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18 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fc2eb78580b9/
Changeset: fc2eb78580b9
User: guerler
Date: 2014-06-18 12:53:16
Summary: Charts: Pad y axis
Affected #: 1 file
diff -r 9896943ec1d8ef895b973d496ff6e124bbd46f06 -r fc2eb78580b90809ead1ecde5efa68899205b359 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
@@ -25,6 +25,9 @@
axes: {
xaxis: {
min : -1
+ },
+ yaxis: {
+ pad : 1.2
}
}
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1
0
commit/galaxy-central: guerler: Charts: Fix formatting option
by commits-noreply＠bitbucket.org 18 Jun '14
by commits-noreply＠bitbucket.org 18 Jun '14
18 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9896943ec1d8/
Changeset: 9896943ec1d8
User: guerler
Date: 2014-06-18 12:50:49
Summary: Charts: Fix formatting option
Affected #: 2 files
diff -r 385c4b53694eb1838c0f2487b38b4e798b16c522 -r 9896943ec1d8ef895b973d496ff6e124bbd46f06 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
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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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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(){for(var e in this.queue)if(this.counter==0){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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.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_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,o=$("<svg/>");o.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var u="",a=0;t.find("svg").each(function(){var e=$(this),t=$('<g transform="translate('+a+', 0)">');t.append(e.clone().find("g").first()),o.append(t),a+=i});var u=s.serializeToString(o[0]);window.location.href="data:none/none;base64,"+btoa(u)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}return{createPNG:t,createSVG:s}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG or SVG file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file-o",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,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=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),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)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+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,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),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.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$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.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<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.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{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 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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'+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),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=t.definition;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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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(){for(var e in this.queue)if(this.counter==0){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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));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,100),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(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.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_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,o=$("<svg/>");o.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var u="",a=0;t.find("svg").each(function(){var e=$(this),t=$('<g transform="translate('+a+', 0)">');t.append(e.clone().find("g").first()),o.append(t),a+=i});var u=s.serializeToString(o[0]);window.location.href="data:none/none;base64,"+btoa(u)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}return{createPNG:t,createSVG:s}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG or SVG file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file-o",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(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)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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.del(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="ui-table '+e.cls+'">'+"<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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_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({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div 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t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{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 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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h=D.yScale().invert(i.mouseY),p=Math.abs(D.yScale().domain()[0]-D.yScale().domain()[1]),d=.03*p,m=e.nearestValueIndex(c.map(function(e){return e.value}),h,d);m!==null&&(c[m].highlight=!0)}var g=n.tickFormat()(D.x()(s,f),f);o.tooltip.position({left:l+u.left,top:i.mouseY+u.top}).chartContainer(A.parentNode).enabled(v).valueFormatter(function(e,t){return r.tickFormat()(e)}).data({value:g,series:c})(),o.renderGuideLine(l)}),o.dispatch.on("elementMouseout",function(e){k.tooltipHide(),t.clearHighlights()}),k.on("tooltipShow",function(e){v&&_(e,A.parentNode)}),k.on("changeState",function(e){typeof e.disabled!="undefined"&&(b.forEach(function(t,n){t.disabled=e.disabled[n]}),x.disabled=e.disabled),typeof e.index!