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commit/galaxy-central: guerler: Charts: Fix resizing
by commits-noreply＠bitbucket.org 17 May '14

17 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/632087d47985/ Changeset: 632087d47985 User: guerler Date: 2014-05-17 16:45:14 Summary: Charts: Fix resizing Affected #: 6 files diff -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 -r 632087d479859d0a8152267f6c21a623722bc875 config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -54,13 +54,13 @@ display: inline-block; } -.charts-viewport .container { +.charts-viewport .charts-viewport-container { float: left; display: block; height: 100%; } -.charts-viewport .canvas { +.charts-viewport .charts-viewport-canvas { display: block; width:100%; height: inherit; diff -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 -r 632087d479859d0a8152267f6c21a623722bc875 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ 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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}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new 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r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var 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href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$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.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)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}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var 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heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bar/config","plugin/charts/nvd3_bar_stacked/config","plugin/charts/nvd3_bar_horizontal/config","plugin/charts/nvd3_bar_horizontal_stacked/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_histogram_discrete/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,highcharts_boxplot:p,heatmap:d}})}),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 3bdd01eda31d3f9b195b11982b31c58bc37254e8 -r 632087d479859d0a8152267f6c21a623722bc875 config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js @@ -23,7 +23,7 @@ }, y: { index: index++ - }, + } } } diff -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 -r 632087d479859d0a8152267f6c21a623722bc875 config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js @@ -1,12 +1,13 @@ define(['plugin/charts/nvd3/config'], function(nvd3_config) { return $.extend(true, {}, nvd3_config, { - title : 'Histogram', - category : 'Histograms', - execute : 'histogram_discrete', + title : 'Histogram (discrete)', + category : 'Data processing (requires \'charts\' tool from Toolshed)', + execute : 'histogramdiscrete', columns : { y : { - title : 'Observations' + title : 'Observations', + is_label : true } }, settings : { diff -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 -r 632087d479859d0a8152267f6c21a623722bc875 config/plugins/visualizations/charts/static/charts/types.js --- a/config/plugins/visualizations/charts/static/charts/types.js +++ b/config/plugins/visualizations/charts/static/charts/types.js @@ -4,6 +4,7 @@ 'plugin/charts/nvd3_bar_horizontal/config', 'plugin/charts/nvd3_bar_horizontal_stacked/config', 'plugin/charts/nvd3_histogram/config', + 'plugin/charts/nvd3_histogram_discrete/config', 'plugin/charts/nvd3_line/config', 'plugin/charts/nvd3_line_focus/config', 'plugin/charts/nvd3_pie/config', @@ -18,6 +19,7 @@ nvd3_bar_horizontal, nvd3_bar_horizontal_stacked, nvd3_histogram, + nvd3_histogram_discrete, nvd3_line, nvd3_line_focus, nvd3_pie, @@ -46,6 +48,7 @@ 'nvd3_scatter' : nvd3_scatter, 'nvd3_pie' : nvd3_pie, 'nvd3_histogram' : nvd3_histogram, + //'nvd3_histogram_discrete' : nvd3_histogram_discrete, 'highcharts_boxplot' : highcharts_boxplot, 'heatmap' : heatmap } diff -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 -r 632087d479859d0a8152267f6c21a623722bc875 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 @@ -282,9 +282,9 @@ // template svg/div element _templateContainer: function(tag, width) { - return '<div class="container" style="width:' + width + '%;">' + + return '<div class="charts-viewport-container" style="width:' + width + '%;">' + '<div id="menu"/>' + - '<' + tag + ' id="canvas" class="canvas">' + + '<' + tag + ' id="canvas" class="charts-viewport-canvas">' + '</div>'; } 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: greg: I meant to make this file a .sample file.
by commits-noreply＠bitbucket.org 17 May '14

17 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3bdd01eda31d/ Changeset: 3bdd01eda31d User: greg Date: 2014-05-17 16:10:23 Summary: I meant to make this file a .sample file. Affected #: 3 files diff -r 2e6e51179f7177b743bd970095be7e261ae62700 -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml --- a/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml +++ /dev/null @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<user> - <email>admin(a)test.org</email> - <password>testuser</password> - <username>admin</username> -</user> diff -r 2e6e51179f7177b743bd970095be7e261ae62700 -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample @@ -0,0 +1,12 @@ +<?xml version="1.0"?> + +<user> + <email>admin(a)test.org</email> + <password>testuser</password> + <username>admin</username> +</user> diff -r 2e6e51179f7177b743bd970095be7e261ae62700 -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 run_tool_shed.sh --- a/run_tool_shed.sh +++ b/run_tool_shed.sh @@ -15,6 +15,7 @@ tool_sheds_conf.xml.sample openid_conf.xml.sample universe_wsgi.ini.sample + lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample tool-data/shared/ncbi/builds.txt.sample tool-data/shared/ensembl/builds.txt.sample tool-data/shared/ucsc/builds.txt.sample 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: martenson: data libraries: permissions UI and API work, library router fixes, security addition for retrieving paginated roles for given dataset
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e6e51179f71/ Changeset: 2e6e51179f71 User: martenson Date: 2014-05-17 00:13:26 Summary: data libraries: permissions UI and API work, library router fixes, security addition for retrieving paginated roles for given dataset Affected #: 14 files diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -208,6 +208,75 @@ roles.add( role ) return self.sort_by_attr( [ role for role in roles ], 'name' ) + def get_valid_dataset_roles( self, trans, dataset, query, page, page_limit ): + """ + This method retrieves the list of possible roles that user can select + in the dataset permissions form. Admins can select any role so the + results are paginated in order to save the bandwidth and to speed + things up. + Standard users can select their own private role, any fo their + sharing roles and any public role (not private and not sharing). + """ + roles = [] + if query is not None: + query = query.replace( '_', '/_' ).replace( '%', '/%' ).replace( '/', '//' ) + search_query = query + '%' + # Limit the query only to get the page needed + limit = page * page_limit + + # Admins see it all + if trans.user_is_admin(): + # Add all roles that fit the query + db_query = trans.sa_session.query( trans.app.model.Role ).filter( self.model.Role.table.c.deleted == False ) + if query is not None: + db_query = db_query.filter( self.model.Role.table.c.name.like( search_query, escape='/' ) ) + for role in ( db_query.order_by( self.model.Role.table.c.name ).limit( limit ) ): + roles.append( role ) + # Take last page of the selection + roles = roles[ ( -page_limit ): ] + + # Non-admins see the list of relevant roles + else: + if self.dataset_is_public( dataset ): + # Add the current user's private role + roles.append( self.get_private_user_role( trans.user ) ) + # Add the current user's sharing roles + for role in self.get_sharing_roles( trans.user ): + roles.append( role ) + # Add all remaining non-private, non-sharing roles + for role in trans.sa_session.query( trans.app.model.Role ) \ + .filter( and_( self.model.Role.table.c.deleted == False, + self.model.Role.table.c.type != self.model.Role.types.PRIVATE, + self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ + .order_by( self.model.Role.table.c.name ): + roles.append( role ) + + else: + # If item has roles associated with the access permission, we need to start with them. + access_roles = dataset.get_access_roles( trans ) + for role in access_roles: + if trans.user_is_admin() or self.ok_to_display( trans.user, role ): + roles.append( role ) + # Each role potentially has users. We need to find all roles that each of those users have. + for ura in role.users: + user = ura.user + for ura2 in user.roles: + if trans.user_is_admin() or self.ok_to_display( trans.user, ura2.role ): + roles.append( ura2.role ) + # Each role also potentially has groups which, in turn, have members ( users ). We need to + # find all roles that each group's members have. + for gra in role.groups: + group = gra.group + for uga in group.users: + user = uga.user + for ura in user.roles: + if trans.user_is_admin() or self.ok_to_display( trans.user, ura.role ): + roles.append( ura.role ) + + # Omit duplicated roles by converting to set + return_roles = set( roles ) + return self.sort_by_attr( [ role for role in return_roles ], 'name' ) + def get_legitimate_roles( self, trans, item, cntrller ): """ Return a sorted list of legitimate roles that can be associated with a permission on diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -75,9 +75,16 @@ for a given dataset permission. """ current_user_roles = trans.get_current_user_roles() - page = int( kwd.get( 'page', None ) ) - page_limit = int( kwd.get( 'page_limit', None ) ) - query = kwd.get ( 'q', None ) + + page = kwd.get( 'page', None ) + if page is not None: + page = int( page ) + + page_limit = kwd.get( 'page_limit', None ) + if page_limit is not None: + page_limit = int( page_limit ) + + query = kwd.get( 'q', None ) if page is None: page = 1 @@ -96,11 +103,8 @@ if not can_manage: raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to access permissions.' ) - cntrller = 'standard_user' - if trans.user_is_admin(): - cntrller = 'library_admin' + roles = trans.app.security_agent.get_valid_dataset_roles( trans, dataset, query, page, page_limit ) - roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) total_roles = len( roles ) return_roles = [] for role in roles: @@ -109,6 +113,23 @@ return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) @expose_api + def get_roles( self, trans, encoded_dataset_id, **kwd ): + try: + library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) + except Exception, e: + raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) + dataset = library_dataset.library_dataset_dataset_association.dataset + + roles = dataset.get_access_roles( trans ) + + # roles = dataset.get_manage_permissions_roles( trans ) + + # roles = trans.app.security_agent.get_current_dataset_roles( trans, dataset, trans.app.security_agent.permitted_actions.DATASET_ACCESS ) + # Omit duplicated roles by converting to set + roles = set( roles ) + return [ role.name for role in roles ] + + @expose_api def delete( self, trans, encoded_dataset_id, **kwd ): """ delete( self, trans, encoded_dataset_id, **kwd ): diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -224,6 +224,12 @@ action='show_roles', conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'show_legitimate_lda_roles', + '/api/libraries/datasets/:encoded_dataset_id/permissions/current', + controller='lda_datasets', + action='get_roles', + conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'delete_lda_item', '/api/libraries/datasets/:encoded_dataset_id', controller='lda_datasets', diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -74,6 +74,7 @@ library_router: null, folderToolbarView: null, folderListView: null, + datasetView: null, initialize : function(){ Galaxy.libraries = this; @@ -106,10 +107,17 @@ }); this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ - new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}) + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); }); + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ - new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}) + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); }); Backbone.history.start({pushState: false}); diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -20,10 +20,15 @@ events: { "click .toolbtn_modify_dataset" : "enableModification", "click .toolbtn_cancel_modifications" : "render", - "click .toolbtn_change_permissions" : "showPermissions", "click .toolbtn-download-dataset" : "downloadDataset", "click .toolbtn-import-dataset" : "importIntoHistory", - "click .toolbtn-share-dataset" : "shareDataset" + "click .toolbtn-share-dataset" : "shareDataset", + + // missing features below + "click .toolbtn_save_modifications" : "comingSoon", + "click .btn-remove-restrictions" : "comingSoon", + "click .btn-make-private" : "comingSoon", + "click .btn-share-dataset" : "comingSoon" }, @@ -132,7 +137,7 @@ }, importCurrentIntoHistory: function(){ - var self = this; + // var self = this; var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); var historyItem = new mod_library_model.HistoryItem(); historyItem.url = historyItem.urlRoot + history_id + '/contents'; @@ -165,88 +170,102 @@ mod_toastr.info('Feature coming soon.'); }, + goBack: function(){ + Galaxy.libraries.library_router.back(); + }, + showPermissions: function(){ $(".tooltip").remove(); var template = this.templateDatasetPermissions(); this.$el.html(template({item: this.model})); + // Select works different for admins + var is_admin = false; + if (Galaxy.currUser){ + is_admin = Galaxy.currUser.isAdmin(); + } + var self = this; - this.access_perm = new mod_select.View({ - css: 'access_perm', - multiple:true, - placeholder: 'Click to select a role', - container: self.