - - // create chart models this.types = new Types(); this.chart = new Chart(); - this.charts = new Charts(); - this.group = new Group(); - // create dataset handler + // + // libraries + // + this.jobs = new Jobs(this); this.datasets = new Datasets(this); + this.storage = new Storage(this); - // create views - this.charts_view = new ChartsView(this); - this.group_view = new GroupView(this); - this.chart_view = new ChartView(this); - this.viewport_view = new ViewportView(this); - - // append view port to charts viewer - this.charts_view.append(this.viewport_view.$el); - - // create portlet - if (!this.options.config.widget) { - this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'}); - } else { - this.portlet = $('<div></div>'); - } + // + // views + // + this.viewer_view = new ViewerView(this); + this.editor_view = new EditorView(this); // append views - this.portlet.append(this.charts_view.$el); - this.portlet.append(this.group_view.$el); - this.portlet.append(this.chart_view.$el); - - // set element - if (!this.options.config.widget) { - this.setElement(this.portlet.$el); + this.$el.append(this.viewer_view.$el); + this.$el.append(this.editor_view.$el); + + // pick start screen + if (!this.storage.load()) { + // show editor + this.go('editor'); } else { - this.setElement(this.portlet); + // show viewport + this.go('viewer'); + + // draw chart + var self = this; + this.chart.deferred.execute(function() { + self.chart.trigger('redraw'); + }); } - - // hide views - this.group_view.$el.hide(); - this.charts_view.$el.hide(); - - // events - var self = this; - this.config.on('change:current_view', function() { - self._showCurrent(); - }); }, - // current view - _showCurrent: function() { + // loads a view and makes sure that all others are hidden + go: function(view_id) { + // hide all tooltips + $('.tooltip').hide(); + // pick view + switch (view_id) { + case 'editor' : + this.editor_view.show(); + this.viewer_view.hide(); + break; + case 'viewer' : + this.editor_view.hide(); + this.viewer_view.show(); + break; + } }, // execute command diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/build-app.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -0,0 +1,6 @@ +// Underscore.js 1.4.4 +// http://underscorejs.org +// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. +// Underscore may be freely distributed under the MIT license. + +(function(){var 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t=this.buttonList[e];this.$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.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$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 n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{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 btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:a,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+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 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/_nvd3/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/_nvd3/config.js @@ -0,0 +1,218 @@ +define([], function() { + +return { + title : '', + columns : { + y : { + title : 'Values for y-axis' + } + }, + settings : { + separator_label : { + title : 'X axis', + type : 'separator' + }, + x_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'X-axis', + placeholder : 'Axis label' + }, + x_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + hide : 'x_axis_tick' + }, + { + label : 'Auto', + value : 'auto', + hide : 'x_axis_tick' + }, + { + label : 'Float', + value : 'f', + show : 'x_axis_tick' + }, + { + label : 'Exponent', + value : 'e', + show : 'x_axis_tick' + }, + { + label : 'Integer', + value : 'd', + hide : 'x_axis_tick' + }, + { + label : 'Percentage', + value : 'p', + show : 'x_axis_tick' + }, + { + label : 'Rounded', + value : 'r', + show : 'x_axis_tick' + }, + { + label : 'SI-prefix', + value : 's', + show : 'x_axis_tick' + } + ] + }, + x_axis_tick : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '.1', + data : [ + { + label : '0.00001', + value : '.5' + }, + { + label : '0.0001', + value : '.4' + }, + { + label : '0.001', + value : '.3' + }, + { + label : '0.01', + value : '.2' + }, + { + label : '0.1', + value : '.1' + }, + { + label : '1', + value : '1' + } + ] + + }, + separator_tick : { + title : 'Y axis', + type : 'separator' + }, + y_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'Y-axis', + placeholder : 'Axis label' + }, + y_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + hide : 'y_axis_tick' + }, + { + label : 'Auto', + value : 'auto', + hide : 'y_axis_tick' + }, + { + label : 'Float', + value : 'f', + show : 'y_axis_tick' + }, + { + label : 'Exponent', + value : 'e', + show : 