="undefined"&&(M.i=e.index,M.x=O(M.i),x.index=e.index,tt.data([M])),typeof e.rescaleY!="undefined"&&(y=e.rescaleY),D.update()})}),D}function P(e,n){return n.map(function(n,r){if(!n.values)return n;var i=n.values[e];if(i==null)return n;var s=t.y()(i,e);return 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return arguments.length?(l=e,C):l},C.showLegend=function(e){return arguments.length?(c=e,C):c},C.showXAxis=function(e){return arguments.length?(h=e,C):h},C.showYAxis=function(e){return arguments.length?(p=e,C):p},C.tooltip=function(e){return arguments.length?(m=e,C):m},C.tooltips=function(e){return arguments.length?(v=e,C):v},C.tooltipContent=function(e){return arguments.length?(m=e,C):m},C.state=function(e){return arguments.length?(b=e,C):b},C.defaultState=function(e){return arguments.length?(w=e,C):w},C.noData=function(e){return arguments.length?(E=e,C):E},C.transitionDuration=function(e){return arguments.length?(T=e,C):T},C},e.models.multiChart=function(){function C(e){return e.each(function(e){var u=d3.select(this),f=this;C.update=function(){u.call(C)},C.container=this;var 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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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:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{init:"true",hide:!0}}})}),define("plugin/charts/nvd3/stackedarea_full/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea_stream/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts",zoomable:!0,keywords:"default small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/histogram_discrete/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",query_limit:1e4,settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:2e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{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:"Wysiwyg",value:"wysiwyg"}]}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),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/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{jqplot_bar:p,nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f,jqplot_line:d,jqplot_scatter:v,jqplot_boxplot:m,others_heatmap:g,others_heatmap_cluster:y}})}),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()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 385c4b53694eb1838c0f2487b38b4e798b16c522 -r 9896943ec1d8ef895b973d496ff6e124bbd46f06 config/plugins/visualizations/charts/static/charts/forms/default.js
--- a/config/plugins/visualizations/charts/static/charts/forms/default.js
+++ b/config/plugins/visualizations/charts/static/charts/forms/default.js
@@ -80,7 +80,7 @@
title : 'Axis tick format',
info : 'Select the tick format for the axis.',
type : 'select',
- init : '.1',
+ init : '1',
data : [
{
label : '0.00001',
@@ -181,7 +181,7 @@
title : 'Axis tick format',
info : 'Select the tick format for the axis.',
type : 'select',
- init : '.1',
+ init : '1',
data : [
{
label : '0.00001',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts: Fix jqplot bar axis
by commits-noreply＠bitbucket.org 18 Jun '14
by commits-noreply＠bitbucket.org 18 Jun '14
18 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/385c4b53694e/
Changeset: 385c4b53694e
User: guerler
Date: 2014-06-18 12:42:11
Summary: Charts: Fix jqplot bar axis
Affected #: 4 files
diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
@@ -20,7 +20,12 @@
makeConfig : function(groups, plot_config){
$.extend(true, plot_config, {
seriesDefaults: {
- renderer : $.jqplot.BarRenderer
+ renderer : $.jqplot.BarRenderer
+ },
+ axes: {
+ xaxis: {
+ min : -1
+ }
}
});
}
diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
@@ -16,8 +16,8 @@
showLine : true, // whether to render the line segments or not.
rendererOptions: {
shadowDepth : 0,
- //barDirection : 'horizontal',
- barWidth : 1
+ barWidth : 3,
+ barPadding : 3
},
markerRenderer : $.jqplot.MarkerRenderer,
markerOptions: {
@@ -56,7 +56,6 @@
angle : chart.settings.get('use_panels') === 'true' ? 0 : -30,
showGridline : chart.settings.get('x_axis_grid') === 'true'
},
- tickInterval : 1,
pad : 0
},
yaxis: {
diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
@@ -134,7 +134,7 @@
formatter : function(formatter) {
if (formatter) {
plot_config.axes[id + 'axis'].tickOptions.formatter = function(format, value) {
- return formatter(value);
+ return formatter(value);
};
}
}
diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 config/plugins/visualizations/charts/static/charts/tools.js
--- a/config/plugins/visualizations/charts/static/charts/tools.js
+++ b/config/plugins/visualizations/charts/static/charts/tools.js
@@ -361,6 +361,9 @@
// add handler
svg.call(d3zoom).on('dblclick.zoom', unzoomed);
+
+ // return
+ return d3zoom;
};
// return
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Fix typo in b267ce103960.
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/45963b149ddb/
Changeset: 45963b149ddb
User: jmchilton
Date: 2014-06-18 00:22:55
Summary: Fix typo in b267ce103960.
Affected #: 1 file
diff -r b267ce1039608f0c8fbbd42f148a372871668c22 -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
--- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
+++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
@@ -6,7 +6,7 @@
GALAXY_SLOTS="$SLURM_NTASKS"
elif [ -n "$NSLOTS" ]; then
GALAXY_SLOTS="$NSLOTS"
-elif [ -n "$PBS_NCPUS" ] then
+elif [ -n "$PBS_NCPUS" ]; then
GALAXY_SLOTS="$PBS_NCPUS"
elif [ -f "$PBS_NODEFILE" ]; then
GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots.