$el.find('#access_perm'), - ajax: { - url: "/api/libraries/datasets/5969b1f7201f12ae/permissions", - dataType: 'json', - quietMillis: 100, - data: function (term, page) { // page is the one-based page number tracked by Select2 - return { - q: term, //search term - page_limit: 10, // page size - page: page // page number - }; - }, - results: function (data, page) { - var more = (page * 10) < data.total; // whether or not there are more results available - // notice we return the value of more so Select2 knows if more results can be loaded - return {results: data.roles, more: more}; - } - }, - formatResult : function roleFormatResult(role) { - return role.name; - }, + // load all current permissions + $.get( "/api/libraries/datasets/" + self.id + "/permissions/current").done(function(fetched_permissions) { + var selected_roles = []; + for (var i = 0; i < fetched_permissions.length; i++) { + selected_roles.push(fetched_permissions[i] + ':' + fetched_permissions[i]); + } + // ACCESS PERMISSIONS + if (is_admin){ // Admin has a special select that allows remote searching + var access_select_options = { + minimumInputLength: 1, + css: 'access_perm', + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#access_perm'), + ajax: { + url: "/api/libraries/datasets/" + self.id + "/permissions", + dataType: 'json', + quietMillis: 100, + data: function (term, page) { // page is the one-based page number tracked by Select2 + return { + q: term, //search term + page_limit: 10, // page size + page: page // page number + }; + }, + results: function (data, page) { + var more = (page * 10) < data.total; // whether or not there are more results available + // notice we return the value of more so Select2 knows if more results can be loaded + return {results: data.roles, more: more}; + } + }, + formatResult : function roleFormatResult(role) { + return role.name + ' type: ' + role.type; + }, - formatSelection: function roleFormatSelection(role) { - return role.name; - }, - initSelection: function(element, callback) { - // the input tag has a value attribute preloaded that points to a preselected role's id - // this function resolves that id attribute to an object that select2 can render - // using its formatResult renderer - that way the role name is shown preselected - var data = []; - $(element.val().split(",")).each(function(i) { - var item = this.split(':'); - data.push({ - id: item[1], - name: item[1] - }); + formatSelection: function roleFormatSelection(role) { + return role.name; + }, + initSelection: function(element, callback) { + // the input tag has a value attribute preloaded that points to a preselected role's id + // this function resolves that id attribute to an object that select2 can render + // using its formatResult renderer - that way the role name is shown preselected + var data = []; + $(element.val().split(",")).each(function() { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: selected_roles.join(','), + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + }; + + this.accessSelectObject = new mod_select.View(access_select_options); + } else { // Non-admins have select with pre-loaded options + var template = this.templateAccessSelect(); + $.get( "/api/libraries/datasets/" + self.id + "/permissions", function( data ) { + $('.access_perm').html(template({options:data.roles})); + this.accessSelectObject = $('#access_select').select2(); + }).fail(function() { + mod_toastr.error('An error occurred while fetching data with permissions. :('); }); - callback(data); - }, - initialData: 'marten@bx.psu.edu:marten@bx.psu.edu', - dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + } + }).fail(function(){ + mod_toastr.error('An error occurred while fetching data with permissions. :('); }); - // this.access_perm.$el.append($('<option>', {value:"NEWVAL", text: "New Option Text"})); - // this.modify_perm = new mod_select.View({ - // css: 'modify_perm', - // placeholder: 'Select a role', - // // onchange : function() { - // // self.model.set('access_perm', self.select_genome.value()); - // // }, - // data: [{id:'test',text:'testik'}, {id:'dududu', text:'dadada'}], - // container: self.$el.find('#modify_perm'), - // multiple: true - // // value: self.model.get('access_perm') - // }); - // this.modify_perm.$el.append($('<option>', {value:"NEWVAL", text: "New Option Text"})); - - // this.manage_perm = new mod_select.View({ - // css: 'manage_perm', - // placeholder: 'Select a role', - // // onchange : function() { - // // self.model.set('access_perm', self.select_genome.value()); - // // }, - // data: [{id:'test',text:'testik'}, {id:'dududu', text:'dadada'}], - // container: self.$el.find('#manage_perm'), - // multiple: true - // // value: self.model.get('access_perm') - // }); - // this.manage_perm.$el.append($('<option>', {value:"NEWVAL", text: "New Option Text"})); + //TODO add permissions for modification and management of datasets $("#center [data-toggle]").tooltip(); + //hack to show scrollbars + $("#center").css('overflow','auto'); + }, + + comingSoon: function(){ + mod_toastr.warning('Feature coming soon'); }, @@ -259,7 +278,7 @@ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify dataset" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Change permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Change permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' </div>'); @@ -481,8 +500,8 @@ tmpl_array.push('<div class="library_style_container">'); tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> go to Folder</span></button></a>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> see the Dataset</span></button><a>'); tmpl_array.push(' </div>'); @@ -511,11 +530,16 @@ tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to see the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>'); tmpl_array.push('</p>'); + tmpl_array.push('<p>You can share this dataset with another Galaxy user. '); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to see the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + tmpl_array.push('</p>'); + tmpl_array.push('<h2>Advanced permissions</h2>'); - tmpl_array.push('<p>You can assign any number of roles to any of the following three dataset permissions:</p>'); + tmpl_array.push('<p>You can assign any number of roles to any of the following three dataset permission types. However please read carefully the implications of such actions.</p>'); tmpl_array.push('<h3>Access Roles</h3>'); tmpl_array.push('<div class="alert alert-info">User has to have <strong>all these roles</strong> in order to see this dataset.</div>'); tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); tmpl_array.push('<h3>Modify Roles</h3>'); tmpl_array.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can modify the information about this dataset.</div>'); tmpl_array.push('<div id="modify_perm" class="modify_perm"></div>'); @@ -532,7 +556,7 @@ return _.template(tmpl_array.join('')); }, -templateBulkImportInModal : function(){ + templateBulkImportInModal: function(){ var tmpl_array = []; tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); @@ -545,8 +569,22 @@ tmpl_array.push('</span>'); return _.template(tmpl_array.join('')); + }, + + templateAccessSelect: function(){ + var tmpl_array = []; + + tmpl_array.push('<select id="access_select" multiple>'); + + tmpl_array.push(' <% _.each(options, function(option) { %>'); + tmpl_array.push(' <option value="<%- option.name %>"><%- option.name %></option>'); + tmpl_array.push(' <% }); %>'); + + tmpl_array.push('</select>'); + + + return _.template(tmpl_array.join('')); } - }); return { diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -46,7 +46,7 @@ }, showDatasetDetails : function(){ - this.dataset_view = new mod_library_dataset_view.LibraryDatasetView({id: this.id}); + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: this.id}); }, /** diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 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 @@ -520,7 +520,7 @@ tmpl_array.push('<div class="library_style_container">'); // TOOLBAR tmpl_array.push('<div id="library_toolbar">'); - tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_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" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>'); tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><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="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 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 @@ -118,7 +118,7 @@ tmpl_array.push(' <div id="toolbar_form">'); 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="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted</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(' <% } %>'); diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/mvc/ui/ui-select.js --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -17,6 +17,7 @@ value : null, multiple : false, minimumInputLength : 0, + // example format of initial data: "id:name,55:anotherrole@role.com,27:role@role.com" initialData : '' }, diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view"],function(f,c,h,l,i,a,g,e,j,d){var m=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var k=l.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new k({id:"global-lib-prefs"});this.library_router=new m();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new e.LibraryToolbarView();Galaxy.libraries.libraryListView=new g.LibraryListView()});this.library_router.on("route:folder_content",function(n){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new j.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n})});this.library_router.on("route:download",function(n,o){if($("#folder_list_body").find(":checked").length===0){h.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+n,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(n,o);Galaxy.libraries.library_router.navigate("folders/"+n,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(o,n){new d.LibraryDatasetView({id:n})});this.library_router.on("route:dataset_permissions",function(o,n){new d.LibraryDatasetView({id:n,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view"],function(f,c,h,l,i,a,g,e,j,d){var m=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var k=l.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new k({id:"global-lib-prefs"});this.library_router=new m();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new e.LibraryToolbarView();Galaxy.libraries.libraryListView=new g.LibraryListView()});this.library_router.on("route:folder_content",function(n){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new j.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n})});this.library_router.on("route:download",function(n,o){if($("#folder_list_body").find(":checked").length===0){h.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+n,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(n,o);Galaxy.libraries.library_router.navigate("folders/"+n,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(o,n){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new d.LibraryDatasetView({id:n})});this.library_router.on("route:dataset_permissions",function(o,n){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new d.LibraryDatasetView({id:n,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn_change_permissions":"showPermissions","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=this;var g=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var h=new c.HistoryItem();h.url=h.urlRoot+g+"/contents";var e="/api/histories/"+g+"/set_as_current";$.ajax({url:e,type:"PUT"});h.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(j,i){if(typeof i.responseJSON!=="undefined"){d.error("Dataset not imported. "+i.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},showPermissions:function(){$(".tooltip").remove();var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model}));var e=this;this.access_perm=new b.View({css:"access_perm",multiple:true,placeholder:"Click to select a role",container:e.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/5969b1f7201f12ae/permissions",dataType:"json",quietMillis:100,data:function(i,j){return{q:i,page_limit:10,page:j}},results:function(k,j){var i=(j*10)<k.total;return{results:k.roles,more:i}}},formatResult:function f(i){return i.name},formatSelection:function h(i){return i.name},initSelection:function(i,k){var j=[];$(i.val().split(",")).each(function(l){var m=this.split(":");j.push({id:m[1],name:m[1]})});k(j)},initialData:"marten@bx.psu.edu:marten@bx.psu.edu",dropdownCssClass:"bigdrop"});$("#center [data-toggle]").tooltip()},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify dataset" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Change permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1><%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-success">You have rights to change permissions on this dataset. That means you can control who can access it, who can modify it and also appoint others that can manage permissions on it.</div>');e.push('<div class="dataset_table">');e.push("<h2>Basic permissions</h2>");e.push("<p>You can remove all access restrictions on this dataset. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to see the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>');e.push("</p>");e.push("<p>You can make this dataset private to you. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to see the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>');e.push("</p>");e.push("<h2>Advanced permissions</h2>");e.push("<p>You can assign any number of roles to any of the following three dataset permissions:</p>");e.push("<h3>Access Roles</h3>");e.push('<div class="alert alert-info">User has to have <strong>all these roles</strong> in order to see this dataset.</div>');e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push("<h3>Modify Roles</h3>");e.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can modify the information about this dataset.</div>');e.push('<div id="modify_perm" class="modify_perm"></div>');e.push("<h3>Manage Roles</h3>");e.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can change permissions of this dataset.</div>');e.push('<div id="manage_perm" class="manage_perm"></div>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .toolbtn_save_modifications":"comingSoon","click .btn-remove-restrictions":"comingSoon","click .btn-make-private":"comingSoon","click .btn-share-dataset":"comingSoon"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(){$(".tooltip").remove();var f=this.templateDatasetPermissions();this.$el.html(f({item:this.model}));var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}var e=this;$.get("/api/libraries/datasets/"+e.id+"/permissions/current").done(function(j){var k=[];for(var m=0;m<j.length;m++){k.push(j[m]+":"+j[m])}if(g){var h={minimumInputLength:1,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:e.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+e.id+"/permissions",dataType:"json",quietMillis:100,data:function(i,p){return{q:i,page_limit:10,page:p}},results:function(q,p){var i=(p*10)<q.total;return{results:q.roles,more:i}}},formatResult:function l(i){return i.name+" type: "+i.type},formatSelection:function o(i){return i.name},initSelection:function(i,q){var p=[];$(i.val().split(",")).each(function(){var r=this.split(":");p.push({id:r[1],name:r[1]})});q(p)},initialData:k.join(","),dropdownCssClass:"bigdrop"};this.accessSelectObject=new b.View(h)}else{var n=this.templateAccessSelect();$.get("/api/libraries/datasets/"+e.id+"/permissions",function(i){$(".access_perm").html(n({options:i.roles}));this.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")});$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},comingSoon:function(){d.warning("Feature coming soon")},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify dataset" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Change permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> go to Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> see the Dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1><%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-success">You have rights to change permissions on this dataset. That means you can control who can access it, who can modify it and also appoint others that can manage permissions on it.</div>');e.push('<div class="dataset_table">');e.push("<h2>Basic permissions</h2>");e.push("<p>You can remove all access restrictions on this dataset. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to see the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>');e.push("</p>");e.push("<p>You can make this dataset private to you. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to see the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>');e.push("</p>");e.push("<p>You can share this dataset with another Galaxy user. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to see the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push("</p>");e.push("<h2>Advanced permissions</h2>");e.push("<p>You can assign any number of roles to any of the following three dataset permission types. However please read carefully the implications of such actions.