'y_axis_tick' + }, + { + label : 'Integer', + value : 'd', + hide : 'y_axis_tick' + }, + { + label : 'Percentage', + value : 'p', + show : 'y_axis_tick' + }, + { + label : 'Rounded', + value : 'r', + show : 'y_axis_tick' + }, + { + label : 'SI-prefix', + value : 's', + show : 'y_axis_tick' + } + ] + }, + y_axis_tick : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '.1', + data : [ + { + label : '0.00001', + value : '.5' + }, + { + label : '0.0001', + value : '.4' + }, + { + label : '0.001', + value : '.3' + }, + { + label : '0.01', + value : '.2' + }, + { + label : '0.1', + value : '.1' + }, + { + label : '1', + value : '1' + } + ] + + }, + separator_legend : { + title : 'Others', + type : 'separator' + }, + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'select', + init : 'true', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + } +}; + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js @@ -0,0 +1,80 @@ +// dependencies +define([], function() { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, nvd3_model, chart, request_dictionary, callback) + { + // request data + var self = this; + this.app.datasets.request(request_dictionary, function(data) { + nv.addGraph(function() { + // x axis + self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); + + // x axis label + nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label')); + + // y axis + self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); + + // y axis label + nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label')) + .axisLabelDistance(30); + + // controls + if (chart.groups.length == 1) { + nvd3_model.options({ showControls: false }); + } + + // legend + var legend_visible = true; + if (chart.settings.get('show_legend') == 'false') { + legend_visible = false; + } + nvd3_model.showLegend(legend_visible); + + // custom callback + if (callback) { + callback(nvd3_model); + } + + // parse data to svg + self.options.svg.datum(data) + .call(nvd3_model); + + // refresh on window resize + nv.utils.windowResize(nvd3_model.update); + + // set chart state + chart.state('ok', 'Chart has been drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + }); + }, + + // make axis + _axis: function(axis, type, tick) { + switch (type) { + case 'hide': + axis.tickFormat(function() { return '' }); + break; + case 'auto': + break; + default: + axis.tickFormat(d3.format(tick + type)); + } + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/bardiagram.js --- a/config/plugins/visualizations/charts/static/charts/bardiagram.js +++ /dev/null @@ -1,33 +0,0 @@ -// dependencies -define([], function() { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.d3_chart = nv.models.multiBarChart(); - - self.d3_chart.xAxis.tickFormat(d3.format('.2f')) - self.d3_chart.yAxis.tickFormat(d3.format('.1f')) - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/bardiagram/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/bardiagram/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Bar diagram', +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/histogram/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js @@ -0,0 +1,21 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Histogram', + execute : true, + columns : { + y : { + title : 'Observations' + } + }, + settings : { + x_axis_label : { + init : 'Breaks' + }, + y_axis_label : { + init : 'Density' + } + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/histogram/histogram.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/histogram/histogram.js @@ -0,0 +1,31 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // configure request + var index = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = { + x: index++, + y: index++ + } + } + + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/horizontal.js --- a/config/plugins/visualizations/charts/static/charts/horizontal.js +++ /dev/null @@ -1,33 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.d3_chart = nv.models.multiBarHorizontalChart(); - - self.d3_chart.xAxis.tickFormat(function() { return ''; }); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/horizontal/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/horizontal/config.js @@ -0,0 +1,12 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Bar diagram (horizontal)', + settings : { + x_axis_type : { + init : 'hide' + } + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/line.js --- a/config/plugins/visualizations/charts/static/charts/line.js +++ /dev/null @@ -1,39 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.lineChart(); - - self.chart_3d.xAxis - .tickFormat(d3.format(',f')); - - self.chart_3d.yAxis - .tickFormat(d3.format(',.2f')); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - - return self.chart_3d; - }); - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/line/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/line/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Line chart', +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/line/line.