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b267ce103960/
Changeset: b267ce103960
User: jmchilton
Date: 2014-06-17 22:10:58
Summary: Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots.
Affected #: 1 file
diff -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 -r b267ce1039608f0c8fbbd42f148a372871668c22 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
--- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
+++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
@@ -6,6 +6,8 @@
GALAXY_SLOTS="$SLURM_NTASKS"
elif [ -n "$NSLOTS" ]; then
GALAXY_SLOTS="$NSLOTS"
+elif [ -n "$PBS_NCPUS" ] then
+ GALAXY_SLOTS="$PBS_NCPUS"
elif [ -f "$PBS_NODEFILE" ]; then
GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
elif [ -n "$LSB_DJOB_NUMPROC" ]; then
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Eliminate the use of the repository_util.py module for Galaxy installs from the Tool Shed.
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6294a65d863a/
Changeset: 6294a65d863a
User: greg
Date: 2014-06-17 20:38:02
Summary: Eliminate the use of the repository_util.py module for Galaxy installs from the Tool Shed.
Affected #: 16 files
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -19,6 +19,7 @@
from galaxy.jobs import metrics as job_metrics
from galaxy.web.base import pluginframework
from galaxy.queue_worker import GalaxyQueueWorker
+from tool_shed.galaxy_install import update_repository_manager
import logging
log = logging.getLogger( __name__ )
@@ -80,12 +81,8 @@
# Load Data Manager
self.data_managers = DataManagers( self )
- # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories.
- if self.config.get_bool( 'enable_tool_shed_check', False ):
- from tool_shed.galaxy_install import update_repository_manager
- self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self )
- else:
- self.update_repository_manager = None
+ # Load the update repository manager.
+ self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self )
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
@@ -159,8 +156,7 @@
self.object_store.shutdown()
if self.heartbeat:
self.heartbeat.shutdown()
- if self.update_repository_manager is not None:
- self.update_repository_manager.shutdown()
+ self.update_repository_manager.shutdown()
if self.control_worker:
self.control_worker.shutdown()
try:
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -105,7 +105,6 @@
self.shed_tool_data_path = self.tool_data_path
self.tool_data_table_config_path = [ resolve_path( x, self.root ) for x in kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ).split( ',' ) ]
self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
- self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) )
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
self.hours_between_check = kwargs.get( 'hours_between_check', 12 )
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -24,11 +24,11 @@
from tool_shed.util import metadata_util
from tool_shed.util import readme_util
from tool_shed.util import repository_dependency_util
+from tool_shed.util import repository_maintenance_util
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
from tool_shed.util import workflow_util
from tool_shed.util import xml_util
-from tool_shed.galaxy_install import repository_util
from tool_shed.galaxy_install import install_manager
from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids
@@ -114,7 +114,8 @@
# repository dependencies and tool dependencies will be current. Only allow selecting a different section
# in the tool panel if the repository was uninstalled and it contained tools that should be displayed in
# the tool panel.
- changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( trans.app, repository )
+ changeset_revision_dict = \
+ trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev( repository )
current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None )
current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None )
if current_changeset_revision and current_ctx_rev:
@@ -588,11 +589,10 @@
updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
else:
updated_metadata = None
- repository = repository_util.update_repository_record( trans.app,
- repository=repository,
- updated_metadata_dict=updated_metadata,
- updated_changeset_revision=updating_to_changeset_revision,
- updated_ctx_rev=updating_to_ctx_rev )
+ repository = trans.app.update_repository_manager.update_repository_record( repository=repository,
+ updated_metadata_dict=updated_metadata,
+ updated_changeset_revision=updating_to_changeset_revision,
+ updated_ctx_rev=updating_to_ctx_rev )
if install_tool_dependencies:
tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
repository,
@@ -657,7 +657,7 @@
def manage_repositories( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- tsridslist = repository_util.get_tool_shed_repository_ids( **kwd )
+ tsridslist = common_util.get_tool_shed_repository_ids( **kwd )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if not tsridslist:
@@ -941,7 +941,7 @@
@web.expose
@web.require_admin
def monitor_repository_installation( self, trans, **kwd ):
- tsridslist = repository_util.get_tool_shed_repository_ids( **kwd )
+ tsridslist = common_util.get_tool_shed_repository_ids( **kwd )
if not tsridslist:
tsridslist = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=False )