</p>");e.push("<h3>Access Roles</h3>");e.push('<div class="alert alert-info">User has to have <strong>all these roles</strong> in order to see this dataset.</div>');e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("<h3>Modify Roles</h3>");e.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can modify the information about this dataset.</div>');e.push('<div id="modify_perm" class="modify_perm"></div>');e.push("<h3>Manage Roles</h3>");e.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can change permissions of this dataset.</div>');e.push('<div id="manage_perm" class="manage_perm"></div>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 static/scripts/packed/mvc/library/library-folderrow-view.js --- a/static/scripts/packed/mvc/library/library-folderrow-view.js +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){this.dataset_view=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}}); \ No newline at end of file diff -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 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","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$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 g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}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=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".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("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<div id="library_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><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="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" 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 dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" 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(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');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(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" 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","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("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(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},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);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;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 l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<div id="library_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><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="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" 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 dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" 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(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');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(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" 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 6d45e4c17643f86a5b7c572a9bd423ac46fb446e -r 2e6e51179f7177b743bd970095be7e261ae62700 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(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.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(d){return d.name!==""},check_include_deleted:function(d){if(d.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">');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(""))},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("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.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(d){return d.name!==""},check_include_deleted:function(d){if(d.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">');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"> include deleted</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(""))},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("")}});return{LibraryToolbarView:c}}); \ 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: jmchilton: Update LWR client through LWR changeset f7d15f0.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d45e4c17643/ Changeset: 6d45e4c17643 User: jmchilton Date: 2014-05-16 23:17:08 Summary: Update LWR client through LWR changeset f7d15f0. Adds new LWR file action type - rewrite - that allows paths to be simply rewritten during paramater replacement or command rewriting. Affected #: 5 files diff -r f61263482700499fd79238b6468c18e6915aaf08 -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -132,6 +132,24 @@ self.mappers = mappers_from_dicts(config.get("paths", [])) self.files_endpoint = config.get("files_endpoint", None) + def action(self, path, type, mapper=None): + mapper = self.__find_mapper(path, type, mapper) + action_class = self.__action_class(path, type, mapper) + file_lister = DEFAULT_FILE_LISTER + action_kwds = {} + if mapper: + file_lister = mapper.file_lister + action_kwds = mapper.action_kwds + action = action_class(path, file_lister=file_lister, **action_kwds) + self.__process_action(action, type) + return action + + def unstructured_mappers(self): + """ Return mappers that will map 'unstructured' files (i.e. go beyond + mapping inputs, outputs, and config files). + """ + return filter(lambda m: path_type.UNSTRUCTURED in m.path_types, self.mappers) + def to_dict(self): return dict( default_action=self.default_action, @@ -153,18 +171,19 @@ config = load(open(path, 'rb')) self.mappers = mappers_from_dicts(config.get('paths', [])) - def action(self, path, type, mapper=None): - action_type = self.default_action if type in ACTION_DEFAULT_PATH_TYPES else "none" - file_lister = DEFAULT_FILE_LISTER - normalized_path = abspath(path) + def __find_mapper(self, path, type, mapper=None): if not mapper: + normalized_path = abspath(path) for query_mapper in self.mappers: if query_mapper.matches(normalized_path, type): mapper = query_mapper break + return mapper + + def __action_class(self, path, type, mapper): + action_type = self.default_action if type in ACTION_DEFAULT_PATH_TYPES else "none" if mapper: action_type = mapper.action_type - file_lister = mapper.file_lister if type in ["workdir", "output_workdir"] and action_type == "none": # We are changing the working_directory relative to what # Galaxy would use, these need to be copied over. @@ -174,15 +193,7 @@ message_template = "Unknown action_type encountered %s while trying to map path %s" message_args = (action_type, path) raise Exception(message_template % message_args) - action = action_class(path, file_lister=file_lister) - self.__process_action(action, type) - return action - - def unstructured_mappers(self): - """ Return mappers that will map 'unstructured' files (i.e. go beyond - mapping inputs, outputs, and config files). - """ - return filter(lambda m: path_type.UNSTRUCTURED in m.path_types, self.mappers) + return action_class def __process_action(self, action, file_type): """ Extension point to populate extra action information after an @@ -198,19 +209,30 @@ url = "%s&path=%s&file_type=%s" % (url_base, action.path, file_type) action.url = url +REQUIRED_ACTION_KWD = object() + class BaseAction(object): + action_spec = {} def __init__(self, path, file_lister=None): self.path = path self.file_lister = file_lister or DEFAULT_FILE_LISTER - def unstructured_map(self): + def unstructured_map(self, path_helper): unstructured_map = self.file_lister.unstructured_map(self.path) - # To ensure uniqueness, prepend unique prefix to each name - prefix = unique_path_prefix(self.path) - for path, name in unstructured_map.iteritems(): - unstructured_map[path] = join(prefix, name) + if self.staging_needed: + # To ensure uniqueness, prepend unique prefix to each name + prefix = unique_path_prefix(self.path) + for path, name in unstructured_map.iteritems(): + unstructured_map[path] = join(prefix, name) + else: + path_rewrites = {} + for path in unstructured_map: + rewrite = self.path_rewrite(path_helper, path) + if rewrite: + path_rewrites[path] = rewrite + unstructured_map = path_rewrites return unstructured_map @property @@ -230,6 +252,56 @@ action_type = "none" staging = STAGING_ACTION_NONE + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return NoneAction(path=action_dict["path"]) + + def path_rewrite(self, path_helper, path=None): + return None + + +class RewriteAction(BaseAction): + """ This actin indicates the LWR server should simply rewrite the path + to the specified file. + """ + action_spec = dict( + source_directory=REQUIRED_ACTION_KWD, + destination_directory=REQUIRED_ACTION_KWD + ) + action_type = "rewrite" + staging = STAGING_ACTION_NONE + + def __init__(self, path, file_lister=None, source_directory=None, destination_directory=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + self.source_directory = source_directory + self.destination_directory = destination_directory + + def to_dict(self): + return dict( + path=self.path, + action_type=self.action_type, + source_directory=self.source_directory, + destination_directory=self.destination_directory, + ) + + @classmethod + def from_dict(cls, action_dict): + return RewriteAction( + path=action_dict["path"], + source_directory=action_dict["source_directory"], + destination_directory=action_dict["destination_directory"], + ) + + def path_rewrite(self, path_helper, path=None): + if not path: + path = self.path + new_path = path_helper.from_posix_with_new_base(self.path, self.source_directory, self.destination_directory) + return None if new_path == self.path else new_path + class TransferAction(BaseAction): """ This actions indicates that the LWR client should initiate an HTTP @@ -353,7 +425,18 @@ class BasePathMapper(object): def __init__(self, config): - self.action_type = config.get('action', DEFAULT_MAPPED_ACTION) + action_type = config.get('action', DEFAULT_MAPPED_ACTION) + action_class = actions.get(action_type, None) + action_kwds = action_class.action_spec.copy() + for key, value in action_kwds.items(): + if key in config: + action_kwds[key] = config[key] + elif value is REQUIRED_ACTION_KWD: + message_template = "action_type %s requires key word argument %s" + message = message_template % (action_type, key) + raise Exception( message ) + self.action_type = action_type + self.action_kwds = action_kwds path_types_str = config.get('path_types', "*defaults*") path_types_str = path_types_str.replace("*defaults*", ",".join(ACTION_DEFAULT_PATH_TYPES)) path_types_str = path_types_str.replace("*any*", ",".join(ALL_PATH_TYPES)) @@ -368,9 +451,10 @@ base_dict = dict( action=self.action_type, path_types=",".join(self.path_types), - match_type=self.match_type, - **self.file_lister.to_dict() + match_type=self.match_type ) + base_dict.update(self.file_lister.to_dict()) + base_dict.update(self.action_kwds) base_dict.update(**kwds) return base_dict @@ -464,10 +548,11 @@ ACTION_CLASSES = [ NoneAction, + RewriteAction, TransferAction, CopyAction, RemoteCopyAction, - RemoteTransferAction + RemoteTransferAction, ] actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) diff -r f61263482700499fd79238b6468c18e6915aaf08 -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -48,6 +48,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) + log.debug("Consuming queue '%s'", queue) while check: try: with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: diff -r f61263482700499fd79238b6468c18e6915aaf08 -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e lib/galaxy/jobs/runners/lwr_client/path_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/path_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/path_mapper.py @@ -59,7 +59,7 @@ path = str(local_path) # Use false_path if needed. action = self.action_mapper.action(path, path_type.UNSTRUCTURED) if not action.staging_needed: - return None, [] + return action.path_rewrite(self.path_helper), [] unique_names = action.unstructured_map() name = unique_names[path] remote_path = self.path_helper.remote_join(self.unstructured_files_directory, name) @@ -70,12 +70,16 @@ """ path = str(dataset_path) # Use false_path if needed. action = self.action_mapper.action(path, dataset_path_type) - remote_path_rewrite = None if action.staging_needed: if name is None: name = os.path.basename(path) remote_directory = self.__remote_directory(dataset_path_type) remote_path_rewrite = self.path_helper.remote_join(remote_directory, name) + else: + # Actions which don't require staging MUST define a path_rewrite + # method. + remote_path_rewrite = action.path_rewrite(self.path_helper) + return remote_path_rewrite def __action(self, dataset_path, dataset_path_type): diff -r f61263482700499fd79238b6468c18e6915aaf08 -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e lib/galaxy/jobs/runners/lwr_client/staging/up.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py @@ -78,9 +78,11 @@ self.job_inputs = JobInputs(self.command_line, self.config_files) self.action_mapper = FileActionMapper(client) - self.transfer_tracker = TransferTracker(client, self.action_mapper, self.job_inputs, rewrite_paths=self.rewrite_paths) self.__handle_setup(job_config) + + self.transfer_tracker = TransferTracker(client, self.path_helper, self.action_mapper, self.job_inputs, rewrite_paths=self.rewrite_paths) + self.__initialize_referenced_tool_files() if self.rewrite_paths: self.__initialize_referenced_arbitrary_files() @@ -142,7 +144,7 @@ referenced_arbitrary_path_mappers[path] = mapper for path, mapper in referenced_arbitrary_path_mappers.iteritems(): action = self.action_mapper.action(path, path_type.UNSTRUCTURED, mapper) - unstructured_map = action.unstructured_map() + unstructured_map = action.unstructured_map(self.path_helper) self.arbitrary_files.update(unstructured_map) def __upload_tool_files(self): @@ -330,8 +332,9 @@ class TransferTracker(object): - def __init__(self, client, action_mapper, job_inputs, rewrite_paths): + def __init__(self, client, path_helper, action_mapper, job_inputs, rewrite_paths): self.client = client + self.path_helper = path_helper self.action_mapper = action_mapper self.job_inputs = job_inputs @@ -357,6 +360,11 @@ register = self.rewrite_paths or type == 'tool' # Even if inputs not rewritten, tool must be. if register: self.register_rewrite(path, get_path(), type, force=True) + elif self.rewrite_paths: + path_rewrite = action.path_rewrite(self.path_helper) + if path_rewrite: + self.register_rewrite(path, path_rewrite, type, force=True) + # else: # No action for this file def __add_remote_staging_input(self, action, name, type): diff -r f61263482700499fd79238b6468c18e6915aaf08 -r 6d45e4c17643f86a5b7c572a9bd423ac46fb446e lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -107,6 +107,12 @@ 'moo/cow' >>> nt_path_helper.local_name("moo\\\\cow") 'moo/cow' + >>> posix_path_helper.from_posix_with_new_base("/galaxy/data/bowtie/hg19.fa", "/galaxy/data/", "/work/galaxy/data") + '/work/galaxy/data/bowtie/hg19.fa' + >>> posix_path_helper.from_posix_with_new_base("/galaxy/data/bowtie/hg19.fa", "/galaxy/data", "/work/galaxy/data") + '/work/galaxy/data/bowtie/hg19.fa' + >>> posix_path_helper.from_posix_with_new_base("/galaxy/data/bowtie/hg19.fa", "/galaxy/data", "/work/galaxy/data/") + '/work/galaxy/data/bowtie/hg19.fa' ''' def __init__(self, separator, local_path_module=os.path): @@ -123,6 +129,22 @@ def remote_join(self, *args): return self.separator.join(args) + def from_posix_with_new_base(self, posix_path, old_base, new_base): + # TODO: Test with new_base as a windows path against nt_path_helper. + if old_base.endswith("/"): + old_base = old_base[:-1] + if not posix_path.startswith(old_base): + message_template = "Cannot compute new path for file %s, does not start with %s." + message = message_template % (posix_path, old_base) + raise Exception(message) + stripped_path = posix_path[ len(old_base): ] + while stripped_path.startswith("/"): + stripped_path = stripped_path[1:] + path_parts = stripped_path.split(self.separator) + if new_base.endswith(self.separator): + new_base = new_base[:-len(self.separator)] + return self.remote_join(new_base, *path_parts) + class TransferEventManager(object): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a script for creating a new user and an associated API key to streamline the process of setting up a new local development tool shed.