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/line/line.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/linewithfocus.js --- a/config/plugins/visualizations/charts/static/charts/linewithfocus.js +++ /dev/null @@ -1,37 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.lineWithFocusChart(); - - self.chart_3d.xAxis - .tickFormat(d3.format(',f')); - - self.chart_3d.yAxis - .tickFormat(d3.format(',.2f')); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - }); - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/linewithfocus/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Line with focus', +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js @@ -0,0 +1,21 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/piechart.js --- a/config/plugins/visualizations/charts/static/charts/piechart.js +++ /dev/null @@ -1,51 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // loop through data groups - for (var key in data) { - // get group - var group = data[key]; - - // format chart data - var pie_data = []; - for (var key in group.values) { - var value = group.values[key]; - pie_data.push ({ - key : value.x, - y : value.y - }); - } - - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.pieChart() - .donut(true) - .showLegend(false); - - d3.select(self.options.svg_id) - .datum(pie_data) - .call(self.chart_3d); - - nv.utils.windowResize(self.chart_3d.update); - - return self.chart_3d; - }); - } - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/piechart/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/piechart/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Pie chart', +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/piechart/piechart.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/piechart/piechart.js @@ -0,0 +1,57 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // request data + var self = this; + this.app.datasets.request(request_dictionary, function(data) { + + // loop through data groups + for (var key in request_dictionary.groups) { + // get group + var group = request_dictionary.groups[key]; + + // format chart data + var pie_data = []; + for (var key in group.values) { + var value = group.values[key]; + pie_data.push ({ + key : value.x, + y : value.y + }); + } + + // add graph to screen + nv.addGraph(function() { + self.chart_3d = nv.models.pieChart() + .donut(true) + .showLegend(false); + + self.options.svg.datum(pie_data) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + + // set chart state + chart.state('ok', 'Pie chart drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + } + }); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/scatterplot.js --- a/config/plugins/visualizations/charts/static/charts/scatterplot.js +++ /dev/null @@ -1,37 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.d3_chart = nv.models.scatterChart() - .showDistX(true) - .showDistY(true) - .color(d3.scale.category10().range()); - - self.d3_chart.xAxis.tickFormat(d3.format('.02f')) - self.d3_chart.yAxis.tickFormat(d3.format('.02f')) - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/scatterplot/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/scatterplot/config.js @@ -0,0 +1,12 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Scatter plot', + columns : { + x : { + title : 'Values for x-axis' + } + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js @@ -0,0 +1,25 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) { + nvd3_model.showDistX(true) + .showDistY(true) + .color(d3.scale.category10().range()); + }); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/stackedarea.js --- a/config/plugins/visualizations/charts/static/charts/stackedarea.js +++ /dev/null @@ -1,59 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - this.chart = options.chart; - }, - - // render - refresh : function(data) - { - // add graph to screen - var self = this; - nv.addGraph(function() { - // check data - var valid = true; - var length = 0; - for (var key in data) { - // evalute length - if (length == 0) { - length = data[key].values.length; - } else { - if (length != data[key].values.length) { - valid = false; - break; - } - } - } - if (!valid) { - return; - } - - // make plot - self.d3_chart = nv.models.stackedAreaChart() - .x(function(d) { - return d.x - }) - .y(function(d) { - return d.y - }) - .clipEdge(true); - - self.d3_chart.xAxis.tickFormat(function() { return ''; }); - - d3.select(self.options.svg_id) - .datum(data) - .call(self.d3_chart); - - nv.utils.windowResize(self.d3_chart.update); - }); - } -}); - -}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/stackedarea/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/stackedarea/config.js @@ -0,0 +1,7 @@ +define(['plugin/charts/_nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Stacked area' +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js @@ -0,0 +1,26 @@ +// dependencies +define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) { + // make plot + nvd3_model.x(function(d) { return d.x }) + .y(function(d) { return d.y }) + .clipEdge(true); + }); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/types.