kwd[ 'tool_shed_repository_ids' ] = tsridslist
@@ -1062,11 +1062,10 @@
decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
# Now that the user has decided whether they will handle dependencies, we can update
# the repository to the latest revision.
- repository = repository_util.update_repository_record( trans.app,
- repository=repository,
- updated_metadata_dict=decoded_updated_metadata,
- updated_changeset_revision=updating_to_changeset_revision,
- updated_ctx_rev=updating_to_ctx_rev )
+ repository = trans.app.update_repository_manager.update_repository_record( repository=repository,
+ updated_metadata_dict=decoded_updated_metadata,
+ updated_changeset_revision=updating_to_changeset_revision,
+ updated_ctx_rev=updating_to_ctx_rev )
install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
if includes_tool_dependencies:
install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
@@ -1081,7 +1080,7 @@
tool_path=tool_path,
tool_shed_url=tool_shed_url )
created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
- repository_util.handle_tool_shed_repositories( trans.app, installation_dict, using_api=False )
+ irm.handle_tool_shed_repositories( installation_dict, using_api=False )
if created_or_updated_tool_shed_repositories:
installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
filtered_repo_info_dicts=filtered_repo_info_dicts,
@@ -1367,16 +1366,17 @@
tool_dependencies = metadata.get( 'tool_dependencies', None )
else:
tool_dependencies = None
- repo_info_dict = repository_util.create_repo_info_dict( app=trans.app,
- repository_clone_url=repository_clone_url,
- changeset_revision=tool_shed_repository.changeset_revision,
- ctx_rev=ctx_rev,
- repository_owner=tool_shed_repository.owner,
- repository_name=tool_shed_repository.name,
- repository=None,
- repository_metadata=None,
- tool_dependencies=tool_dependencies,
- repository_dependencies=repository_dependencies )
+ repo_info_dict = \
+ repository_maintenance_util.create_repo_info_dict( app=trans.app,
+ repository_clone_url=repository_clone_url,
+ changeset_revision=tool_shed_repository.changeset_revision,
+ ctx_rev=ctx_rev,
+ repository_owner=tool_shed_repository.owner,
+ repository_name=tool_shed_repository.name,
+ repository=None,
+ repository_metadata=None,
+ tool_dependencies=tool_dependencies,
+ repository_dependencies=repository_dependencies )
if repo_info_dict not in repo_info_dicts:
repo_info_dicts.append( repo_info_dict )
# Make sure all tool_shed_repository records exist.
@@ -1581,16 +1581,17 @@
repository_dependencies = \
repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans.app,
tool_shed_repository )
- repo_info_dict = repository_util.create_repo_info_dict( app=trans.app,
- repository_clone_url=repository_clone_url,
- changeset_revision=tool_shed_repository.installed_changeset_revision,
- ctx_rev=tool_shed_repository.ctx_rev,
- repository_owner=tool_shed_repository.owner,
- repository_name=tool_shed_repository.name,
- repository=None,
- repository_metadata=None,
- tool_dependencies=tool_dependencies,
- repository_dependencies=repository_dependencies )
+ repo_info_dict = \
+ repository_maintenance_util.create_repo_info_dict( app=trans.app,
+ repository_clone_url=repository_clone_url,
+ changeset_revision=tool_shed_repository.installed_changeset_revision,
+ ctx_rev=tool_shed_repository.ctx_rev,
+ repository_owner=tool_shed_repository.owner,
+ repository_name=tool_shed_repository.name,
+ repository=None,
+ repository_metadata=None,
+ tool_dependencies=tool_dependencies,
+ repository_dependencies=repository_dependencies )
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
@@ -2024,11 +2025,10 @@
return self.install_tool_dependencies_with_update( trans, **new_kwd )