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f61263482700/ Changeset: f61263482700 User: greg Date: 2014-05-16 23:14:24 Summary: Add a script for creating a new user and an associated API key to streamline the process of setting up a new local development tool shed. Affected #: 2 files diff -r 9fbe2754793109a1680239131b5507614d431870 -r f61263482700499fd79238b6468c18e6915aaf08 lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py @@ -0,0 +1,158 @@ +#!/usr/bin/env python + +import ConfigParser +import logging +import os +import re +import sys + +from optparse import OptionParser + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) +eggs.require( 'mercurial' ) + +from galaxy.web import security +import galaxy.webapps.tool_shed.config as tool_shed_config +from galaxy.webapps.tool_shed.model import mapping +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9\-]+$" ) +VALID_EMAIL_RE = re.compile( "[^@]+@[^@]+\.[^@]+" ) + + +class BootstrapApplication( object ): + """ + Creates a basic Tool Shed application in order to discover the database connection and use SQL + to create a user and API key. + """ + + def __init__( self, config ): + self.config = config + if not self.config.database_connection: + self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str( config.database ) + print 'Using database connection: ', self.config.database_connection + # Setup the database engine and ORM + self.model = mapping.init( self.config.file_path, + self.config.database_connection, + engine_options={}, + create_tables=False ) + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + self.hgweb_config_manager = self.model.hgweb_config_manager + self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir + print 'Using hgweb.config file: ', self.hgweb_config_manager.hgweb_config + + @property + def sa_session( self ): + """Returns a SQLAlchemy session.""" + return self.model.context.current + + def shutdown( self ): + pass + +def create_api_key( app, user ): + api_key = app.security.get_new_guid() + new_key = app.model.APIKeys() + new_key.user_id = user.id + new_key.key = api_key + app.sa_session.add( new_key ) + app.sa_session.flush() + return api_key + +def create_user( app ): + user_info_config = os.path.abspath( os.path.join( app.config.root, 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) ) + email = None + password = None + username = None + tree, error_message = xml_util.parse_xml( user_info_config ) + if tree is None: + print "The XML file ", user_info_config, " seems to be invalid, using defaults." + email = 'admin(a)test.org' + password = 'testuser' + username = 'admin' + else: + root = tree.getroot() + for elem in root: + if elem.tag == 'email': + email = elem.text + elif elem.tag == 'password': + password = elem.text + elif elem.tag == 'username': + username = elem.text + if email and password and username: + invalid_message = validate( email, password, username ) + if invalid_message: + print invalid_message + else: + user = app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + app.sa_session.add( user ) + app.sa_session.flush() + app.model.security_agent.create_private_user_role( user ) + return user + else: + print "Missing required values for email: ", email, ", password: ", password, ", username: ", username + return None + +def validate( email, password, username ): + message = validate_email( email ) + if not message: + message = validate_password( password ) + if not message: + message = validate_publicname( username ) + return message + +def validate_email( email ): + """Validates the email format.""" + message = '' + if not( VALID_EMAIL_RE.match( email ) ): + message = "Please enter a real email address." + elif len( email ) > 255: + message = "Email address exceeds maximum allowable length." + return message + +def validate_password( password ): + if len( password ) < 6: + return "Use a password of at least 6 characters" + return '' + +def validate_publicname( username ): + """""Validates the public username.""" + if len( username ) < 3: + return "Public name must be at least 3 characters in length" + if len( username ) > 255: + return "Public name cannot be more than 255 characters in length" + if not( VALID_PUBLICNAME_RE.match( username ) ): + return "Public name must contain only lower-case letters, numbers and '-'" + return '' + +if __name__ == "__main__": + parser = OptionParser() + ( options, args ) = parser.parse_args() + try: + ini_file = args[ 0 ] + except IndexError: + print "Usage: python %s <tool shed .ini file> [options]" % sys.argv[ 0 ] + exit( 127 ) + config_parser = ConfigParser.ConfigParser( { 'here':os.getcwd() } ) + print "Reading ini file: ", ini_file + config_parser.read( ini_file ) + config_dict = {} + for key, value in config_parser.items( "app:main" ): + config_dict[ key ] = value + config = tool_shed_config.Configuration( **config_dict ) + app = BootstrapApplication( config ) + user = create_user( app ) + if user is not None: + api_key = create_api_key( app, user ) + print "Created new user with public username '", user.username, ". An API key was also created and associated with the user." + else: + print "Problem creating a new user and an associated API key." diff -r 9fbe2754793109a1680239131b5507614d431870 -r f61263482700499fd79238b6468c18e6915aaf08 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<user> + <email>admin(a)test.org</email> + <password>testuser</password> + <username>admin</username> +</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.

1 0

commit/galaxy-central: dan: Fix for checking dataset access permissions when reruning a tool by job_id.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fbe27547931/ Changeset: 9fbe27547931 User: dan Date: 2014-05-16 21:13:29 Summary: Fix for checking dataset access permissions when reruning a tool by job_id. Affected #: 1 file diff -r 1b06ee57191c56cd50c0248239f876f4c5311831 -r 9fbe2754793109a1680239131b5507614d431870 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 @@ -118,6 +118,11 @@ job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) except: error( "Invalid value for 'job_id' parameter" ) + if not trans.user_is_admin(): + for data_assoc in job.output_datasets: + #only allow rerunning if user is allowed access to the dataset. + if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data_assoc.dataset.dataset ): + error( "You are not allowed to rerun this job" ) param_error_text = "Failed to get parameters for job id %d " % job_id else: if not id: @@ -130,7 +135,6 @@ id = trans.security.decode_id( id ) except: error( "Invalid value for 'id' parameter" ) - # Get the dataset object data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id ) #only allow rerunning if user is allowed access to the dataset. 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: jmchilton: A bit more LWR client logging.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1b06ee57191c/ Changeset: 1b06ee57191c User: jmchilton Date: 2014-05-16 17:24:54 Summary: A bit more LWR client logging. Affected #: 1 file diff -r 2f592b5f1883520d62fc6ceab6a1657edd188294 -r 1b06ee57191c56cd50c0248239f876f4c5311831 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -313,7 +313,9 @@ # before queueing. setup_params = _setup_params_from_job_config(job_config) launch_params["setup_params"] = setup_params - return self.client_manager.exchange.publish("setup", launch_params) + response = self.client_manager.exchange.publish("setup", launch_params) + log.info("Job published to setup message queue.") + return response def clean(self): del self.client_manager.status_cache[self.job_id] 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: jmchilton: Update LWR client and behavior through LWR changeset 8ea7265.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f592b5f1883/ Changeset: 2f592b5f1883 User: jmchilton Date: 2014-05-16 17:14:52 Summary: Update LWR client and behavior through LWR changeset 8ea7265. LWR now informed of job submission failures in MQ mode so jobs shouldn't sit in queued state forever if job fails to queue remotely. Also small fixes and more logging. Affected #: 4 files diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -28,6 +28,7 @@ NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "LWR misconfiguration - LWR client configured to set metadata remotely, but remote LWR isn't properly configured with a galaxy_home directory." NO_REMOTE_DATATYPES_CONFIG = "LWR client is configured to use remote datatypes configuration when setting metadata externally, but LWR is not configured with this information. Defaulting to datatypes_conf.xml." +GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server." # Is there a good way to infer some default for this? Can only use # url_for from web threads. https://gist.github.com/jmchilton/9098762 @@ -266,7 +267,7 @@ if failed: job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) except Exception: - message = "Failed to communicate with remote job server." + message = GENERIC_REMOTE_ERROR job_wrapper.fail( message, exception=True ) log.exception("failure finishing job %d" % job_wrapper.job_id) return @@ -284,7 +285,7 @@ Seperated out so we can use the worker threads for it. """ self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) - job_state.job_wrapper.fail( job_state.fail_message ) + job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) ) def check_pid( self, pid ): try: diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -300,7 +300,7 @@ launch_params = dict(command_line=command_line, job_id=self.job_id) submit_params_dict = submit_params(self.destination_params) if submit_params_dict: - launch_params['params'] = submit_params_dict + launch_params['submit_params'] = submit_params_dict if dependencies_description: launch_params['dependencies_description'] = dependencies_description.to_dict() if env: diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -97,6 +97,7 @@ try: if "job_id" in body: self.status_cache[body["job_id"]] = body + log.debug("Handling asynchronous status update from remote LWR.") callback(body) except Exception: log.exception("Failure processing job status update message.") @@ -104,6 +105,7 @@ def run(): self.exchange.consume("status_update", callback_wrapper, check=self) + log.debug("Leaving LWR client status update thread, no additional LWR updates will be processed.") thread = threading.Thread( name="lwr_client_%s_status_update_callback" % self.manager_name, diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,7 @@ contents.append(name) return contents + def parse_amqp_connect_ssl_params(params): ssl = None rval = 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.

1 0

commit/galaxy-central: greg: Fix query filters for various Tool Shed "latest revision" grids by making sure revisions have actually been tested by the install and test framework, and not sure prepared the framework's preparation scripts.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26b9fe985ee7/ Changeset: 26b9fe985ee7 User: greg Date: 2014-05-16 15:48:50 Summary: Fix query filters for various Tool Shed "latest revision" grids by making sure revisions have actually been tested by the install and test framework, and not sure prepared the framework's preparation scripts. Affected #: 1 file diff -r 7e95105c466051432e5c47ff977826a19758b867 -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -1940,8 +1940,8 @@ of type repository_suite_definition and tool_dependency_definition. """ repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata \ - and repository_metadata.tool_test_results is not None \ + if repository_metadata is not None \ + and has_been_tested( repository_metadata ) \ and not repository_metadata.missing_test_components \ and not repository_metadata.tools_functionally_correct \ and not repository_metadata.test_install_error: @@ -1957,7 +1957,9 @@ tool_dependency_definition. """ repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata and repository_metadata.missing_test_components: + if repository_metadata is not None \ + and has_been_tested( repository_metadata ) \ + and repository_metadata.missing_test_components: return repository_metadata.changeset_revision return None @@ -1968,9 +1970,10 @@ and tool_dependency_definition. """ repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata is not None and \ - not repository_metadata.missing_test_components and \ - repository_metadata.tools_functionally_correct: + if repository_metadata is not None \ + and has_been_tested( repository_metadata ) \ + and not repository_metadata.missing_test_components \ + and repository_metadata.tools_functionally_correct: return repository_metadata.changeset_revision return None @@ -1993,7 +1996,9 @@ """ repository_metadata = get_latest_downloadable_repository_metadata_if_it_has_test_install_errors( trans, repository ) # Filter further by eliminating repositories that are missing test components. - if repository_metadata is not None and not repository_metadata.missing_test_components: + if repository_metadata is not None \ + and has_been_tested( repository_metadata ) \ + and not repository_metadata.missing_test_components: return repository_metadata.changeset_revision return None @@ -2067,7 +2072,9 @@ well as types repository_suite_definition and tool_dependency_definition. """ repository_metadata = get_latest_downloadable_repository_metadata( trans, repository ) - if repository_metadata is not None and repository_metadata.test_install_error: + if repository_metadata is not None \ + and has_been_tested( repository_metadata ) \ + and repository_metadata.test_install_error: return repository_metadata return None @@ -2104,3 +2111,25 @@ if metadata is not None and 'invalid_tools' in metadata: return repository_metadata return None + +def has_been_tested( repository_metadata ): + """ + Return True if the received repository_metadata record'd tool_test_results column was populated by + the Tool Shed's install and test framework. + """ + tool_test_results = repository_metadata.tool_test_results + if tool_test_results is None: + return False + # The install and test framework's preparation scripts will populate the tool_test_results column + # with something like this: + # [{"test_environment": + # {"time_tested": "2014-05-15 16:15:18", + # "tool_shed_database_version": 22, + # "tool_shed_mercurial_version": "2.2.3", + # "tool_shed_revision": "13459:9a1415f8108f"} + # }] + tool_test_results = listify( tool_test_results ) + for test_results_dict in tool_test_results: + if len( test_results_dict ) > 1: + return True + 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.