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/types.js @@ -0,0 +1,39 @@ +// dependencies +define(['plugin/charts/bardiagram/config', + //'plugin/charts/boxplot/config', + 'plugin/charts/histogram/config', + 'plugin/charts/horizontal/config', + 'plugin/charts/line/config', + 'plugin/charts/linewithfocus/config', + 'plugin/charts/piechart/config', + 'plugin/charts/scatterplot/config', + 'plugin/charts/stackedarea/config', + ], function(bardiagram, + //boxplot, + histogram, + horizontal, + line, + linewithfocus, + piechart, + scatterplot, + stackedarea + ) { + +// widget +return Backbone.Model.extend( +{ + // types + defaults: { + 'bardiagram' : bardiagram, + //'boxplot' : boxplot, + 'horizontal' : horizontal, + 'histogram' : histogram, + 'line' : line, + 'linewithfocus' : linewithfocus, + 'piechart' : piechart, + 'scatterplot' : scatterplot, + 'stackedarea' : stackedarea + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/datasets.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/datasets.js @@ -0,0 +1,149 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.Collection.extend( +{ + // list of datasets + list: {}, + + // initialize + initialize: function(app, options) + { + // link app + this.app = app; + + // configure options + this.options = Utils.merge(options, this.optionsDefault); + }, + + // wait + request: function(options, success, error) { + // link this + var self = this; + + // check if column data is requested + if (options.groups) { + this._fetch(options, success); + } else { + // check if dataset is available from cache + var dataset = this.list[options.id]; + if (dataset) { + success(dataset); + return; + } + + // request dataset + Utils.request('GET', config.root + 'api/datasets/' + options.id, {}, function(dataset) { + switch (dataset.state) { + case 'error': + if (error) { + error(dataset); + } + break; + default: + self.list[options.id] = dataset; + success(dataset); + } + }); + } + }, + + // fetch data columns into dataset object + _fetch: function(options, callback) { + // set offset + var offset = options.start ? options.start : 0; + + // set limit + var limit = Math.abs(options.end - options.start); + var query_limit = this.app.config.get('query_limit'); + if (!limit || limit > query_limit) { + limit = query_limit; + } + + // get column indices + var index_string = ''; + var index_map = {}; + var index_count = 0; + for (var i in options.groups) { + var group = options.groups[i]; + for (var key in group.columns) { + var column = group.columns[key]; + + // add to index string + index_string += column + ','; + + // add to dictionary + index_map[column] = index_count; + + // increase counter + index_count++; + } + } + if (index_count == 0) { + callback({}); + return; + } + index_string = index_string.substring(0, index_string.length - 1); + + // initialize result dictionary + var result = options.groups.slice(0); + for (var i in result) { + result[i].values = []; + } + + // make request + var self = this; + Utils.request('GET', config.root + 'api/datasets/' + options.id, { + data_type : 'raw_data', + provider : 'dataset-column', + limit : limit, + offset : offset, + indeces : index_string + }, function(response) { + + // loop through rows + for (var i in response.data) { + // get row + var row = response.data[i]; + + // collect all data into the defined groups + for (var j in options.groups) { + // get group + var group = options.groups[j]; + + // initialize value + var value = { + x : parseInt(i) + offset + }; + + // fill value + for (var key in group.columns) { + // get column + var column = group.columns[key]; + + // identify column + var index = index_map[column]; + + // read value from row + var v = row[index]; + if(isNaN(v) || !v) { + v = 0; + } + + // add value to dictionary + value[key] = v; + } + + // add to result + result[j].values.push(value); + } + } + + // callback + callback(result); + }); + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/deferred.