# Updates received did not include any newly defined repository dependencies or newly defined
# tool dependencies that need to be installed.
- repository = repository_util.update_repository_record( trans.app,
- repository=repository,
- updated_metadata_dict=metadata_dict,
- updated_changeset_revision=latest_changeset_revision,
- updated_ctx_rev=latest_ctx_rev )
+ repository = trans.app.update_repository_manager.update_repository_record( repository=repository,
+ updated_metadata_dict=metadata_dict,
+ updated_changeset_revision=latest_changeset_revision,
+ updated_ctx_rev=latest_ctx_rev )
message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \
( name, latest_changeset_revision )
else:
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -1,3 +1,4 @@
+import json
import logging
import os
import tarfile
@@ -6,13 +7,11 @@
from galaxy import eggs
from galaxy import util
from galaxy import web
-from galaxy.util import json
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import HTTPBadRequest
from galaxy.web.framework.helpers import time_ago
import tool_shed.repository_types.util as rt_util
import tool_shed.util.shed_util_common as suc
-from tool_shed.galaxy_install import repository_util
from tool_shed.util import basic_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
@@ -192,7 +191,10 @@
includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, \
has_repository_dependencies_only_if_compiling_contained_td = \
- repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision )
+ repository_maintenance_util.get_repo_info_dict( trans.app,
+ trans.user,
+ encoded_repository_id,
+ changeset_revision )
return repository_dict, repository_metadata_dict, repo_info_dict
else:
log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \
@@ -465,7 +467,7 @@
results = handle_repository( trans, repository, results )
stop_time = strftime( "%Y-%m-%d %H:%M:%S" )
results[ 'stop_time' ] = stop_time
- return json.to_json_string( results, sort_keys=True, indent=4 )
+ return json.dumps( results, sort_keys=True, indent=4 )
@web.expose_api
def reset_metadata_on_repository( self, trans, payload, **kwd ):
@@ -504,7 +506,7 @@
results = handle_repository( trans, start_time, repository )
stop_time = strftime( "%Y-%m-%d %H:%M:%S" )
results[ 'stop_time' ] = stop_time
- return json.to_json_string( results, sort_keys=True, indent=4 )
+ return json.dumps( results, sort_keys=True, indent=4 )
@web.expose_api_anonymous
def show( self, trans, id, **kwd ):
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -31,7 +31,7 @@
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
from tool_shed.util import workflow_util
-from tool_shed.galaxy_install import repository_util
+from tool_shed.galaxy_install import install_manager
from galaxy.webapps.tool_shed.util import ratings_util
import galaxy.tools
import tool_shed.grids.repository_grids as repository_grids
@@ -1761,7 +1761,7 @@
repository_id, changeset_revision = tup
repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \
cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \
- repository_util.get_repo_info_dict( trans, repository_id, changeset_revision )
+ repository_maintenance_util.get_repo_info_dict( trans.app, trans.user, repository_id, changeset_revision )
if cur_has_repository_dependencies and not has_repository_dependencies:
has_repository_dependencies = True
if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td:
@@ -1881,7 +1881,7 @@
"""
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_id = trans.security.encode_id( repository.id )
- repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if not repository_metadata:
@@ -1892,16 +1892,16 @@
after_changeset_revision=changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
- repo_info_dict = repository_util.create_repo_info_dict( app=trans.app,
- repository_clone_url=repository_clone_url,
- changeset_revision=changeset_revision,
- ctx_rev=str( ctx.rev() ),
- repository_owner=repository.user.username,
- repository_name=repository.name,
- repository=repository,
- repository_metadata=repository_metadata,
- tool_dependencies=None,
- repository_dependencies=None )
+ repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=trans.app,
+ repository_clone_url=repository_clone_url,
+ changeset_revision=changeset_revision,
+ ctx_rev=str( ctx.rev() ),
+ repository_owner=repository.user.username,
+ repository_name=repository.name,
+ repository=repository,
+ repository_metadata=repository_metadata,
+ tool_dependencies=None,
+ repository_dependencies=None )
includes_data_managers = False
includes_datatypes = False
includes_tools = False
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -20,14 +20,17 @@
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import container_util
+from tool_shed.util import data_manager_util
+from tool_shed.util import datatype_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
+from tool_shed.util import metadata_util
+from tool_shed.util import repository_dependency_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
from tool_shed.util import xml_util
-from tool_shed.galaxy_install import repository_util
from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment
from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager
@@ -488,6 +491,136 @@
repo_info_dicts = [ repo_info_dict ]
return repository_revision_dict, repo_info_dicts
+ def handle_repository_contents( self, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir,
+ tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False ):
+ """
+ Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy
+ (never the tool shed) when an administrator is installing a new repository or reinstalling an uninstalled repository.