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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d81156abc40/ Changeset: 0d81156abc40 User: jmchilton Date: 2014-05-16 07:57:31 Summary: Helper method for creating JobWrappers in JobHandler. Affected #: 1 file diff -r b94bb858d29b39f5d8127414bd703ee8e4905281 -r 0d81156abc40773643f5f8d72af521fe5d1b5d9d lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -84,6 +84,13 @@ self.monitor_thread.start() log.info( "job handler queue started" ) + def job_wrapper( self, job ): + return JobWrapper( job, self ) + + def job_wrapper_for_id( self, id ): + job = self.sa_session.query( model.Job ) + return self.job_wrapper( job ) + def __check_jobs_at_startup( self ): """ Checks all jobs that are in the 'new', 'queued' or 'running' state in @@ -110,7 +117,7 @@ for job in jobs_at_startup: if job.tool_id not in self.app.toolbox.tools_by_id: log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) ) - JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) + self.job_wrapper( job ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) elif job.job_runner_name is not None and job.job_runner_external_id is None: # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner. log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id ) @@ -122,7 +129,7 @@ elif job.job_runner_name is not None and job.job_runner_external_id is not None and job.destination_id is None: # This is the first start after upgrading from URLs to destinations, convert the URL to a destination and persist # TODO: test me extensively - job_wrapper = JobWrapper( job, self ) + job_wrapper = self.job_wrapper( job ) job_destination = self.dispatcher.url_to_destination(job.job_runner_name) if job_destination.id is None: job_destination.id = 'legacy_url' @@ -138,7 +145,7 @@ self.queue.put( ( job.id, job.tool_id ) ) else: # Already dispatched and running - job_wrapper = JobWrapper( job, self ) + job_wrapper = self.job_wrapper( job ) job_wrapper.job_runner_mapper.cached_job_destination = JobDestination(id=job.destination_id, runner=job.job_runner_name, params=job.destination_params) self.dispatcher.recover( job, job_wrapper ) if self.sa_session.dirty: @@ -296,21 +303,21 @@ continue # don't run jobs for which the input dataset was deleted if idata.deleted: - self.job_wrappers.pop(job.id, JobWrapper( job, self )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) return JOB_INPUT_DELETED # an error in the input data causes us to bail immediately elif idata.state == idata.states.ERROR: - self.job_wrappers.pop(job.id, JobWrapper( job, self )).fail( "input data %s is in error state" % ( idata.hid ) ) + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) return JOB_INPUT_ERROR elif idata.state == idata.states.FAILED_METADATA: - self.job_wrappers.pop(job.id, JobWrapper( job, self )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) return JOB_INPUT_ERROR elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): # need to requeue return JOB_WAIT # Create the job wrapper so that the destination can be set if job.id not in self.job_wrappers: - self.job_wrappers[job.id] = JobWrapper(job, self) + self.job_wrappers[job.id] = self.job_wrapper( job ) # Cause the job_destination to be set and cached by the mapper try: self.job_wrappers[job.id].job_destination https://bitbucket.org/galaxy/galaxy-central/commits/6b565d3fc2a7/ Changeset: 6b565d3fc2a7 User: jmchilton Date: 2014-05-16 07:57:31 Summary: PEP-8 fixes for JobManager. Affected #: 1 file diff -r 0d81156abc40773643f5f8d72af521fe5d1b5d9d -r 6b565d3fc2a7f4f0db9f7a911e762e139c7fbb67 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -3,20 +3,12 @@ """ import logging -import os -import random -import threading -import time -from Queue import Empty, Queue - -from galaxy import model -from galaxy.util.sleeper import Sleeper -from galaxy.jobs import handler, JobWrapper, NoopQueue -from galaxy.util.json import from_json_string +from galaxy.jobs import handler, NoopQueue log = logging.getLogger( __name__ ) + class JobManager( object ): """ Highest level interface to job management. @@ -35,14 +27,18 @@ self.job_handler = NoopHandler() self.job_queue = self.job_stop_queue = NoopQueue() self.job_handler.start() + def shutdown( self ): self.job_handler.shutdown() + class NoopHandler( object ): def __init__( self, *args, **kwargs ): self.job_queue = NoopQueue() self.job_stop_queue = NoopQueue() + def start( self ): pass + def shutdown( self, *args ): pass https://bitbucket.org/galaxy/galaxy-central/commits/7c668716a412/ Changeset: 7c668716a412 User: jmchilton Date: 2014-05-16 07:57:31 Summary: Handle LWR failed state in asynchronous MQ updates. Affected #: 1 file diff -r 6b565d3fc2a7f4f0db9f7a911e762e139c7fbb67 -r 7c668716a4125c583c0000d11a4aae9347dc8606 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -98,6 +98,9 @@ if lwr_status == "complete": self.mark_as_finished(job_state) return None + if lwr_status == "failed": + self.fail_job(job_state) + return None if lwr_status == "running" and not job_state.running: job_state.running = True job_state.job_wrapper.change_state( model.Job.states.RUNNING ) https://bitbucket.org/galaxy/galaxy-central/commits/21a568dac530/ Changeset: 21a568dac530 User: jmchilton Date: 2014-05-16 07:57:31 Summary: Correct 'abstract' method definition in AsynchronousJobRunner. Affected #: 1 file diff -r 7c668716a4125c583c0000d11a4aae9347dc8606 -r 21a568dac530aefb54e49238da2fac0934cb9308 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -400,7 +400,7 @@ self.watched = new_watched # Subclasses should implement this unless they override check_watched_items all together. - def check_watched_item(self): + def check_watched_item(self, job_state): raise NotImplementedError() def finish_job( self, job_state ): https://bitbucket.org/galaxy/galaxy-central/commits/7e95105c4660/ Changeset: 7e95105c4660 User: jmchilton Date: 2014-05-16 07:57:31 Summary: Simplified, truely asynchronous LWR MQ status updates. In addition to eliminating some egregious hacks, this reworked functionality should allow any LWR handler process to consume update messages for any job (so LWR jobs don't have to be bound to a particular handler). Affected #: 2 files diff -r 21a568dac530aefb54e49238da2fac0934cb9308 -r 7e95105c466051432e5c47ff977826a19758b867 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -87,9 +87,9 @@ def job_wrapper( self, job ): return JobWrapper( job, self ) - def job_wrapper_for_id( self, id ): - job = self.sa_session.query( model.Job ) - return self.job_wrapper( job ) + def job_pair_for_id( self, id ): + job = self.sa_session.query( model.Job ).get( id ) + return job, self.job_wrapper( job ) def __check_jobs_at_startup( self ): """ diff -r 21a568dac530aefb54e49238da2fac0934cb9308 -r 7e95105c466051432e5c47ff977826a19758b867 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -43,8 +43,6 @@ def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) - self.async_status_updates = dict() - self._init_monitor_thread() self._init_worker_threads() amqp_connect_ssl_args = {} amqp_consumer_timeout = False @@ -65,6 +63,10 @@ client_manager_kwargs['amqp_consumer_timeout'] = float(kwds['amqp_consumer_timeout']) self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) + if url: + self.client_manager.ensure_has_status_update_callback(self.__async_update) + else: + self._init_monitor_thread() def url_to_destination( self, url ): """Convert a legacy URL to a job destination""" @@ -73,18 +75,6 @@ def check_watched_item(self, job_state): try: client = self.get_client_from_state(job_state) - - if hasattr(self.client_manager, 'ensure_has_status_update_callback'): - # Message queue implementation. - - # TODO: Very hacky now, refactor after Dannon merges in his - # message queue work, runners need the ability to disable - # check_watched_item like this and instead a callback needs to - # be issued post job recovery allowing a message queue - # consumer to be setup. - self.client_manager.ensure_has_status_update_callback(self.__async_update) - return job_state - status = client.get_status() except Exception: # An orphaned job was put into the queue at app startup, so remote server went down @@ -108,26 +98,9 @@ def __async_update( self, full_status ): job_id = full_status[ "job_id" ] - job_state = self.__find_watched_job( job_id ) - if not job_state: - # Probably finished too quickly, sleep and try again. - # Kind of a hack, why does monitor queue need to no wait - # get and sleep instead of doing a busy wait that would - # respond immediately. - sleep( 2 ) - job_state = self.__find_watched_job( job_id ) - if not job_state: - log.warn( "Failed to find job corresponding to status %s in %s" % ( full_status, self.watched ) ) - else: - self.__update_job_state_for_lwr_status(job_state, full_status["status"]) - - def __find_watched_job( self, job_id ): - found_job = None - for async_job_state in self.watched: - if str( async_job_state.job_id ) == job_id: - found_job = async_job_state - break - return found_job + job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id( job_id ) + job_state = self.__job_state( job, job_wrapper ) + self.__update_job_state_for_lwr_status(job_state, full_status["status"]) def queue_job(self, job_wrapper): job_destination = job_wrapper.job_destination @@ -358,12 +331,8 @@ def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" - job_state = AsynchronousJobState() - job_state.job_id = str( job.get_job_runner_external_id() ) - job_state.runner_url = job_wrapper.get_job_runner_url() - job_state.job_destination = job_wrapper.job_destination + job_state = self.__job_state( job, job_wrapper ) job_wrapper.command_line = job.get_command_line() - job_state.job_wrapper = job_wrapper state = job.get_state() if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) @@ -375,6 +344,14 @@ super( LwrJobRunner, self ).shutdown() self.client_manager.shutdown() + def __job_state( self, job, job_wrapper ): + job_state = AsynchronousJobState() + job_state.job_id = str( job.get_job_runner_external_id() ) + job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination + job_state.job_wrapper = job_wrapper + return job_state + def __client_outputs( self, client, job_wrapper ): work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) output_files = self.get_output_files( job_wrapper ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix for previous commit.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b94bb858d29b/ Changeset: b94bb858d29b User: jmchilton Date: 2014-05-16 05:05:04 Summary: Fix for previous commit. Affected #: 1 file diff -r 933d0f2847332024f1fdf40234e74930014794e6 -r b94bb858d29b39f5d8127414bd703ee8e4905281 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -76,7 +76,7 @@ def __init__(self, **kwds): self.url = kwds.get('url') - self.manager_name = kwds.get("manager", "_default_") + self.manager_name = kwds.get("manager", None) or "_default_" self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) timeout = kwds.get('amqp_consumer_timeout', False) if timeout is 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: jmchilton: Bugfix: LWR - Fix manager name not passed into MQClientManager.