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -0,0 +1,85 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// deferred process handler +return Backbone.Model.extend( +{ + // queue + queue: [], + + // list of currently registered processes + process: {}, + + // process counter + counter: 0, + + // initialize + initialize: function() + { + // loop through queue and check states + this.on('refresh', function() { + if (this.counter == 0) { + for (var index in this.queue) { + // execute callback + this.queue[index](); + + // remove callback + this.queue.splice(index, 1); + } + } + }); + }, + + // executes callback once all processes are unregistered + execute: function(callback) { + // add wrapper to queue + this.queue.push(callback); + + // trigger change + this.trigger('refresh'); + }, + + // register process + register: function() { + // create unique id + var id = Utils.uuid(); + + // add process to queue + this.process[id] = true; + + // increase process counter + this.counter++; + + // log + console.debug('Deferred:register() - Registering ' + id); + + // return unique id + return id; + }, + + // unregister process + done: function(id) { + // delete tag + delete this.process[id]; + + // decrease process counter + this.counter--; + + // log + console.debug('Deferred:done() - Unregistering ' + id); + + // trigger change + this.trigger('refresh'); + }, + + // ready + ready: function() { + if (this.counter == 0) { + return true; + } else { + return false; + } + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/jobs.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -0,0 +1,152 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.Model.extend( +{ + // initialize + initialize: function(app, options) { + // link app + this.app = app; + + // link options + this.options = Utils.merge(options, this.optionsDefault); + }, + + // clean + cleanup: function(chart) { + // cleanup previous dataset file + var previous = chart.get('dataset_id_job'); + if (previous != '') { + var self = this; + Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() { + // update galaxy history + self._refreshHdas(); + }); + + // reset id + chart.set('dataset_id_job', ''); + } + }, + + // create job + submit: function(chart, settings_string, columns_string, success, error) { + // link this + var self = this; + + // backup chart details + var chart_id = chart.id; + var chart_type = chart.get('type'); + + // get chart settings + var chart_settings = this.app.types.get(chart_type); + + // configure tool + data = { + 'tool_id' : 'chartskit', + 'inputs' : { + 'input' : { + 'id' : chart.get('dataset_id'), + 'src' : 'hda' + }, + 'module' : chart_type, + 'columns' : columns_string, + 'settings' : settings_string + } + } + + // set chart state + chart.state('wait', 'Sending job request...'); + + // post job + Utils.request('POST', config.root + 'api/tools', data, + // success handler + function(response) { + if (!response.outputs || response.outputs.length == 0) { + chart.state('failed', 'Job submission failed. No response.'); + + // call error + error && error(); + } else { + // update galaxy history + self._refreshHdas(); + + // get dataset + var job = response.outputs[0]; + + // check dataset + chart.state('wait', 'Job has been queued...'); + + // backup resulting dataset id + chart.set('dataset_id_job', job.id); + + // save + this.app.storage.save(); + + // wait for job completion + self._loop(job.id, function(job) { + switch (job.state) { + case 'ok': + // update state + chart.state('wait', 'Job completed successfully...'); + + // execute success + success(job); + + // stop loop + return true; + case 'error': + // update state + chart.state('failed', 'Job has failed. Please check the history for details.'); + + // call error + error && error(); + + // stop loop + return true; + case 'running': + // wait + chart.state('wait', 'Job is running...'); + + // continue loop + return false; + } + }); + } + }, + // error handler + function(response) { + var message = ''; + if (response && response.message && response.message.data && response.message.data.input) { + message = response.message.data.input + '.'; + } + // update state + chart.state('failed', 'This visualization requires the Charts-Kit. Please make sure it is installed. ' + message); + + // call error + error && error(); + + } + ); + }, + + // request job details + _loop: function(id, callback) { + var self = this; + Utils.request('GET', config.root + 'api/datasets/' + id, {}, function(job) { + if (!callback(job)) { + setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout')); + } + }); + }, + + // refresh history panel + _refreshHdas: function() { + // update galaxy history + if (Galaxy && Galaxy.currHistoryPanel) { + Galaxy.currHistoryPanel.refreshHdas(); + } + } +}); + +}); \ No newline at end of file diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/portlet.js --- a/config/plugins/visualizations/charts/static/library/portlet.js +++ /dev/null @@ -1,171 +0,0 @@ -// dependencies -define(['library/utils'], function(Utils) { - -// return -return Backbone.View.extend( -{ - // visibility - visible: false, - - // defaults options - optionsDefault: { - label : '', - icon : 'fa-tasks', - buttons : null, - body : null, - height : null, - operations : null, - placement : 'bottom', - overflow : 'auto' - }, - - // content - $content : null, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this.template(this.options)); - - // link content - this.