galaxy-commits June 2014

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ca297d98ab45/ Changeset: ca297d98ab45 Branch: stable User: natefoo Date: 2014-06-02 22:24:53 Summary: Added tag latest_2014.04.14 for changeset 68a8b0397947 Affected #: 1 file diff -r 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 -r ca297d98ab45f650b817acc613050530247c429c .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,3 +7,4 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 +68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 https://bitbucket.org/galaxy/galaxy-central/commits/9874065b40c6/ Changeset: 9874065b40c6 Branch: next-stable User: natefoo Date: 2014-06-02 22:26:48 Summary: Close next-stable branch. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/7e257c7b10ba/ Changeset: 7e257c7b10ba Branch: stable User: natefoo Date: 2014-06-02 22:27:48 Summary: Update stable branch from next-stable for release. 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this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var 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id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" 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e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" 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No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_svg();var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg_el=this.$el.find("svg"),this.svg=d3.select(this.svg_el[0])},_draw:function(e){var t=this;this._create_svg(),e.state("wait","Please wait...");var n=e.deferred.register(),r=e.get("type"),i=this.app.types.get(r);if(!i.execute||i.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var s=new r(t.app,{svg:t.svg});i.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){s.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):s.draw(n,e,t._defaultRequestDictionary(e)):s.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart 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u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new 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btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<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 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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_histogram_discrete/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram (discrete)",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",columns:{y:{title:"Observations",is_label:!0}},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_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 ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/_nvd3/config.js --- a/config/plugins/visualizations/charts/static/charts/_nvd3/config.js +++ /dev/null @@ -1,218 +0,0 @@ -define([], function() { - -return { - title : '', - columns : { - y : { - title : 'Values for y-axis' - } - }, - settings : { - separator_label : { - title : 'X axis', - type : 'separator' - }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - x_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : 'x_axis_tick' - }, - { - label : 'Auto', - value : 'auto', - hide : 'x_axis_tick' - }, - { - label : 'Float', - value : 'f', - show : 'x_axis_tick' - }, - { - label : 'Exponent', - value : 'e', - show : 'x_axis_tick' - }, - { - label : 'Integer', - value : 'd', - hide : 'x_axis_tick' - }, - { - label : 'Percentage', - value : 'p', - show : 'x_axis_tick' - }, - { - label : 'Rounded', - value : 'r', - show : 'x_axis_tick' - }, - { - label : 'SI-prefix', - value : 's', - show : 'x_axis_tick' - } - ] - }, - x_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - - }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - }, - y_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : 'y_axis_tick' - }, - { - label : 'Auto', - value : 'auto', - hide : 'y_axis_tick' - }, - { - label : 'Float', - value : 'f', - show : 'y_axis_tick' - }, - { - label : 'Exponent', - value : 'e', - show : 'y_axis_tick' - }, - { - label : 'Integer', - value : 'd', - hide : 'y_axis_tick' - }, - { - label : 'Percentage', - value : 'p', - show : 'y_axis_tick' - }, - { - label : 'Rounded', - value : 'r', - show : 'y_axis_tick' - }, - { - label : 'SI-prefix', - value : 's', - show : 'y_axis_tick' - } - ] - }, - y_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - - }, - separator_legend : { - title : 'Others', - type : 'separator' - }, - show_legend : { - title : 'Show legend', - info : 'Would you like to add a legend?', - type : 'select', - init : 'true', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] - }, - } -}; - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js --- a/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js +++ /dev/null @@ -1,80 +0,0 @@ -// dependencies -define([], function() { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, nvd3_model, chart, request_dictionary, callback) - { - // request data - var self = this; - this.app.datasets.request(request_dictionary, function(data) { - nv.addGraph(function() { - // x axis - self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); - - // x axis label - nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label')); - - // y axis - self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); - - // y axis label - nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label')) - .axisLabelDistance(30); - - // controls - if (chart.groups.length == 1) { - nvd3_model.options({ showControls: false }); - } - - // legend - var legend_visible = true; - if (chart.settings.get('show_legend') == 'false') { - legend_visible = false; - } - nvd3_model.showLegend(legend_visible); - - // custom callback - if (callback) { - callback(nvd3_model); - } - - // parse data to svg - self.options.svg.datum(data) - .call(nvd3_model); - - // refresh on window resize - nv.utils.windowResize(nvd3_model.update); - - // set chart state - chart.state('ok', 'Chart has been drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - }); - }, - - // make axis - _axis: function(axis, type, tick) { - switch (type) { - case 'hide': - axis.tickFormat(function() { return '' }); - break; - case 'auto': - break; - default: - axis.tickFormat(d3.format(tick + type)); - } - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js --- a/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js +++ /dev/null @@ -1,21 +0,0 @@ -// dependencies -define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/bardiagram/config.js --- a/config/plugins/visualizations/charts/static/charts/bardiagram/config.js +++ /dev/null @@ -1,7 +0,0 @@ -define(['plugin/charts/_nvd3/config'], function(nvd3_config) { - -return $.extend(true, {}, nvd3_config, { - title : 'Bar diagram', -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/heatmap/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js @@ -0,0 +1,195 @@ +define([], function() { + +return { + title : 'Heatmap', + category : 'Data processing (requires \'charts\' tool from Toolshed)', + library : '', + tag : 'div', + use_panels : true, + execute : 'heatmap', + + // columns + columns : { + row_label : { + title : 'Row labels', + is_label : true + }, + col_label : { + title : 'Column labels', + is_label : true + }, + value : { + title : 'Observations' + }, + }, + + // settings + settings: { + /*limit : { + title : 'Limit', + info : 'Which to ranked clusters would you like to visualize', + type : 'select', + init : '20', + data : [ + { + label : '20', + value : '20' + }, + { + label : '30', + value : '30' + }, + { + label : '40', + value : '40' + }, + { + label : '50', + value : '50' + }, + { + label : '60', + value : '60' + }, + { + label : '70', + value : '70' + }, + { + label : '80', + value : '80' + }, + { + label : '90', + value : '90' + }, + { + label : '100', + value : '100' + } + ] + },*/ + color_set : { + title : 'Color scheme', + info : 'Select a color scheme for your heatmap', + type : 'select', + init : 'ocean', + data : [ + { + label : 'Cold-to-Hot', + value : 'hot' + }, + { + label : 'Cool', + value : 'cool' + }, + { + label : 'Copper', + value : 'copper' + }, + { + label : 'Gebco', + value : 'gebco' + }, + { + label : 'Globe', + value : 'globe' + }, + { + label : 'Gray scale', + value : 'gray' + }, + { + label : 'Haxby', + value : 'haxby' + }, + { + label : 'Jet', + value : 'jet' + }, + { + label : 'No-Green', + value : 'no_green' + }, + { + label : 'Ocean', + value : 'ocean' + }, + { + label : 'Polar', + value : 'polar' + }, + { + label : 'Rainbow', + value : 'rainbow' + }, + { + label : 'Red-to-Green', + value : 'redgreen' + }, + { + label : 'Red-to-green (saturated)', + value : 'red2green' + }, + { + label : 'Relief', + value : 'relief' + }, + { + label : 'Seismograph', + value : 'seis' + }, + { + label : 'Sealand', + value : 'sealand' + }, + { + label : 'Split', + value : 'split' + }, + { + label : 'Topo', + value : 'topo' + }, + { + label : 'Wysiwyg', + value : 'wysiwyg' + } + ] + }, + + sorting : { + title : 'Sorting', + info : 'How should the columns be clustered?', + type : 'select', + init : 'hclust', + data : [ + { + label : 'Read from dataset', + value : 'hclust' + }, + { + label : 'Sort column and row labels', + value : 'byboth' + }, + { + label : 'Sort column labels', + value : 'bycolumns' + }, + { + label : 'Sort by rows', + value : 'byrow' + } + ] + } + }, + + // menu definition + menu : function() { + return { + color_set : this.settings.color_set + } + } +}; + +}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js @@ -0,0 +1,52 @@ +// dependencies +define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { + +// color palettes +var colorSets = { + seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'], + + sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'], + + redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'], + + ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'], + + cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'], + + copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'], + + gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'], + + globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'], + + gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'], + + haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'], + + hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'], + + jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'], + + no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'], + + polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'], + + rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'], + + red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'], + + relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'], + + split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'], + + topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'], + + wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF'] +} + +// return +return { + colorSets: colorSets +} + +}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -0,0 +1,739 @@ +// dependencies +define(['utils/utils'], +function(Utils) { + +// widget +return Backbone.View.extend( +{ + // number of columns and rows + colNumber: 0, + rowNumber: 0, + + // indices + rowIndex: [], + colIndex: [], + + // labels + rowLabel: [], + colLabel: [], + + // cell size + cellSize: 0, + + // font size + fontSize: 0, + + // color buckets + nColors: 0, + + // margins as cells + margin : { + top : 5, + right : 5, + bottom : 5, + left : 5 + }, + + // default settings + optionsDefault: { + title : '', + pace : 1000, + }, + + // initialize + initialize: function(options) { + // link this + var self = this; + + // load options + this.options = Utils.merge(options, this.optionsDefault) + + // check requirements + if (!this.options.data || !this.options.div || !this.options.colors) { + console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.'); + return; + } + + // link data + this.data = this.options.data; + + // set element + this.setElement(this.options.div); + + // + // data indexing + // + + // labels (in alphabetical order) + this.rowLabel = []; + this.colLabel = []; + + // index (order from original dataset) + this.rowIndex = []; + this.colIndex = []; + + // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting) + this.colRank = {}; + this.rowRank = {}; + + // + // identify and parse labels + // + for (var i in this.data) { + var cell = this.data[i]; + + // add label to index list + var col_label = cell.col_label; + if (this.colRank[col_label] === undefined) { + this.colRank[col_label] = true; + this.colLabel.push(col_label); + this.colIndex.push(col_label); + } + var row_label = cell.row_label; + if (this.rowRank[row_label] === undefined) { + this.rowRank[row_label] = true; + this.rowLabel.push(row_label); + this.rowIndex.push(row_label); + } + } + + // + // sort labels and update rank dictionary + // + + // set sizes + this.rowNumber = this.rowLabel.length + this.colNumber = this.colLabel.length + + // sort labels alphabetical + this.rowLabel.sort(); + this.colLabel.sort(); + + // generate sorted key list for rows + for (var i in this.rowLabel) { + var row_label = this.rowLabel[i]; + var row = parseInt(i); + this.rowRank[row_label] = row; + } + + // generate sorted key list for columns + for (var i in this.colLabel) { + var col_label = this.colLabel[i]; + var col = parseInt(i); + this.colRank[col_label] = col; + } + + // + // parse indexing from rank dictionary to cells + // + + // min/max + this.max = undefined; + this.min = undefined + + // add indices to data + for (var i in this.data) { + // get cell data + var cell = this.data[i]; + + // add rank + cell.col = this.colRank[cell.col_label]; + cell.row = this.rowRank[cell.row_label]; + + // identify max/min values + if (this.min == undefined || this.min > cell.value) { + this.min = cell.value; + } + if (this.max == undefined || this.max < cell.value) { + this.max = cell.value; + } + } + + // + // translate original create cluster from order in original data + // + + // generate sorted key list for columns + for (var i in this.colIndex) { + this.colIndex[i] = this.colRank[this.colIndex[i]]; + } + // generate sorted key list for columns + for (var i in this.rowIndex) { + this.rowIndex[i] = this.rowRank[this.rowIndex[i]]; + } + + // middle + this.mid = (this.max + this.min) / 2; + + // + // set colors + // + + // identify buckets + this.nColors = this.options.colors.length; + + // color scale + this.colorScale = d3.scale.quantile() + .domain([this.min, this.mid, this.max]) + .range(this.options.colors); + + // + // add ui elements + // + // create tooltip + this.$tooltip = $(this._templateTooltip()); + this.$el.append(this.$tooltip); + + // + // finally draw the heatmap + // + this._build(); + + // catch window resize event + $(window).resize(function () { + self._build(); + }); + }, + + _build: function() { + // link this + var self = this; + + // container (full draw area) + this.widthContainer = this.