by commits-noreply＠bitbucket.org 16 May '14

16 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/933d0f284733/ Changeset: 933d0f284733 User: jmchilton Date: 2014-05-16 04:57:54 Summary: Bugfix: LWR - Fix manager name not passed into MQClientManager. Affected #: 1 file diff -r 559c5f4d1bdb694f90826896e5ebc837afa9b4f2 -r 933d0f2847332024f1fdf40234e74930014794e6 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -51,7 +51,13 @@ for kwd in kwds.keys(): if kwd.startswith('amqp_connect_ssl_'): amqp_connect_ssl_args[kwd] = kwds[kwd] - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} + client_manager_kwargs = { + 'transport_type': transport, + 'cache': string_as_bool_or_none(cache), + "url": url, + 'amqp_connect_ssl_args': amqp_connect_ssl_args or None, + 'manager': kwds.get("manager", None), + } if 'amqp_consumer_timeout' in kwds: if kwds['amqp_consumer_timeout'] == 'None': client_manager_kwargs['amqp_consumer_timeout'] = 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: 2 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fcd83883072c/ Changeset: fcd83883072c User: jmchilton Date: 2014-05-15 22:58:12 Summary: Fix GALAXY_SLOTS calculation for LSF. Thanks to Ilya Sytchev for the patch. Affected #: 1 file diff -r 47786821cd22eed10d1db9227b2ac18eff760374 -r fcd83883072c64b96ea0f12582fde3d05060b0f4 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -8,6 +8,8 @@ GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` +elif [ -n "$LSB_DJOB_NUMPROC" ]; then + GALAXY_SLOTS="$LSB_DJOB_NUMPROC" else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED https://bitbucket.org/galaxy/galaxy-central/commits/559c5f4d1bdb/ Changeset: 559c5f4d1bdb User: jmchilton Date: 2014-05-15 22:58:58 Summary: Merge. Affected #: 1 file diff -r fcd83883072c64b96ea0f12582fde3d05060b0f4 -r 559c5f4d1bdb694f90826896e5ebc837afa9b4f2 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -473,6 +473,20 @@ dbkey = dbkey[0] file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] file_formats.sort() + + def __ok_to_edit_metadata( ldda_id ): + #prevent modifying metadata when dataset is queued or running as input/output + #This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now + for job_to_dataset_association in trans.sa_session.query( self.app.model.JobToInputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all() \ + + trans.sa_session.query( self.app.model.JobToOutputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all(): + if job_to_dataset_association.job.state not in [ job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED ]: + return False + return True + # See if we have any associated templates widgets = [] info_association, inherited = ldda.get_info_association() @@ -480,14 +494,18 @@ widgets = ldda.get_template_widgets( trans ) if params.get( 'change', False ): # The user clicked the Save button on the 'Change data type' form - if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: - trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.sa_session.flush() - message = "Data type changed for library dataset '%s'." % ldda.name - status = 'done' + if __ok_to_edit_metadata( ldda.id ): + if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: + trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) + trans.sa_session.flush() + message = "Data type changed for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + status = 'error' else: - message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - status = 'error' + message = "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." + status = "error" elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form old_name = ldda.name @@ -501,33 +519,40 @@ ldda.name = new_name ldda.info = new_info ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_setting_metadata( ldda ) + message = "Attributes updated for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata." + status = 'warning' trans.sa_session.flush() - message = "Attributes updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + message = "Attributes have been queued to be updated for library dataset '%s'." % ldda.name + status = 'done' + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':ldda } ) + else: + message = "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them." + status = 'error' trans.sa_session.flush() - message = "Information updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'change_extended_metadata', False): em_string = util.restore_text( params.get("extended_metadata", "") ) if len(em_string): 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: Have auto-detect metadata option in library use external set metadata process.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/331232edbe8f/ Changeset: 331232edbe8f User: dan Date: 2014-05-15 22:25:44 Summary: Have auto-detect metadata option in library use external set metadata process. Affected #: 1 file diff -r 47786821cd22eed10d1db9227b2ac18eff760374 -r 331232edbe8f30eef4814cc01ac1cb3db4bd09e7 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -473,6 +473,20 @@ dbkey = dbkey[0] file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] file_formats.sort() + + def __ok_to_edit_metadata( ldda_id ): + #prevent modifying metadata when dataset is queued or running as input/output + #This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now + for job_to_dataset_association in trans.sa_session.query( self.app.model.JobToInputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all() \ + + trans.sa_session.query( self.app.model.JobToOutputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all(): + if job_to_dataset_association.job.state not in [ job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED ]: + return False + return True + # See if we have any associated templates widgets = [] info_association, inherited = ldda.get_info_association() @@ -480,14 +494,18 @@ widgets = ldda.get_template_widgets( trans ) if params.get( 'change', False ): # The user clicked the Save button on the 'Change data type' form - if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: - trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.sa_session.flush() - message = "Data type changed for library dataset '%s'." % ldda.name - status = 'done' + if __ok_to_edit_metadata( ldda.id ): + if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: + trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) + trans.sa_session.flush() + message = "Data type changed for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + status = 'error' else: - message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - status = 'error' + message = "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." + status = "error" elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form old_name = ldda.name @@ -501,33 +519,40 @@ ldda.name = new_name ldda.info = new_info ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_setting_metadata( ldda ) + message = "Attributes updated for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata." + status = 'warning' trans.sa_session.flush() - message = "Attributes updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + message = "Attributes have been queued to be updated for library dataset '%s'." % ldda.name + status = 'done' + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':ldda } ) + else: + message = "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them." + status = 'error' trans.sa_session.flush() - message = "Information updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'change_extended_metadata', False): em_string = util.restore_text( params.get("extended_metadata", "") ) if len(em_string): 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: jmchilton: Fix incorrect LWR comment.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47786821cd22/ Changeset: 47786821cd22 User: jmchilton Date: 2014-05-15 21:59:57 Summary: Fix incorrect LWR comment. Affected #: 1 file diff -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 -r 47786821cd22eed10d1db9227b2ac18eff760374 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -108,7 +108,7 @@ sleep( 2 ) job_state = self.__find_watched_job( job_id ) if not job_state: - log.warn( "Failed to find job corresponding to final status %s in %s" % ( full_status, self.watched ) ) + log.warn( "Failed to find job corresponding to status %s in %s" % ( full_status, self.watched ) ) else: self.__update_job_state_for_lwr_status(job_state, full_status["status"]) 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: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #389)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a50b64b9d707/ Changeset: a50b64b9d707 User: jmchilton Date: 2014-05-15 20:49:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #389) Small Column Parameter Enhancements Affected #: 2 files diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,97 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/707b69b09eb4/ Changeset: 707b69b09eb4 User: jmchilton Date: 2014-05-12 19:01:14 Summary: Unit test case for tool column parameters. Ever more duplication in these parameters tests, I need to find some time to refactor... Affected #: 1 file diff -r 8e2135ee278aa44eb5a8da04a392bfa44efc0279 -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,89 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param https://bitbucket.org/galaxy/galaxy-central/commits/6171bcdb7333/ Changeset: 6171bcdb7333 User: jmchilton Date: 2014-05-12 19:01:14 Summary: Allow c to appear in default value for Column parameters, allow specification with value attribute. Ideas purposed by Peter Cock here - http://dev.list.galaxyproject.org/Default-value-for-data-column-not-working…. Affected #: 2 files diff -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac -r 6171bcdb7333fd7a1bfa3986768ad425e28cf8f6 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac -r 6171bcdb7333fd7a1bfa3986768ad425e28cf8f6 test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -38,6 +38,14 @@ self.other_attributes = "default_value='2'" self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + def setUp( self ): self.setup_app( mock_model=False ) self.mock_tool = bunch.Bunch( https://bitbucket.org/galaxy/galaxy-central/commits/a50b64b9d707/ Changeset: a50b64b9d707 User: jmchilton Date: 2014-05-15 20:49:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #389) Small Column Parameter Enhancements Affected #: 2 files diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,97 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #387)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44ac8fc8f7b6/ Changeset: 44ac8fc8f7b6 User: jmchilton Date: 2014-05-15 20:43:43 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #387) Recursive Tool Parameter Dictification Affected #: 2 files diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): @@ -517,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,49 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_info = self._show_valid_tool( "cat1" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) 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 15 May '14

15 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73b85f86a9d5/ Changeset: 73b85f86a9d5 User: jmchilton Date: 2014-05-09 00:55:00 Summary: Improvements to to_dict for Repeat tool parameters. Expand out nested parameters and more information about the repeat itself. Affected #: 2 files diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,23 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_show_response = self._get( "tools/cat1", data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) https://bitbucket.org/galaxy/galaxy-central/commits/b411c3c86936/ Changeset: b411c3c86936 User: jmchilton Date: 2014-05-09 00:55:00 Summary: Improvements to to_dict for Conditional tool parameters. Expand out nested test_param parameter and cases. Affected #: 2 files diff -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 -r b411c3c8693660a3291f0f537c61ba0b978e1813 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -530,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 -r b411c3c8693660a3291f0f537c61ba0b978e1813 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -27,10 +27,7 @@ @skip_without_tool( "cat1" ) def test_show_repeat( self ): - tool_show_response = self._get( "tools/cat1", data=dict( io_details=True ) ) - self._assert_status_code_is( tool_show_response, 200 ) - tool_info = tool_show_response.json() - self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + tool_info = self._show_valid_tool( "cat1" ) parameters = tool_info[ "inputs" ] assert len( parameters ) == 2 assert parameters[ 0 ][ "name" ] == "input1" @@ -42,6 +39,35 @@ assert len( repeat_params ) == 1 assert repeat_params[ 0 ][ "name" ] == "input2" + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) https://bitbucket.org/galaxy/galaxy-central/commits/44ac8fc8f7b6/ Changeset: 44ac8fc8f7b6 User: jmchilton Date: 2014-05-15 20:43:43 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #387) Recursive Tool Parameter Dictification Affected #: 2 files diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): @@ -517,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,49 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_info = self._show_valid_tool( "cat1" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Change paired collections terminology from left/right to forward/reverse.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f24bb5dde1f5/ Changeset: f24bb5dde1f5 User: jmchilton Date: 2014-05-15 20:01:36 Summary: Change paired collections terminology from left/right to forward/reverse. If you have paired datasets in your database they will no longer work - send me an e-mail and I can give you an SQL update statement. Affected #: 5 files diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 lib/galaxy/dataset_collections/types/paired.py --- a/lib/galaxy/dataset_collections/types/paired.py +++ b/lib/galaxy/dataset_collections/types/paired.py @@ -2,8 +2,10 @@ from galaxy.model import DatasetCollectionElement -LEFT_IDENTIFIER = "left" -RIGHT_IDENTIFIER = "right" +FORWARD_IDENTIFIER = "forward" +REVERSE_IDENTIFIER = "reverse" + +INVALID_IDENTIFIERS_MESSAGE = "Paired instance must define '%s' and '%s' datasets ." % ( FORWARD_IDENTIFIER, REVERSE_IDENTIFIER ) class PairedDatasetCollectionType( BaseDatasetCollectionType ): @@ -16,16 +18,16 @@ pass def build_collection( self, elements ): - left_dataset = elements.get("left", None) - right_dataset = elements.get("right", None) - if not left_dataset or not right_dataset: - self._validation_failed("Paired instance must define 'left' and 'right' datasets .") + forward_dataset = elements.get( FORWARD_IDENTIFIER, None ) + reverse_dataset = elements.get( REVERSE_IDENTIFIER, None ) + if not forward_dataset or not reverse_dataset: + self._validation_failed( INVALID_IDENTIFIERS_MESSAGE ) left_association = DatasetCollectionElement( - element=left_dataset, - element_identifier=LEFT_IDENTIFIER, + element=forward_dataset, + element_identifier=FORWARD_IDENTIFIER, ) right_association = DatasetCollectionElement( - element=right_dataset, - element_identifier=RIGHT_IDENTIFIER, + element=reverse_dataset, + element_identifier=REVERSE_IDENTIFIER, ) return self._new_collection_for_elements([left_association, right_association]) diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -292,8 +292,8 @@ hda1, hda2 = self.