$content = this.$el.find('#content'); - - // set content height - if (this.options.height) { - this.$el.find('#body').css('height', this.options.height); - this.$el.find('#content').css('overflow', this.options.overflow); - } - - // append buttons - this.$buttons = $(this.el).find('#buttons'); - if (this.options.buttons) { - // link functions - var self = this; - $.each(this.options.buttons, function(name, item) { - item.$el.prop('id', name); - self.$buttons.append(item.$el); - }); - } else { - this.$buttons.remove(); - } - - // append operations - this.$operations = $(this.el).find('#operations'); - if (this.options.operations) { - // link functions - var self = this; - $.each(this.options.operations, function(name, item) { - item.$el.prop('id', name); - self.$operations.append(item.$el); - }); - } - - // add body - if(this.options.body) { - this.append(this.options.body); - } - }, - - // append - append: function($el) { - this.$content.append(Utils.wrap($el)); - }, - - // content - content: function() { - return this.$content; - }, - - // hide modal - show: function(){ - // fade in - this.$el.fadeIn('fast'); - - // set flag - this.visible = true; - }, - - // hide modal - hide: function(){ - // fade out - this.$el.fadeOut('fast'); - - // set flag - this.visible = false; - }, - - // enable buttons - enableButton: function(id) { - this.$buttons.find('#' + id).prop('disabled', false); - }, - - // disable buttons - disableButton: function(id) { - this.$buttons.find('#' + id).prop('disabled', true); - }, - - // enable operation - hideOperation: function(id) { - this.$operations.find('#' + id).hide(); - }, - - // disable operation - showOperation: function(id) { - this.$operations.find('#' + id).show(); - }, - - // set operation - setOperation: function(id, callback) { - var $el = this.$operations.find('#' + id); - $el.off('click'); - $el.on('click', callback); - }, - - // label - label: function(new_label) { - var $el = this.$el.find('#label'); - if (new_label) { - $el.html(new_label); - } - return $el.html(); - }, - - // fill regular modal template - template: function(options) { - var tmpl = '<div class="toolForm">'; - - if (options.label || options.icon) { - tmpl += '<div id="title" class="toolFormTitle" style="overflow:hidden;">' + - '<div id="operations" style="float: right;"></div>' + - '<div style="overflow: hidden">'; - - if (options.icon) - tmpl += '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; - - tmpl += '<div id="label" style="padding-top: 2px; float: left;">' + options.label + '</div>'; - - tmpl += '</div>' + - '</div>'; - } - tmpl += '<div id="body" class="toolFormBody">'; - - if (options.placement == 'top') { - tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; - } - - tmpl += '<div id="content" class="content" style="height: inherit; padding: 10px;"></div>'; - - if (options.placement == 'bottom') { - tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; - } - - tmpl += '</div>' + - '</div>'; - return tmpl; - } -}); - -}); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/1ad62c772728/ Changeset: 1ad62c772728 Branch: stable User: natefoo Date: 2014-04-15 01:28:10 Summary: Added tag release_2014.04.14 for changeset 9e53251b0b7e Affected #: 1 file diff -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc -r 1ad62c7727285084e46ee3572835483e34c551a5 .hgtags --- a/.hgtags +++ b/.hgtags @@ -6,3 +6,4 @@ 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 +9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 https://bitbucket.org/galaxy/galaxy-central/commits/3b3365a39194/ Changeset: 3b3365a39194 User: natefoo Date: 2014-04-15 01:28:45 Summary: Merge stable to default Affected #: 1 file diff -r 855b03513ca92f33be6d4da54afffadad294a9cc -r 3b3365a391944f848b403412f226ee9e5499c0d5 .hgtags --- a/.hgtags +++ b/.hgtags @@ -6,3 +6,4 @@ 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 +9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Merged in hillrunner2008/galaxy-central (pull request #367)