+ """
+ install_model = self.app.install_model
+ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf )
+ metadata_dict, invalid_file_tups = \
+ metadata_util.generate_metadata_for_changeset_revision( app=self.app,
+ repository=tool_shed_repository,
+ changeset_revision=tool_shed_repository.changeset_revision,
+ repository_clone_url=repository_clone_url,
+ shed_config_dict=shed_config_dict,
+ relative_install_dir=relative_install_dir,
+ repository_files_dir=None,
+ resetting_all_metadata_on_repository=False,
+ updating_installed_repository=False,
+ persist=True )
+ tool_shed_repository.metadata = metadata_dict
+ # Update the tool_shed_repository.tool_shed_status column in the database.
+ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository )
+ if tool_shed_status_dict:
+ tool_shed_repository.tool_shed_status = tool_shed_status_dict
+ install_model.context.add( tool_shed_repository )
+ install_model.context.flush()
+ if 'tool_dependencies' in metadata_dict and not reinstalling:
+ tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app,
+ tool_shed_repository,
+ relative_install_dir,
+ set_status=True )
+ if 'sample_files' in metadata_dict:
+ sample_files = metadata_dict.get( 'sample_files', [] )
+ tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
+ tool_data_table_conf_filename, tool_data_table_elems = \
+ tool_util.install_tool_data_tables( self.app, tool_shed_repository, tool_index_sample_files )
+ if tool_data_table_elems:
+ self.app.tool_data_tables.add_new_entries_from_config_file( tool_data_table_conf_filename,
+ None,
+ self.app.config.shed_tool_data_table_config,
+ persist=True )
+ if 'tools' in metadata_dict:
+ tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section )
+ sample_files = metadata_dict.get( 'sample_files', [] )
+ tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
+ tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path )
+ sample_files_copied = [ str( s ) for s in tool_index_sample_files ]
+ repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict )
+ if repository_tools_tups:
+ # Handle missing data table entries for tool parameters that are dynamically generated select lists.
+ repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app,
+ relative_install_dir,
+ tool_path,
+ repository_tools_tups )
+ # Handle missing index files for tool parameters that are dynamically generated select lists.
+ repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app,
+ tool_path,
+ sample_files,
+ repository_tools_tups,
+ sample_files_copied )
+ # Copy remaining sample files included in the repository to the ~/tool-data directory of the
+ # local Galaxy instance.
+ tool_util.copy_sample_files( self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied )
+ tool_util.add_to_tool_panel( app=self.app,
+ repository_name=tool_shed_repository.name,
+ repository_clone_url=repository_clone_url,
+ changeset_revision=tool_shed_repository.installed_changeset_revision,
+ repository_tools_tups=repository_tools_tups,
+ owner=tool_shed_repository.owner,
+ shed_tool_conf=shed_tool_conf,
+ tool_panel_dict=tool_panel_dict,
+ new_install=True )
+ if 'data_manager' in metadata_dict:
+ new_data_managers = data_manager_util.install_data_managers( self.app,
+ self.app.config.shed_data_manager_config_file,
+ metadata_dict,
+ shed_config_dict,
+ relative_install_dir,
+ tool_shed_repository,
+ repository_tools_tups )
+ if 'datatypes' in metadata_dict:
+ tool_shed_repository.status = install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
+ if not tool_shed_repository.includes_datatypes:
+ tool_shed_repository.includes_datatypes = True
+ install_model.context.add( tool_shed_repository )
+ install_model.context.flush()
+ files_dir = relative_install_dir
+ if shed_config_dict.get( 'tool_path' ):
+ files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir )
+ datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir )
+ # Load data types required by tools.
+ converter_path, display_path = \
+ datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, files_dir, override=False )
+ if converter_path or display_path:
+ # Create a dictionary of tool shed repository related information.