__datasets( history_id, count=2, contents=contents ) element_identifiers = [ - dict( name="left", src="hda", id=hda1[ "id" ] ), - dict( name="right", src="hda", id=hda2[ "id" ] ), + dict( name="forward", src="hda", id=hda1[ "id" ] ), + dict( name="reverse", src="hda", id=hda2[ "id" ] ), ] return element_identifiers diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -204,8 +204,8 @@ first_object = first_element[ "object" ] assert first_object[ "collection_type" ] == "paired" assert len( first_object[ "elements" ] ) == 2 - first_object_left_element = first_object[ "elements" ][ 0 ] - self.assertEquals( outputs[ 0 ][ "id" ], first_object_left_element[ "object" ][ "id" ] ) + first_object_forward_element = first_object[ "elements" ][ 0 ] + self.assertEquals( outputs[ 0 ][ "id" ], first_object_forward_element[ "object" ][ "id" ] ) @skip_without_tool( "cat1" ) def test_map_over_two_collections( self ): diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/functional/tools/collection_mixed_param.xml --- a/test/functional/tools/collection_mixed_param.xml +++ b/test/functional/tools/collection_mixed_param.xml @@ -13,8 +13,8 @@ <test><param name="f1"><collection type="paired"> - <element name="left" value="simple_line.txt" /> - <element name="right" value="simple_line_alternative.txt" /> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /></collection></param><param name="f2" value="simple_lines_both.txt" /> diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/functional/tools/collection_paired_test.xml --- a/test/functional/tools/collection_paired_test.xml +++ b/test/functional/tools/collection_paired_test.xml @@ -1,6 +1,6 @@ <tool id="collection_paired_test" name="paired_test" version="0.1.0"><command> - cat #for $f in $f1# ${f} #end for# >> $out1; + cat $f1.forward $f1.reverse >> $out1; </command><inputs><param name="f1" type="data_collection" collection_type="paired" /> @@ -12,8 +12,8 @@ <test><param name="f1"><collection type="paired"> - <element name="left" value="simple_line.txt" /> - <element name="right" value="simple_line_alternative.txt" /> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /></collection></param><output name="out1"> 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: 4 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ef71c8b55a5/ Changeset: 6ef71c8b55a5 User: jmchilton Date: 2014-05-15 19:04:58 Summary: Bugfix: Copying datasets to existing and new history at same time. Previously would give error about set not having an append method. Affected #: 1 file diff -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 -r 6ef71c8b55a56be844a5a57aad9fe91a4222663e lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1000,7 +1000,7 @@ elif target_history_ids: if not isinstance( target_history_ids, list ): target_history_ids = target_history_ids.split(",") - target_history_ids = set([ trans.security.decode_id(h) for h in target_history_ids if h ]) + target_history_ids = list(set([ trans.security.decode_id(h) for h in target_history_ids if h ])) else: target_history_ids = [] done_msg = error_msg = "" https://bitbucket.org/galaxy/galaxy-central/commits/e1a1ffe4bfaf/ Changeset: e1a1ffe4bfaf User: jmchilton Date: 2014-05-15 19:04:58 Summary: Allow 'Copy Datasets' page to copy collections as well. Affected #: 2 files diff -r 6ef71c8b55a56be844a5a57aad9fe91a4222663e -r e1a1ffe4bfaf06b1c0ab293d0057c6e793fee493 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -981,7 +981,7 @@ return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects, upgrade_messages=upgrade_messages, has_parameter_errors=has_parameter_errors ) @web.expose - def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): + def copy_datasets( self, trans, source_history=None, source_content_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): user = trans.get_user() if source_history is not None: history = self.get_history(trans, source_history) @@ -989,12 +989,16 @@ else: history = current_history = trans.get_history() refresh_frames = [] - if source_dataset_ids: - if not isinstance( source_dataset_ids, list ): - source_dataset_ids = source_dataset_ids.split(",") - source_dataset_ids = set(map( trans.security.decode_id, source_dataset_ids )) + if source_content_ids: + if not isinstance( source_content_ids, list ): + source_content_ids = source_content_ids.split(",") + encoded_dataset_collection_ids = [ s[ len("dataset_collection|"): ] for s in source_content_ids if s.startswith("dataset_collection|") ] + encoded_dataset_ids = [ s[ len("dataset|"): ] for s in source_content_ids if s.startswith("dataset|") ] + decoded_dataset_collection_ids = set(map( trans.security.decode_id, encoded_dataset_collection_ids )) + decoded_dataset_ids = set(map( trans.security.decode_id, encoded_dataset_ids )) else: - source_dataset_ids = [] + decoded_dataset_collection_ids = [] + decoded_dataset_ids = [] if target_history_id: target_history_ids = [ trans.security.decode_id(target_history_id) ] elif target_history_ids: @@ -1006,8 +1010,8 @@ done_msg = error_msg = "" new_history = None if do_copy: - invalid_datasets = 0 - if not source_dataset_ids or not ( target_history_ids or new_history_name ): + invalid_contents = 0 + if not ( decoded_dataset_ids or decoded_dataset_collection_ids ) or not ( target_history_ids or new_history_name ): error_msg = "You must provide both source datasets and target histories. " else: if new_history_name: @@ -1023,18 +1027,22 @@ target_histories = [ history ] if len( target_histories ) != len( target_history_ids ): error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) ) - source_hdas = map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, source_dataset_ids ) - source_hdas.sort(key=lambda hda: hda.hid) - for hda in source_hdas: - if hda is None: + source_contents = map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, decoded_dataset_ids ) + source_contents.extend( map( trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get, decoded_dataset_collection_ids ) ) + source_contents.sort(key=lambda content: content.hid) + for content in source_contents: + if content is None: error_msg = error_msg + "You tried to copy a dataset that does not exist. " - invalid_datasets += 1 - elif hda.history != history: + invalid_contents += 1 + elif content.history != history: error_msg = error_msg + "You tried to copy a dataset which is not in your current history. " - invalid_datasets += 1 + invalid_contents += 1 else: for hist in target_histories: - hist.add_dataset( hda.copy( copy_children = True ) ) + if content.history_content_type == "dataset": + hist.add_dataset( content.copy( copy_children=True ) ) + else: + hist.add_dataset_collection( content.copy( ) ) if current_history in target_histories: refresh_frames = ['history'] trans.sa_session.flush() @@ -1042,21 +1050,21 @@ ( url_for( controller="history", action="switch_to_history", \ hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \ for hist in target_histories ] ) - num_source = len( source_dataset_ids ) - invalid_datasets + num_source = len( source_content_ids ) - invalid_contents num_target = len(target_histories) done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) trans.sa_session.refresh( history ) - source_datasets = history.visible_datasets + source_contents = history.active_contents target_histories = [history] if user: target_histories = user.active_histories return trans.fill_template( "/dataset/copy_view.mako", source_history = history, current_history = current_history, - source_dataset_ids = source_dataset_ids, + source_content_ids = source_content_ids, target_history_id = target_history_id, target_history_ids = target_history_ids, - source_datasets = source_datasets, + source_contents = source_contents, target_histories = target_histories, new_history_name = new_history_name, done_msg = done_msg, diff -r 6ef71c8b55a56be844a5a57aad9fe91a4222663e -r e1a1ffe4bfaf06b1c0ab293d0057c6e793fee493 templates/webapps/galaxy/dataset/copy_view.mako --- a/templates/webapps/galaxy/dataset/copy_view.mako +++ b/templates/webapps/galaxy/dataset/copy_view.mako @@ -59,17 +59,18 @@ </select></div><div class="toolFormBody"> - %if len(source_datasets) > 0: - %for data in source_datasets: + %if source_contents: + %for data in source_contents: <% checked = "" encoded_id = trans.security.encode_id(data.id) - if data.id in source_dataset_ids: + input_id = "%s|%s" % ( data.history_content_type, encoded_id ) + if input_id in source_content_ids: checked = " checked='checked'" %><div class="form-row"> - <input type="checkbox" name="source_dataset_ids" id="dataset_${encoded_id}" value="${encoded_id}"${checked}/> - <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label> + <input type="checkbox" name="source_content_ids" id="${input_id}" value="${input_id}"${checked}/> + <label for="${input_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label></div> %endfor %else: https://bitbucket.org/galaxy/galaxy-central/commits/1f35c462c606/ Changeset: 1f35c462c606 User: jmchilton Date: 2014-05-15 19:04:58 Summary: PEP-8 fixes for DatasetInterface.copy_datasets. Affected #: 1 file diff -r e1a1ffe4bfaf06b1c0ab293d0057c6e793fee493 -r 1f35c462c606dca541e5f5f16d2c3f4e33334cfe lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1047,9 +1047,9 @@ refresh_frames = ['history'] trans.sa_session.flush() hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' % - ( url_for( controller="history", action="switch_to_history", \ - hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \ - for hist in target_histories ] ) + ( url_for( controller="history", action="switch_to_history", + hist_id=trans.security.encode_id( hist.id ) ), hist.name ) + for hist in target_histories ] ) num_source = len( source_content_ids ) - invalid_contents num_target = len(target_histories) done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) @@ -1057,19 +1057,19 @@ source_contents = history.active_contents target_histories = [history] if user: - target_histories = user.active_histories + target_histories = user.active_histories return trans.fill_template( "/dataset/copy_view.mako", - source_history = history, - current_history = current_history, - source_content_ids = source_content_ids, - target_history_id = target_history_id, - target_history_ids = target_history_ids, - source_contents = source_contents, - target_histories = target_histories, - new_history_name = new_history_name, - done_msg = done_msg, - error_msg = error_msg, - refresh_frames = refresh_frames ) + source_history=history, + current_history=current_history, + source_content_ids=source_content_ids, + target_history_id=target_history_id, + target_history_ids=target_history_ids, + source_contents=source_contents, + target_histories=target_histories, + new_history_name=new_history_name, + done_msg=done_msg, + error_msg=error_msg, + refresh_frames=refresh_frames ) def _copy_datasets( self, trans, dataset_ids, target_histories, imported=False ): """ Helper method for copying datasets. """ https://bitbucket.org/galaxy/galaxy-central/commits/b5a1cd130f71/ Changeset: b5a1cd130f71 User: jmchilton Date: 2014-05-15 19:04:58 Summary: Order history.{active,visible}_dataset_collections by hid instead of id. Affected #: 1 file diff -r 1f35c462c606dca541e5f5f16d2c3f4e33334cfe -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1461,9 +1461,9 @@ model.HistoryDatasetCollectionAssociation, primaryjoin=( ( model.HistoryDatasetCollectionAssociation.table.c.history_id ) == model.History.table.c.id ) & not_( model.HistoryDatasetCollectionAssociation.table.c.deleted ), - order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.id ), + order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.hid ), viewonly=True, - ), # TODO:orderbyhid + ), visible_datasets=relation( model.HistoryDatasetAssociation, primaryjoin=( ( model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id ) & not_( model.HistoryDatasetAssociation.table.c.deleted ) & model.HistoryDatasetAssociation.table.c.visible ), @@ -1473,7 +1473,7 @@ visible_dataset_collections=relation( model.HistoryDatasetCollectionAssociation, primaryjoin=( ( model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id ) & not_( model.HistoryDatasetCollectionAssociation.table.c.deleted ) & model.HistoryDatasetCollectionAssociation.table.c.visible ), - order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.id ), + order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.hid ), viewonly=True, ), tags=relation( model.HistoryTagAssociation, order_by=model.HistoryTagAssociation.table.c.id, backref="histories" ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Fix multipanels in heatmap
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2300bcd6008/ Changeset: d2300bcd6008 User: guerler Date: 2014-05-15 17:57:43 Summary: Charts: Fix multipanels in heatmap Affected #: 3 files diff -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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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}}),p=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:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)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}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$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)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw 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u(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 o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),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",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),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:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",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 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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_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for 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Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:f,nvd3_stackedarea_full:l,nvd3_stackedarea_stream:c,nvd3_line:s,nvd3_line_focus:o,nvd3_scatter:a,nvd3_pie:u,nvd3_histogram:i,highcharts_boxplot:h,heatmap:p}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$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 +define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var 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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$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:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),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.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=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}}),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:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=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>"}}),l=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>"}}),c=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.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$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}}),p=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:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)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}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" 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r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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i=$("<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.