$el.width(); + this.heightContainer = this.$el.height(); + + // get grid dimensions + this.width = this.widthContainer; + this.height = this.heightContainer; + + // calculate cell size + this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)), + (this.width / (this.colNumber + this.margin.left + this.margin.right))); + + // set font size + this.fontSize = Math.min(this.cellSize, 16); + + // set width/height for plugin + this.width = this.cellSize * this.colNumber; + this.height = this.cellSize * this.rowNumber; + + // get dimensions + var margin = this.options.margin; + var width = this.width; + var height = this.height; + + // reset svg + if (this.svg !== undefined) { + this.$el.find('svg').remove(); + } + + // add main group and translate + this.svg = d3.select(this.$el[0]).append('svg') + .append('g') + .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' + + (this.heightContainer - height) / 2 + ')'); + + // reset sorting + this.rowSortOrder = false; + this.colSortOrder = false; + + // build + this.d3RowLabels = this._buildRowLabels(); + this.d3ColLabels = this._buildColLabels(); + this.d3HeatMap = this._buildHeatMap(); + this.d3Legend = this._buildLegend(); + this.d3Title = this._buildTitle(); + }, + + // build title + _buildTitle: function() { + // link this + var self = this; + + // gather data + var height = this.height; + var width = this.width; + var cellSize = this.cellSize; + var fontSize = this.fontSize; + var title = this.options.title; + + // add title + return this.svg.append('g') + .append('text') + .attr('x', width / 2) + .attr('y', height + 3 * cellSize + fontSize + 3) + .attr('text-anchor', 'middle') + .text(title); + }, + + // build legend + _buildLegend: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var fontSize = this.fontSize; + var height = this.height; + var legendCellWidth = this.width / this.nColors; + + // create range labels + var dataRange = []; + for(var i = 0; i < this.nColors; i++) { + dataRange.push(''); + } + + // prepare indices + var dataRangeMin = 0; + var dataRangeMid = parseInt((dataRange.length - 1) / 2); + var dataRangeMax = dataRange.length - 1; + + // add labels + dataRange[dataRangeMin] = this.min; + dataRange[dataRangeMid] = this.mid; + dataRange[dataRangeMax] = this.max; + + // create legend + var legend = this.svg.selectAll('.legend') + .data(dataRange) + .enter().append('g') + .attr('class', 'legend'); + + // add boxes + legend.append('rect') + .attr('x', function(d, i) { + return legendCellWidth * i; + }) + .attr('y', height + cellSize) + .attr('width', legendCellWidth) + .attr('height', cellSize) + .style('fill', function(d, i) { + return self.options.colors[i]; + }); + + // add text + legend.append('text') + .attr('class', 'mono') + .text(function(d) { + return d; + }) + .attr('width', legendCellWidth) + .attr('x', function(d, i) { + return legendCellWidth * i; + }) + .attr('y', height + cellSize - 3) + .style('font-size', fontSize + 'px'); + + // return + return legend; + }, + + // build column labels + _buildColLabels: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var fontSize = this.fontSize; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // column labels + var colLabels = this.svg.append('g') + .selectAll('.colLabelg') + .data(colLabel) + .enter() + .append('text') + .text(function (d) { + return d; + }) + .attr('x', 0) + .attr('y', function (d, i) { + return colIndex.indexOf(i) * cellSize; + }) + .style('font-size', fontSize + 'px') + .style('text-anchor', 'left') + .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') + .attr('class', function (d, i) { + return 'colLabel mono c' + i; + }) + .on('mouseover', function(d) { + d3.select(this).classed('text-hover',true); + }) + .on('mouseout' , function(d) { + d3.select(this).classed('text-hover',false); + }) + .on('click', function(d, i) { + self.colSortOrder=!self.colSortOrder; + self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder); + d3.select('#order').property('selectedIndex', 4).node().focus(); + }); + + // return + return colLabels; + }, + + // build row labels + _buildRowLabels: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var fontSize = this.fontSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + + // draw labels + var rowLabels = this.svg.append('g') + .selectAll('.rowLabelg') + .data(rowLabel) + .enter() + .append('text') + .text(function (d) { + return d; + }) + .attr('x', 0) + .attr('y', function (d, i) { + return rowIndex.indexOf(i) * cellSize; + }) + .style('font-size', fontSize + 'px') + .style('text-anchor', 'end') + .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') + .attr('class', function (d, i) { + return 'rowLabel mono r' + i; + } ) + .on('mouseover', function(d) { + d3.select(this).classed('text-hover',true); + }) + .on('mouseout' , function(d) { + d3.select(this).classed('text-hover',false); + }) + .on('click', function(d, i) { + self.rowSortOrder=!self.rowSortOrder; + self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder); + d3.select('#order').property('selectedIndex', 4).node().focus(); + }); + + // return + return rowLabels; + }, + + // build heat map + _buildHeatMap: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // heat map + var heatmap = this.svg.append('g').attr('class','g3') + .selectAll('.cellg') + .data(self.data, function(d) { + return d.row + ':' + d.col; + }) + .enter() + .append('rect') + .attr('x', function(d) { + return colIndex.indexOf(d.col) * cellSize; + }) + .attr('y', function(d) { + return rowIndex.indexOf(d.row) * cellSize; + }) + .attr('class', function(d){ + return 'cell cell-border cr' + d.row + ' cc' + d.col; + }) + .attr('width', cellSize) + .attr('height', cellSize) + .style('fill', function(d) { + return self.colorScale(d.value); + }) + .on('mouseover', function(d){ + // highlight text + d3.select(this).classed('cell-hover',true); + d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);}); + d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);}); + + // update the tooltip position and value + d3.select('#heatmap-tooltip') + .style('left', (d3.event.pageX+10) + 'px') + .style('top', (d3.event.pageY-10) + 'px') + .select('#value') + .