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/855b03513ca9/ Changeset: 855b03513ca9 User: dan Date: 2014-04-14 22:56:48 Summary: Merged in hillrunner2008/galaxy-central (pull request #367) added support for the visualization of gtf file format in IGB Affected #: 2 files diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56dee1c67384/ Changeset: 56dee1c67384 User: dcnorris Date: 2014-04-14 16:05:03 Summary: adding support for the visualization of gtf file format in IGB Affected #: 2 files diff -r 6ae3b10ec63e21b0df60f9428ab312ecad0e4e62 -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r 6ae3b10ec63e21b0df60f9428ab312ecad0e4e62 -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/fe0335898665/ Changeset: fe0335898665 User: dcnorris Date: 2014-04-14 22:43:49 Summary: converted tabs to spaces Affected #: 2 files diff -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 -r fe03358986651d3e4bac287cd69e77a925d05cb3 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,7 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> - <display file="igb/gtf.xml" /> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 -r fe03358986651d3e4bac287cd69e77a925d05cb3 display_applications/igb/gtf.xml --- a/display_applications/igb/gtf.xml +++ b/display_applications/igb/gtf.xml @@ -1,17 +1,17 @@ <display id="igb_gtf" version="1.0.0" name="display in IGB"> - <link id="View" name="View"> - <url>$bioviz</url> - <param type="data" name="gtf_file_for_name" viewable="False"/> - <param type="template" name="niceName" viewable="False" strip="True"> - #import re - #set nm=$gtf_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> - - <param type="template" name="bioviz" strip="True" > - http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} </param> - </link> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link></display> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/855b03513ca9/ Changeset: 855b03513ca9 User: dan Date: 2014-04-14 22:56:48 Summary: Merged in hillrunner2008/galaxy-central (pull request #367) added support for the visualization of gtf file format in IGB Affected #: 2 files diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: merge next stable
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c2a2ce95501c/ Changeset: c2a2ce95501c User: dan Date: 2014-04-14 22:34:16 Summary: merge next stable Affected #: 1 file diff -r 12265c0cca1f20c5c87c909a4e6faaff089c70ee -r c2a2ce95501c9e1a3da2550ce963376a49449481 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -708,14 +708,6 @@ # Enable enforcement of quotas. Quotas can be set from the Admin interface. #enable_quotas = False -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - # This option allows users to see the full path of datasets via the "View # Details" option in the history. Administrators can always see this. #expose_dataset_path = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Remove duplicated enable_unique_workflow_defaults from universe_wsgi.ini.sample.
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1165a5a1221a/ Changeset: 1165a5a1221a Branch: next-stable User: dan Date: 2014-04-14 22:33:57 Summary: Remove duplicated enable_unique_workflow_defaults from universe_wsgi.ini.sample. Affected #: 1 file diff -r 52f8e109315ae84a36999586d333e1758511477f -r 1165a5a1221ac538bcbfd4e046a33e5bbfb1106a universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -708,14 +708,6 @@ # Enable enforcement of quotas. Quotas can be set from the Admin interface. #enable_quotas = False -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - # This option allows users to see the full path of datasets via the "View # Details" option in the history. Administrators can always see this. #expose_dataset_path = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: merge next stable
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12265c0cca1f/ Changeset: 12265c0cca1f User: dan Date: 2014-04-14 22:30:29 Summary: merge next stable Affected #: 1 file diff -r a48baeee4ff4014ea42a65adc73f3e5f6184f9a4 -r 12265c0cca1f20c5c87c909a4e6faaff089c70ee 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 @@ -192,7 +192,12 @@ #This needs to be done recursively through grouping parameters def rerun_callback( input, value, prefixed_name, prefixed_label ): if isinstance( value, UnvalidatedValue ): - return str( value ) + try: + return input.to_html_value( value.value, trans.app ) + except Exception, e: + # Need to determine when (if ever) the to_html_value call could fail. + log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) ) + return str( value ) if isinstance( input, DataToolParameter ): if isinstance(value,list): values = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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