$el),u.append('<div class="toolParamHelp" 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$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",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),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:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",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_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others"})}),define("plugin/charts/nvd3_line_focus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others"})}),define("plugin/charts/nvd3_pie/config",[],function(){return{title:"Pie chart",library:"nvd3.js",category:"Area charts",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_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bar/config","plugin/charts/nvd3_bar_stacked/config","plugin/charts/nvd3_bar_horizontal/config","plugin/charts/nvd3_bar_horizontal_stacked/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:f,nvd3_stackedarea_full:l,nvd3_stackedarea_stream:c,nvd3_line:s,nvd3_line_focus:o,nvd3_scatter:a,nvd3_pie:u,nvd3_histogram:i,highcharts_boxplot:h,heatmap:p}})}),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 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js @@ -20,51 +20,66 @@ // loop through data groups var index = 0; for (var group_index in request_dictionary.groups) { + + // configure request + var tmp_dict = { + id : request_dictionary.id, + groups : [{ + key : request_dictionary.groups[group_index].key, + columns : { + row_label: { + index : index++, + is_label : true + }, + col_label: { + index : index++, + is_label : true + }, + value: { + index : index++ + } + } + }] + }; - // configure request - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - row_label: { - index : index++, - is_label : true - }, - col_label: { - index : index++, - is_label : true - }, - value: { - index : index++ - } - } - } - - // request data - this.app.datasets.request(request_dictionary, function() { + // target div + var group_div = self.options.canvas[group_index]; - // get group - var group = request_dictionary.groups[group_index]; - var div = self.options.canvas[group_index]; - - // draw plot - var heatmap = new HeatmapPlugin({ - 'title' : group.key, - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : div - }); - - // check if done + // draw group + this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) { if (group_index == request_dictionary.groups.length - 1) { // set chart state chart.state('ok', 'Heat map drawn.'); - + // unregister process chart.deferred.done(process_id); } }); } + }, + + // draw group + _draw_group: function(group_index, div, chart, request_dictionary, callback) { + // link this + var self = this; + + // request data + this.app.datasets.request(request_dictionary, function() { + + // get group + var group = request_dictionary.groups[0]; + + // draw plot + var heatmap = new HeatmapPlugin({ + 'title' : group.key, + 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], + 'data' : group.values, + 'div' : div + }); + + // callback on completion + callback (group_index); + }); } }); diff -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 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 @@ -198,8 +198,12 @@ var group_index = 0; var self = this; chart.groups.each(function(group) { + // increase group counter + group_index++; + + // add selected columns to column string for (var key in self.chart_settings.columns) { - request_string += key + '_' + (++group_index) + ':' + (parseInt(group.get(key)) + 1) + ', '; + request_string += key + '_' + group_index + ':' + (parseInt(group.get(key)) + 1) + ', '; } }); @@ -244,13 +248,13 @@ // add columns var columns = {}; - for (var key in self.chart_settings.columns) { + for (var column_key in self.chart_settings.columns) { // get settings for column - var column_settings = self.chart_settings.columns[key]; + var column_settings = self.chart_settings.columns[column_key]; // add to columns - columns[key] = { - index : group.get(key), + columns[column_key] = { + index : group.get(column_key), is_label : column_settings.is_label } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Merged in erasche2/galaxy-central (pull request #393)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f6110335f4e/ Changeset: 5f6110335f4e User: natefoo Date: 2014-05-15 17:33:20 Summary: Merged in erasche2/galaxy-central (pull request #393) Added rolling restart script to kill servers sequentially Affected #: 1 file diff -r 0d2c45f321ed234115a15d46c255818192ba41a2 -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 rolling_restart.sh --- /dev/null +++ b/rolling_restart.sh @@ -0,0 +1,49 @@ +#!/bin/bash +cd `dirname $0` + +check_if_not_started(){ + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [[ $latest_pid -eq $current_pid_in_file ]]; + then + echo 0; + else + echo 1; + fi +} + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` +for server in $servers; +do + # If there's a pid + if [[ -e $server.pid ]] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [[ $result -eq 1 ]] + do + result=$(check_if_not_started $server.log $server.pid) + echo -n "." + sleep 1 + done + echo "" +done + 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: 6 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a2892895e566/ Changeset: a2892895e566 User: erasche2 Date: 2014-05-14 21:48:26 Summary: Added rolling restart script to kill servers sequentially Affected #: 1 file diff -r b483d9df129c00480fc72253a277de18ab67b27d -r a2892895e566ebad6edc1401519c72b83138a2a9 rolling_restart.sh --- /dev/null +++ b/rolling_restart.sh @@ -0,0 +1,49 @@ +#!/bin/bash +cd `dirname $0` + +check_if_not_started(){ + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep 'Starting server in PID [0-9]+' $1 -o | sed 's/Starting server in PID //g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [[ $latest_pid -eq $current_pid_in_file ]]; + then + echo 0; + else + echo 1; + fi +} + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` +for server in $servers; +do + # If there's a pid + if [[ -e $server.pid ]] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ & + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [[ $result -eq 1 ]] + do + result=$(check_if_not_started $server.log $server.pid) + echo -n "." + sleep 1 + done + echo "" +done + https://bitbucket.org/galaxy/galaxy-central/commits/8bd0ea03bc28/ Changeset: 8bd0ea03bc28 User: erasche2 Date: 2014-05-14 22:23:26 Summary: Removed detach as --daemon flag will detach process Affected #: 1 file diff -r a2892895e566ebad6edc1401519c72b83138a2a9 -r 8bd0ea03bc2877bc7a9fc6880337c3a07706e655 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -31,7 +31,7 @@ echo "$server not running" fi # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ & + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ # Wait for the server to start sleep 1 # Grab the new pid https://bitbucket.org/galaxy/galaxy-central/commits/b189178db4ae/ Changeset: b189178db4ae User: erasche2 Date: 2014-05-14 22:33:44 Summary: Added --daemon flag so user doesn't have to Affected #: 1 file diff -r 8bd0ea03bc2877bc7a9fc6880337c3a07706e655 -r b189178db4aef2a3dbe9fbfbe2be4582911f8597 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -31,7 +31,7 @@ echo "$server not running" fi # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ # Wait for the server to start sleep 1 # Grab the new pid https://bitbucket.org/galaxy/galaxy-central/commits/a3530f2474fc/ Changeset: a3530f2474fc User: erasche2 Date: 2014-05-15 16:43:04 Summary: Added line anchors for performance Affected #: 1 file diff -r b189178db4aef2a3dbe9fbfbe2be4582911f8597 -r a3530f2474fc2ccc0529e35cf154615de4474365 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -3,7 +3,7 @@ check_if_not_started(){ # Search for all pids in the logs and tail for the last one - latest_pid=`egrep 'Starting server in PID [0-9]+' $1 -o | sed 's/Starting server in PID //g' | tail -n 1` + latest_pid=`egrep '^Starting server in PID [0-9]+.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` # Grab the current pid from the file we were given current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs https://bitbucket.org/galaxy/galaxy-central/commits/65ea2c82a973/ Changeset: 65ea2c82a973 User: erasche2 Date: 2014-05-15 16:48:17 Summary: Fixed typo on regex Affected #: 1 file diff -r a3530f2474fc2ccc0529e35cf154615de4474365 -r 65ea2c82a9738f8782a3c06d2ee06d5471ba9bd0 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -3,7 +3,7 @@ check_if_not_started(){ # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` # Grab the current pid from the file we were given current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs https://bitbucket.org/galaxy/galaxy-central/commits/5f6110335f4e/ Changeset: 5f6110335f4e User: natefoo Date: 2014-05-15 17:33:20 Summary: Merged in erasche2/galaxy-central (pull request #393) Added rolling restart script to kill servers sequentially Affected #: 1 file diff -r 0d2c45f321ed234115a15d46c255818192ba41a2 -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 rolling_restart.sh --- /dev/null +++ b/rolling_restart.sh @@ -0,0 +1,49 @@ +#!/bin/bash +cd `dirname $0` + +check_if_not_started(){ + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [[ $latest_pid -eq $current_pid_in_file ]]; + then + echo 0; + else + echo 1; + fi +} + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` +for server in $servers; +do + # If there's a pid + if [[ -e $server.pid ]] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [[ $result -eq 1 ]] + do + result=$(check_if_not_started $server.log $server.pid) + echo -n "." + sleep 1 + done + echo "" +done + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refactoring cleanup in the Tool Shed's package installation framework.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d2c45f321ed/ Changeset: 0d2c45f321ed User: greg Date: 2014-05-15 15:59:55 Summary: Refactoring cleanup in the Tool Shed's package installation framework. Affected #: 4 files diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -26,8 +26,6 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install import repository_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids -from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager import pkg_resources eggs.require( 'mercurial' ) @@ -458,63 +456,16 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) err_msg = '' - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - installed_tool_dependencies = [] - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = tool_dependencies[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( trans.app, - elem, - tool_shed_repository, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ trans.app.install_model.ToolDependency.installation_status.INSTALLED, - trans.app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) - if trans.app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -22,9 +22,6 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util -from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager - from galaxy import eggs eggs.require( 'mercurial' ) @@ -624,58 +621,12 @@ trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir ) - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - repository_tool_dependencies = util.listify( tool_shed_repository.tool_dependencies ) - # elem is a package tag set. - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in repository_tool_dependencies ] - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = repository_tool_dependencies[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=repository_tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( trans.app, - elem, - tool_shed_repository, - tool_dependencies=repository_tool_dependencies, - from_tool_migration_manager=False ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ trans.app.install_model.ToolDependency.installation_status.INSTALLED, - trans.app.install_model.ToolDependency.installation_status.ERROR ]: - if trans.app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -916,72 +867,24 @@ for tool_dependency in repository.missing_tool_dependencies: if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR, trans.install_model.ToolDependency.installation_status.INSTALLING ]: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( trans.app, - tool_dependency=tool_dependency, - status=trans.install_model.ToolDependency.installation_status.UNINSTALLED, - error_message=None, - remove_from_disk=True ) + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( trans.app, + tool_dependency=tool_dependency, + status=trans.install_model.ToolDependency.installation_status.UNINSTALLED, + error_message=None, + remove_from_disk=True ) # Install tool dependencies. suc.update_tool_shed_repository_status( trans.app, repository, trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( trans.app ) ) - installed_tool_dependencies = [] - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if tree is None: - return installed_tool_dependencies - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = tool_dependency_db_records[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( trans.app, - elem, - tool_shed_repository, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, - app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) - if app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=trans.app, + tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -19,8 +19,6 @@ from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util -from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager from galaxy.util.odict import odict log = logging.getLogger( __name__ ) @@ -447,64 +445,12 @@ self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) - installed_tool_dependencies = [] - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - tool_dependency = None - for tool_dependency in tool_dependencies: - if package_name == str( tool_dependency.name ) and package_version == str( tool_dependency.version ): - break - if tool_dependency is not None: - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = tool_dependencies[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( self.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( self.app, - elem, - tool_shed_repository, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=True ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( self.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.INSTALLED, - self.app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) - if self.app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - self.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=self.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=True ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -3,7 +3,6 @@ import os import urllib import urllib2 -from galaxy import eggs from galaxy import util from galaxy import web from galaxy.util import json @@ -18,6 +17,9 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.install_manager import InstallManager +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager + log = logging.getLogger( __name__ ) def activate_repository( trans, repository ): @@ -481,6 +483,73 @@ all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict +def install_specified_packages( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_tool_migration_manager=False ): + """ + Follow the recipe in the received tool_dependencies_config to install specified packages for + repository tools. The received list of tool_dependencies are the database records for those + dependencies defined in the tool_dependencies_config that are to be installed. This list may + be a subset of the set of dependencies defined in the tool_dependencies_config. This allows + for filtering out dependencies that have not been checked for installation on the 'Manage tool + dependencies' page for an installed Tool Shed repository. + """ + attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] + installed_packages = [] + install_manager = InstallManager() + tag_manager = TagManager() + # Parse the tool_dependencies.xml config. + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + log.debug( "The received tool_dependencies.xml file is likely invalid: %s" % str( error_message ) ) + return installed_packages + root = tree.getroot() + for elem in root: + package_name = elem.get( 'name', None ) + package_version = elem.get( 'version', None ) + if package_name and package_version: + # elem is a package tag set. + attr_tup = ( package_name, package_version, 'package' ) + try: + index = attr_tups_of_dependencies_for_install.index( attr_tup ) + except Exception, e: + index = None + if index is not None: + tool_dependency = tool_dependencies[ index ] + tool_dependency, proceed_with_install, action_elem_tuples = \ + tag_manager.process_tag_set( app, + tool_shed_repository, + tool_dependency, + elem, + package_name, + package_version, + from_tool_migration_manager=from_tool_migration_manager, + tool_dependency_db_records=tool_dependencies ) + if proceed_with_install: + try: + tool_dependency = install_manager.install_package( app, + elem, + tool_shed_repository, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=from_tool_migration_manager ) + except Exception, e: + error_message = "Error installing tool dependency package %s version %s: %s" % \ + ( str( package_name ), str( package_version ), str( e ) ) + log.exception( error_message ) + if tool_dependency: + # Since there was an installation error, update the tool dependency status to Error. The + # remove_installation_path option must be left False here. + tool_dependency = \ + tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, + app.install_model.ToolDependency.installation_status.ERROR ]: + installed_packages.append( tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + return installed_packages + def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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