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value); + // show the tooltip + d3.select('#heatmap-tooltip').classed('hidden', false); + }) + .on('mouseout', function(){ + d3.select(this).classed('cell-hover',false); + d3.selectAll('.rowLabel').classed('text-highlight',false); + d3.selectAll('.colLabel').classed('text-highlight',false); + d3.select('#heatmap-tooltip').classed('hidden', true); + }); + + // return + return heatmap; + }, + + // change ordering of cells + _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) { + // get cell size + var cellSize = this.cellSize; + + // define transition / prepare element + var t = this.svg.transition().duration(this.options.pace); + + // create cells + var cells=[]; + for (var i = 0; i < n; i++) { + cells[i] = { + value: this.min - 1 + } + cells[i][rowORcol] = i; + } + + // collect cells + t.selectAll('.c' + rORc + index).filter(function(ce) { + cells[ce[rowORcol]].value = ce.value; + }); + + // sort cells + cells.sort(function(a, b) { + if (sortOrder) { + return b.value - a.value; + } else { + return a.value - b.value; + } + }); + + // get sorted key list + var sorted = []; + for (var i in cells) { + sorted.push(cells[i][rowORcol]); + } + + // rows or columns + if(rORc == 'r') { + // sort cells + t.selectAll('.cell') + .attr('x', function(d) { + return sorted.indexOf(d.col) * cellSize; + }); + + // sort labels + t.selectAll('.colLabel') + .attr('y', function (d, i) { + return sorted.indexOf(i) * cellSize; + }); + } else { + // sort cells + t.selectAll('.cell') + .attr('y', function(d) { + return sorted.indexOf(d.row) * cellSize; + }); + + // sort labels + t.selectAll('.rowLabel') + .attr('y', function (d, i) { + return sorted.indexOf(i) * cellSize; + }); + } + }, + + // sort function + _sortByOrder: function (value) { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // set duration / select element + var t = this.svg.transition().duration(this.options.pace); + if(value=='hclust'){ + t.selectAll('.cell') + .attr('x', function(d) { + return colIndex.indexOf(d.col) * cellSize; + }) + .attr('y', function(d) { + return rowIndex.indexOf(d.row) * cellSize; + }); + + t.selectAll('.rowLabel') + .attr('y', function(d, i) { + return rowIndex.indexOf(i) * cellSize; + }); + + t.selectAll('.colLabel') + .attr('y', function(d, i) { + return colIndex.indexOf(i) * cellSize; + }); + + } else if (value=='byboth') { + t.selectAll('.cell') + .attr('x', function(d) { + return d.col * cellSize; + }) + .attr('y', function(d) { + return d.row * cellSize; + }); + + t.selectAll('.rowLabel') + .attr('y', function (d, i) { + return i * cellSize; + }); + + t.selectAll('.colLabel') + .attr('y', function (d, i) { + return i * cellSize; + }); + } else if (value=='byrow') { + t.selectAll('.cell') + .attr('y', function(d) { + return d.row * cellSize; + }); + + t.selectAll('.rowLabel') + .attr('y', function (d, i) { + return i * cellSize; + }); + } else if (value=='bycol'){ + t.selectAll('.cell') + .attr('x', function(d) { + return d.col * cellSize; + }); + t.selectAll('.colLabel') + .attr('y', function (d, i) { + return i * cellSize; + }); + } + }, + + // selection of cells + _addSelectionTool: function() { + // + // selection + // + var sa=d3.select('.g3') + .on('mousedown', function() { + if( !d3.event.altKey) { + d3.selectAll('.cell-selected').classed('cell-selected', false); + d3.selectAll('.rowLabel').classed('text-selected', false); + d3.selectAll('.colLabel').classed('text-selected', false); + } + var p = d3.mouse(this); + sa.append('rect') + .attr({ + rx : 0, + ry : 0, + class : 'selection', + x : p[0], + y : p[1], + width : 1, + height : 1 + }) + }) + .on('mousemove', function() { + var s = sa.select('rect.selection'); + + if(!s.empty()) { + var p = d3.mouse(this), + d = { + x : parseInt(s.attr('x'), 10), + y : parseInt(s.attr('y'), 10), + width : parseInt(s.attr('width'), 10), + height : parseInt(s.attr('height'), 10) + }, + move = { + x : p[0] - d.x, + y : p[1] - d.y + }; + + if(move.x < 1 || (move.x*2<d.width)) { + d.x = p[0]; + d.width -= move.x; + } else { + d.width = move.x; + } + + if(move.y < 1 || (move.y*2<d.height)) { + d.y = p[1]; + d.height -= move.y; + } else { + d.height = move.y; + } + s.attr(d); + + // deselect all temporary selected state objects + d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false); + d3.selectAll('.text-selection.text-selected').classed('text-selected',false); + d3.selectAll('.cell').filter(function(cell_d, i) { + if(!d3.select(this).classed('cell-selected') && + // inner circle inside selection frame + (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && + (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) + { + d3.select(this) + .classed('cell-selection', true) + .classed('cell-selected', true); + + d3.select('.r' + cell_d.row) + .classed('text-selection',true) + .classed('text-selected',true); + + d3.select('.c' + cell_d.col) + .classed('text-selection',true) + .classed('text-selected',true); + } + }); + } + }) + .on('mouseup', function() { + // remove selection frame + sa.selectAll('rect.selection').remove(); + + // remove temporary selection marker class + d3.selectAll('.cell-selection').classed('cell-selection', false); + d3.selectAll('.text-selection').classed('text-selection', false); + }) + .on('mouseout', function() { + if(d3.event.relatedTarget.tagName=='html') { + // remove selection frame + sa.selectAll('rect.selection').remove(); + + // remove temporary selection marker class + d3.selectAll('.cell-selection').classed('cell-selection', false); + d3.selectAll('.rowLabel').classed('text-selected',false); + d3.selectAll('.colLabel').classed('text-selected',false); + } + }); + }, + + // template + _templateSelect: function() { + return '<select id="order">' + + '<option value="hclust">Cluster</option>' + + '<option value="byboth">Sort by row and column</option>' + + '<option value="byrow">Sort by row label</option>' + + '<option value="bycol">Sort by column label</option>' + + '</select>'; + }, + + // template + _templateTooltip: function() { + return '<div id="heatmap-tooltip" class="hidden">' + + '<p><span id="value"></p>' + '</div>'; + } +}); +}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/heatmap/logo.png Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js @@ -0,0 +1,86 @@ +// dependencies +define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], +function(Utils, HeatmapPlugin, HeatmapParameters) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // link this + var self = this; + + // loop through data groups + var index = 0; + for (var group_index in request_dictionary.groups) { + + // configure request + var tmp_dict = { + id : request_dictionary.id, + groups : [{ + key : request_dictionary.groups[group_index].key, + columns : { + row_label: { + index : index++, + is_label : true + }, + col_label: { + index : index++, + is_label : true + }, + value: { + index : index++ + } + } + }] + }; + + // target div + var group_div = self.options.canvas[group_index]; + + // draw group + this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) { + if (group_index == request_dictionary.groups.length - 1) { + // set chart state + chart.state('ok', 'Heat map drawn.'); + + // unregister process + chart.deferred.done(process_id); + } + }); + } + }, + + // draw group + _draw_group: function(group_index, div, chart, request_dictionary, callback) { + // link this + var self = this; + + // request data + this.app.datasets.request(request_dictionary, function() { + + // get group + var group = request_dictionary.groups[0]; + + // draw plot + var heatmap = new HeatmapPlugin({ + 'title' : group.key, + 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], + 'data' : group.values, + 'div' : div + }); + + // callback on completion + callback (group_index); + }); + } +}); + +}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js @@ -0,0 +1,40 @@ +define([], function() { + +return { + title : 'Box plot', + category : 'Data processing (requires \'charts\' tool from Toolshed)', + library : 'highcharts.js', + tag : 'div', + execute : 'boxplot', + columns : { + y : { + title : 'Observations' + } + }, + settings : { + separator_label : { + title : 'X axis', + type : 'separator' + }, + x_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'X-axis', + placeholder : 'Axis label' + }, + separator_tick : { + title : 'Y axis', + type : 'separator' + }, + y_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'Y-axis', + placeholder : 'Axis label' + } + } +}; + +}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js @@ -0,0 +1,122 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // highcharts configuration + hc_config : { + chart: { + type: 'boxplot' + }, + + title: { + text: '' + }, + + legend: { + enabled: false + }, + + credits: { + enabled: false + }, + + plotOptions: { + series: { + animation: false + } + }, + + xAxis: { + categories: [], + title: { + text: '' + } + }, + + yAxis: { + title: { + text: '' + } + }, + + series: [{ + name: 'Details:', + data: [], + tooltip: { + headerFormat: '<em>{point.key}</em><br/>' + } + }] + }, + + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // configure request + var index = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = null; + group.columns = { + x: { + index: index++ + } + } + } + + // set axis labels + this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label'); + this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label'); + + // request data + var self = this; + this.app.datasets.request(request_dictionary, function() { + + // reset data/categories + var data = []; + var categories = []; + + // loop through data groups + for (var key in request_dictionary.groups) { + // get group + var group = request_dictionary.groups[key]; + + // add category + categories.push(group.key); + + // format chart data + var point = []; + for (var key in group.values) { + point.push(group.values[key].x); + } + + // add to data + data.push (point); + } + + // categories + self.hc_config.xAxis.categories = categories; + + // update data + self.hc_config.series[0].data = data; + + // draw plot + self.options.canvas[0].highcharts(self.hc_config); + + // set chart state + chart.state('ok', 'Box plot drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + } +}); + +}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/histogram/config.js --- a/config/plugins/visualizations/charts/static/charts/histogram/config.js +++ /dev/null @@ -1,21 +0,0 @@ -define(['plugin/charts/_nvd3/config'], function(nvd3_config) { - -return $.extend(true, {}, nvd3_config, { - title : 'Histogram', - execute : true, - columns : { - y : { - title : 'Observations' - } - }, - settings : { - x_axis_label : { - init : 'Breaks' - }, - y_axis_label : { - init : 'Density' - } - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/histogram/histogram.js --- a/config/plugins/visualizations/charts/static/charts/histogram/histogram.js +++ /dev/null @@ -1,31 +0,0 @@ -// dependencies -define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // configure request - var index = 0; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = { - x: index++, - y: index++ - } - } - - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/horizontal/config.js --- a/config/plugins/visualizations/charts/static/charts/horizontal/config.js +++ /dev/null @@ -1,12 +0,0 @@ -define(['plugin/charts/_nvd3/config'], function(nvd3_config) { - -return $.extend(true, {}, nvd3_config, { - title : 'Bar diagram (horizontal)', - settings : { - x_axis_type : { - init : 'hide' - } - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js --- a/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js +++ /dev/null @@ -1,21 +0,0 @@ -// dependencies -define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/line/config.js --- a/config/plugins/visualizations/charts/static/charts/line/config.js +++ /dev/null @@ -1,7 +0,0 @@ -define(['plugin/charts/_nvd3/config'], function(nvd3_config) { - -return $.extend(true, {}, nvd3_config, { - title : 'Line chart', -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/line/line.js --- a/config/plugins/visualizations/charts/static/charts/line/line.js +++ /dev/null @@ -1,21 +0,0 @@ -// dependencies -define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/linewithfocus/config.js --- a/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js +++ /dev/null @@ -1,7 +0,0 @@ -define(['plugin/charts/_nvd3/config'], function(nvd3_config) { - -return $.extend(true, {}, nvd3_config, { - title : 'Line with focus', -}); - -}); \ No newline at end of file diff -r ca297d98ab45f650b817acc613050530247c429c -r 7e257c7b10badb65772b1528cb61d58175a42e47 config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js --- a/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js +++ /dev/null @@ -1,21 +0,0 @@ -// dependencies -define(['plugin/charts/_nvd3/nvd3'], function(NVD3) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary); - } -}); - -}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/75efcf774765/ Changeset: 75efcf774765 Branch: stable User: natefoo Date: 2014-06-02 22:29:08 Summary: Added tags release_2014.06.02 and latest_2014.06.02 for changeset 7e257c7b10ba Affected #: 1 file diff -r 7e257c7b10badb65772b1528cb61d58175a42e47 -r 75efcf77476543a1f5fae8e4c7ece4b551e2eea9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,3 +8,5 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 +7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 +7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b6e1ffaa053/ Changeset: 8b6e1ffaa053 Branch: next-stable User: dannon Date: 2014-06-02 19:16:15 Summary: Fix for when check_binary fails against an actual binary datatype. The logic in upload needs to be revisited per the comments. Affected #: 1 file diff -r f11149134d6dfafcaf7245f543381e60a937578b -r 8b6e1ffaa053f87c944290f3a84e5f73633cd901 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -241,7 +241,11 @@ dataset.name = uncompressed_name data_type = 'zip' if not data_type: - if check_binary( dataset.path ): + # TODO refactor this logic. check_binary isn't guaranteed to be + # correct since it only looks at whether the first 100 chars are + # printable or not. If someone specifies a known unsniffable + # binary datatype and check_binary fails, the file gets mangled. + if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): # We have a binary dataset, but it is not Bam, Sff or Pdf data_type = 'binary' #binary_ok = False https://bitbucket.org/galaxy/galaxy-central/commits/5273e0bf9ae5/ Changeset: 5273e0bf9ae5 User: dannon Date: 2014-06-02 19:16:51 Summary: merge next-stable Affected #: 1 file diff -r 15d426f19dcccb5ee3c06158898f1102c62d365d -r 5273e0bf9ae54599f1dadbce9d943dcac828d0f0 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -241,7 +241,11 @@ dataset.name = uncompressed_name data_type = 'zip' if not data_type: - if check_binary( dataset.path ): + # TODO refactor this logic. check_binary isn't guaranteed to be + # correct since it only looks at whether the first 100 chars are + # printable or not. If someone specifies a known unsniffable + # binary datatype and check_binary fails, the file gets mangled. + if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): # We have a binary dataset, but it is not Bam, Sff or Pdf data_type = 'binary' #binary_ok = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/15d426f19dcc/ Changeset: 15d426f19dcc User: dan Date: 2014-06-02 18:30:46 Summary: merge next-stable Affected #: 1 file diff -r 3b85bc04f24fd4970bc6376a425decb7daf8c03f -r 15d426f19dcccb5ee3c06158898f1102c62d365d templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -54,7 +54,7 @@ ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )} ## grid container - <div id="grid-container"><div> + <div id="grid-container"></div> ## load javascript <script type="text/javascript"> 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: Close grid-container.
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f11149134d6d/ Changeset: f11149134d6d Branch: next-stable User: dan Date: 2014-06-02 18:30:10 Summary: Close grid-container. Affected #: 1 file diff -r 66c38fea170f5dac9fe8fb8296077e400391b28a -r f11149134d6dfafcaf7245f543381e60a937578b templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -54,7 +54,7 @@ ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )} ## grid container - <div id="grid-container"><div> + <div id="grid-container"></div> ## load javascript <script type="text/javascript"> 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: dannon: Merge.
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b85bc04f24f/ Changeset: 3b85bc04f24f User: dannon Date: 2014-06-02 18:27:01 Summary: Merge. Affected #: 1 file diff -r 8caa7f4d72c7abe021ce5312bda46a3118ff68d8 -r 3b85bc04f24fd4970bc6376a425decb7daf8c03f templates/user/openid_manage.mako --- a/templates/user/openid_manage.mako +++ b/templates/user/openid_manage.mako @@ -4,7 +4,8 @@ <%namespace file="login.mako" import="render_openid_form" /><%def name="load()"> - ${parent.load()} <h2>Associate more OpenIDs</h2> ${render_openid_form( kwargs['redirect'], True, kwargs['openid_providers'] )} -</%def> \ No newline at end of file + <br/><br/> + ${parent.load()} +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix OpenID to work post grid refactoring.
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66c38fea170f/ Changeset: 66c38fea170f Branch: next-stable User: dannon Date: 2014-06-02 18:26:12 Summary: Fix OpenID to work post grid refactoring. Affected #: 1 file diff -r 5db75eaf06614909c09a6bbd70fe6f18007a39a8 -r 66c38fea170f5dac9fe8fb8296077e400391b28a templates/user/openid_manage.mako --- a/templates/user/openid_manage.mako +++ b/templates/user/openid_manage.mako @@ -4,7 +4,8 @@ <%namespace file="login.mako" import="render_openid_form" /><%def name="load()"> - ${parent.load()} <h2>Associate more OpenIDs</h2> ${render_openid_form( kwargs['redirect'], True, kwargs['openid_providers'] )} -</%def> \ No newline at end of file + <br/><br/> + ${parent.load()} +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5db75eaf0661/ Changeset: 5db75eaf0661 Branch: next-stable User: dannon Date: 2014-06-02 17:14:18 Summary: Cleanly terminate the control worker. Resolves a buildbot issue. Affected #: 2 files diff -r aeacb40b527f06eb7dc4138ab871b26a88b8d709 -r 5db75eaf06614909c09a6bbd70fe6f18007a39a8 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -159,6 +159,8 @@ self.heartbeat.shutdown() if self.update_manager: self.update_manager.shutdown() + if self.control_worker: + self.control_worker.shutdown() try: # If the datatypes registry was persisted, attempt to # remove the temporary file in which it was written. diff -r aeacb40b527f06eb7dc4138ab871b26a88b8d709 -r 5db75eaf06614909c09a6bbd70fe6f18007a39a8 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -63,6 +63,9 @@ log.warning("Recieved a malformed task message:\n%s" % body) message.ack() + def shutdown(self): + self.should_stop = True + def send_control_task(trans, task, noop_self=False, kwargs={}): log.info("Sending %s control task." % task) https://bitbucket.org/galaxy/galaxy-central/commits/8caa7f4d72c7/ Changeset: 8caa7f4d72c7 User: dannon Date: 2014-06-02 17:14:30 Summary: Merge next-stable. Affected #: 2 files diff -r db4083ef9b77ee8896a164c0120fc16914c6f8d5 -r 8caa7f4d72c7abe021ce5312bda46a3118ff68d8 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -159,6 +159,8 @@ self.heartbeat.shutdown() if self.update_manager: self.update_manager.shutdown() + if self.control_worker: + self.control_worker.shutdown() try: # If the datatypes registry was persisted, attempt to # remove the temporary file in which it was written. diff -r db4083ef9b77ee8896a164c0120fc16914c6f8d5 -r 8caa7f4d72c7abe021ce5312bda46a3118ff68d8 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -63,6 +63,9 @@ log.warning("Recieved a malformed task message:\n%s" % body) message.ack() + def shutdown(self): + self.should_stop = True + def send_control_task(trans, task, noop_self=False, kwargs={}): log.info("Sending %s control task." % task) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Add ucsc_build_sites.txt.sample to setup_buildbot.sh
by commits-noreply＠bitbucket.org 02 Jun '14

02 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db4083ef9b77/ Changeset: db4083ef9b77 User: davebgx Date: 2014-06-02 16:27:58 Summary: Add ucsc_build_sites.txt.sample to setup_buildbot.sh Affected #: 1 file diff -r 667ba7198f66c0ae9ae0eadbb9ce569a1af05199 -r db4083ef9b77ee8896a164c0120fc16914c6f8d5 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -58,6 +58,7 @@ tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/publicbuilds.txt.sample +tool-data/shared/ucsc/ucsc_build_sites.txt.sample " DIRS=" 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 02 Jun '14

02 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3502f3a5dec/ Changeset: e3502f3a5dec User: jmchilton Date: 2014-06-02 07:13:55 Summary: Restore ability to disable LWR-MQ consumer timeout. Mis-translated this parameter when converting it to use runner spec. Affected #: 2 files diff -r cf31fae45bf3a2d3244744d86edabad0c1465729 -r e3502f3a5dec0e5cb11a60bd6473618d23f98b64 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -58,7 +58,7 @@ default=None, ), amqp_consumer_timeout=dict( - map=specs.to_float_or_none, + map=lambda val: None if val == "None" else float(val), default=None, ), amqp_connect_ssl_ca_certs=dict( diff -r cf31fae45bf3a2d3244744d86edabad0c1465729 -r e3502f3a5dec0e5cb11a60bd6473618d23f98b64 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 @@ -84,8 +84,8 @@ connect_ssl=self.connect_ssl, publish_kwds=parse_amqp_publish_kwds(kwds) ) - timeout = kwds.get('amqp_consumer_timeout', None) - if timeout is not None: + timeout = kwds.get('amqp_consumer_timeout', False) + if timeout is not False: exchange_kwds['timeout'] = timeout self.exchange = LwrExchange(self.url, **exchange_kwds) self.status_cache = {} https://bitbucket.org/galaxy/galaxy-central/commits/667ba7198f66/ Changeset: 667ba7198f66 User: jmchilton Date: 2014-06-02 07:13:55 Summary: Move logic for creating LwrExchange out of MessageQueueClientManager... So can reuse server side when connecting server components to AMQP. Affected #: 3 files diff -r e3502f3a5dec0e5cb11a60bd6473618d23f98b64 -r 667ba7198f66c0ae9ae0eadbb9ce569a1af05199 lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py @@ -0,0 +1,32 @@ +from .amqp_exchange import LwrExchange +from .util import filter_destination_params + + +def get_exchange(url, manager_name, params): + connect_ssl = parse_amqp_connect_ssl_params(params) + exchange_kwds = dict( + manager_name=manager_name, + connect_ssl=connect_ssl, + publish_kwds=parse_amqp_publish_kwds(params) + ) + timeout = params.get('amqp_consumer_timeout', False) + if timeout is not False: + exchange_kwds['timeout'] = timeout + exchange = LwrExchange(url, **exchange_kwds) + return exchange + + +def parse_amqp_connect_ssl_params(params): + ssl_params = filter_destination_params(params, "amqp_connect_ssl_") + if not ssl_params: + return + + ssl = __import__('ssl') + if 'cert_reqs' in ssl_params: + value = ssl_params['cert_reqs'] + ssl_params['cert_reqs'] = getattr(ssl, value.upper()) + return ssl_params + + +def parse_amqp_publish_kwds(params): + return filter_destination_params(params, "amqp_publish_") diff -r e3502f3a5dec0e5cb11a60bd6473618d23f98b64 -r 667ba7198f66c0ae9ae0eadbb9ce569a1af05199 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 @@ -13,10 +13,8 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager -from .util import parse_amqp_connect_ssl_params -from .util import parse_amqp_publish_kwds from .destination import url_to_destination_params -from .amqp_exchange import LwrExchange +from .amqp_exchange_factory import get_exchange from logging import getLogger @@ -78,16 +76,7 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", None) or "_default_" - self.connect_ssl = parse_amqp_connect_ssl_params(kwds) - exchange_kwds = dict( - manager_name=self.manager_name, - connect_ssl=self.connect_ssl, - publish_kwds=parse_amqp_publish_kwds(kwds) - ) - timeout = kwds.get('amqp_consumer_timeout', False) - if timeout is not False: - exchange_kwds['timeout'] = timeout - self.exchange = LwrExchange(self.url, **exchange_kwds) + self.exchange = get_exchange(self.url, self.manager_name, kwds) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r e3502f3a5dec0e5cb11a60bd6473618d23f98b64 -r 667ba7198f66c0ae9ae0eadbb9ce569a1af05199 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 @@ -63,22 +63,6 @@ return contents -def parse_amqp_connect_ssl_params(params): - ssl_params = filter_destination_params(params, "amqp_connect_ssl_") - if not ssl_params: - return - - ssl = __import__('ssl') - if 'cert_reqs' in ssl_params: - value = ssl_params['cert_reqs'] - ssl_params['cert_reqs'] = getattr(ssl, value.upper()) - return ssl_params - - -def parse_amqp_publish_kwds(params): - return filter_destination_params(params, "amqp_publish_") - - def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} return dict([(key[len(prefix):], destination_params[key]) 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 02 Jun '14

02 Jun '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/927ebdb27fd1/ Changeset: 927ebdb27fd1 User: jmchilton Date: 2014-06-02 05:34:39 Summary: Build on 1ed8dd5 for even simpler LWR param handling. Affected #: 2 files diff -r 1ed8dd5753212286c1abd168c55708b26da5edbf -r 927ebdb27fd197edb8578bf70d7e5ec049f7abfd lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -89,26 +89,25 @@ def __init__( self, app, nworkers, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers, runner_param_specs=LWR_PARAM_SPECS, **kwds ) - transport = self.runner_params.transport - cache = self.runner_params.cache - url = self.runner_params.url self._init_worker_threads() - client_manager_kwargs = { - 'transport_type': transport, - 'cache': string_as_bool_or_none(cache), - "url": url, - 'manager': kwds.get("manager", None), - } - for kwd in self.runner_params.keys(): - if kwd.startswith('amqp_'): - client_manager_kwargs[kwd] = self.runner_params[kwd] self.galaxy_url = self.runner_params.galaxy_url - self.client_manager = build_client_manager(**client_manager_kwargs) - if url: + self.__init_client_manager() + if self.runner_params.url: + # This is a message queue driven runner, don't monitor + # just setup required callback. self.client_manager.ensure_has_status_update_callback(self.__async_update) else: self._init_monitor_thread() + def __init_client_manager( self ): + client_manager_kwargs = {} + for kwd in 'url', 'manager', 'cache', 'transport': + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + for kwd in self.runner_params.keys(): + if kwd.startswith( 'amqp_' ): + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + self.client_manager = build_client_manager(**client_manager_kwargs) + def url_to_destination( self, url ): """Convert a legacy URL to a job destination""" return JobDestination( runner="lwr", params=url_to_destination_params( url ) ) diff -r 1ed8dd5753212286c1abd168c55708b26da5edbf -r 927ebdb27fd197edb8578bf70d7e5ec049f7abfd 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 @@ -44,7 +44,7 @@ self.job_manager_interface_args = dict(job_manager=kwds['job_manager'], file_cache=kwds['file_cache']) else: self.job_manager_interface_class = HttpLwrInterface - transport_type = kwds.get('transport_type', None) + transport_type = kwds.get('transport', None) transport = get_transport(transport_type) self.job_manager_interface_args = dict(transport=transport) cache = kwds.get('cache', None) @@ -138,7 +138,7 @@ self.interface_args = dict(object_store=kwds['object_store']) else: self.interface_class = HttpLwrInterface - transport_type = kwds.get('transport_type', None) + transport_type = kwds.get('transport', None) transport = get_transport(transport_type) self.interface_args = dict(transport=transport) self.extra_client_kwds = {} https://bitbucket.org/galaxy/galaxy-central/commits/8003903b1f06/ Changeset: 8003903b1f06 User: jmchilton Date: 2014-06-02 05:34:39 Summary: Small tweaks to LWR configuring to reduce code duplication. Refactor amqp_exchange to move logic for SSL into shared spot and rework SSL parsing to reuse similar logic used to parse destination parameters. Affected #: 2 files diff -r 927ebdb27fd197edb8578bf70d7e5ec049f7abfd -r 8003903b1f062ada839e8898b9c04d62488f100b 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 @@ -33,7 +33,13 @@ name _default_. """ - def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): + def __init__( + self, + url, + manager_name, + connect_ssl=None, + timeout=DEFAULT_TIMEOUT, + ): """ """ if not kombu: @@ -54,9 +60,8 @@ while check: heartbeat_thread = None try: - # TODO: configurable heartbeat - with self.connection(self.__url, ssl=self.__connect_ssl, heartbeat=DEFAULT_HEARTBEAT, **connection_kwargs) as connection: - with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']) as consumer: + with self.connection(self.__url, heartbeat=DEFAULT_HEARTBEAT, **connection_kwargs) as connection: + with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): heartbeat_thread = self.__start_heartbeat(queue_name, connection) while check and connection.connected: try: @@ -76,7 +81,7 @@ log.debug('AMQP heartbeat thread exiting') def publish(self, name, payload): - with self.connection(self.__url, ssl=self.__connect_ssl) as connection: + with self.connection(self.__url) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( @@ -88,6 +93,8 @@ ) def connection(self, connection_string, **kwargs): + if "ssl" not in kwargs: + kwargs["ssl"] = self.__connect_ssl return kombu.Connection(connection_string, **kwargs) def __queue(self, name): diff -r 927ebdb27fd197edb8578bf70d7e5ec049f7abfd -r 8003903b1f062ada839e8898b9c04d62488f100b 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 @@ -64,21 +64,15 @@ def parse_amqp_connect_ssl_params(params): - ssl = None - rval = None - ssl_options = [] - if params: - ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) - if ssl_options: - ssl = __import__('ssl') - rval = {} - for option in ssl_options: - value = params.get(option) - option = option.replace('amqp_connect_ssl_', '', 1) - if option == 'cert_reqs': - value = getattr(ssl, value.upper()) - rval[option] = value - return rval + ssl_params = filter_destination_params(params, "amqp_connect_ssl_") + if not ssl_params: + return + + ssl = __import__('ssl') + if 'cert_reqs' in ssl_params: + value = ssl_params['cert_reqs'] + ssl_params['cert_reqs'] = getattr(ssl, value.upper()) + return ssl_params def filter_destination_params(destination_params, prefix): https://bitbucket.org/galaxy/galaxy-central/commits/cf31fae45bf3/ Changeset: cf31fae45bf3 User: jmchilton Date: 2014-06-02 05:34:39 Summary: Allow configuration of more AMQP parameters. In particular ampq_publish_retry can now be set to True to retry disconnected connections on publication. Hopefully, this will fix producer-related disconnect problems seen in production. Affected #: 4 files diff -r 8003903b1f062ada839e8898b9c04d62488f100b -r cf31fae45bf3a2d3244744d86edabad0c1465729 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -77,6 +77,22 @@ map=specs.to_str_or_none, default=None, ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Producer.… + amqp_publish_retry=dict( + map=specs.to_bool, + default=False, + ), + amqp_publish_priority=dict( + map=int, + valid=lambda x: 0 <= x and x <= 9, + default=0, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Exchange.… + amqp_publish_delivery_mode=dict( + map=str, + valid=specs.is_in("transient", "persistent"), + default="persistent", + ) ) diff -r 8003903b1f062ada839e8898b9c04d62488f100b -r cf31fae45bf3a2d3244744d86edabad0c1465729 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 @@ -39,6 +39,7 @@ manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT, + publish_kwds={}, ): """ """ @@ -49,6 +50,7 @@ self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout + self.__publish_kwds = publish_kwds @property def url(self): @@ -90,6 +92,7 @@ exchange=self.__exchange, declare=[self.__exchange], routing_key=key, + **self.__publish_kwds ) def connection(self, connection_string, **kwargs): diff -r 8003903b1f062ada839e8898b9c04d62488f100b -r cf31fae45bf3a2d3244744d86edabad0c1465729 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 @@ -14,6 +14,7 @@ from .transport import get_transport from .util import TransferEventManager from .util import parse_amqp_connect_ssl_params +from .util import parse_amqp_publish_kwds from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -81,6 +82,7 @@ exchange_kwds = dict( manager_name=self.manager_name, connect_ssl=self.connect_ssl, + publish_kwds=parse_amqp_publish_kwds(kwds) ) timeout = kwds.get('amqp_consumer_timeout', None) if timeout is not None: diff -r 8003903b1f062ada839e8898b9c04d62488f100b -r cf31fae45bf3a2d3244744d86edabad0c1465729 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 @@ -75,6 +75,10 @@ return ssl_params +def parse_amqp_publish_kwds(params): + return filter_destination_params(params, "amqp_publish_") + + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} return dict([(key[len(prefix):], destination_params[key]) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits June 2014