+ repository_dict = \
+ datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed,
+ name=tool_shed_repository.name,
+ owner=tool_shed_repository.owner,
+ installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
+ tool_dicts=metadata_dict.get( 'tools', [] ),
+ converter_path=converter_path,
+ display_path=display_path )
+ if converter_path:
+ # Load proprietary datatype converters
+ self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict )
+ if display_path:
+ # Load proprietary datatype display applications
+ self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+
+ def handle_tool_shed_repositories( self, installation_dict, using_api=False ):
+ # The following installation_dict entries are all required.
+ install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ]
+ new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ]
+ no_changes_checked = installation_dict[ 'no_changes_checked' ]
+ repo_info_dicts = installation_dict[ 'repo_info_dicts' ]
+ tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ]
+ tool_path = installation_dict[ 'tool_path' ]
+ tool_shed_url = installation_dict[ 'tool_shed_url' ]
+ created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
+ repository_dependency_util.create_repository_dependency_objects( app=self.app,
+ tool_path=tool_path,
+ tool_shed_url=tool_shed_url,
+ repo_info_dicts=repo_info_dicts,
+ install_repository_dependencies=install_repository_dependencies,
+ no_changes_checked=no_changes_checked,
+ tool_panel_section_id=tool_panel_section_id,
+ new_tool_panel_section_label=new_tool_panel_section_label )
+ return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts
+
def initiate_repository_installation( self, installation_dict ):
install_model = self.app.install_model
# The following installation_dict entries are all required.
@@ -699,9 +832,9 @@
cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
if cloned_ok:
if reinstalling:
- # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated.
- changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( self.app,
- tool_shed_repository )
+ # Since we're reinstalling the repository we need to find the latest changeset revision to
+ # which it can be updated.
+ changeset_revision_dict = self.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev( tool_shed_repository )
current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None )
current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None )
if current_ctx_rev != ctx_rev:
@@ -711,15 +844,14 @@
create=False )
hg_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
hg_util.update_repository( repo, ctx_rev=current_ctx_rev )
- repository_util.handle_repository_contents( self.app,
- tool_shed_repository=tool_shed_repository,
- tool_path=tool_path,
- repository_clone_url=repository_clone_url,
- relative_install_dir=relative_install_dir,
- tool_shed=tool_shed_repository.tool_shed,
- tool_section=tool_section,
- shed_tool_conf=shed_tool_conf,
- reinstalling=reinstalling )
+ self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
+ tool_path=tool_path,
+ repository_clone_url=repository_clone_url,
+ relative_install_dir=relative_install_dir,
+ tool_shed=tool_shed_repository.tool_shed,
+ tool_section=tool_section,
+ shed_tool_conf=shed_tool_conf,
+ reinstalling=reinstalling )
install_model.context.refresh( tool_shed_repository )
metadata = tool_shed_repository.metadata
if 'tools' in metadata:
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/repair_repository_manager.py
--- a/lib/tool_shed/galaxy_install/repair_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py
@@ -4,13 +4,13 @@
log = logging.getLogger( __name__ )
from tool_shed.galaxy_install import install_manager
-from tool_shed.galaxy_install import repository_util
from tool_shed.util import common_install_util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import repository_dependency_util
+from tool_shed.util import repository_maintenance_util
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
@@ -123,16 +123,16 @@
new_tool_panel_section_label=tool_panel_section_name )
else:
tool_dependencies = None
- repo_info_dict = repository_util.create_repo_info_dict( app=self.app,
- repository_clone_url=repository_clone_url,
- changeset_revision=repository.changeset_revision,
- ctx_rev=repository.ctx_rev,
- repository_owner=repository.owner,
- repository_name=repository.name,
- repository=None,
- repository_metadata=None,
- tool_dependencies=tool_dependencies,
- repository_dependencies=repository_dependencies )
+ repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=self.app,
+ repository_clone_url=repository_clone_url,
+ changeset_revision=repository.changeset_revision,
+ ctx_rev=repository.ctx_rev,
+ repository_owner=repository.owner,
+ repository_name=repository.name,
+ repository=None,
+ repository_metadata=None,
+ tool_dependencies=tool_dependencies,
+ repository_dependencies=repository_dependencies )
return repo_info_dict, tool_panel_section_key
def repair_tool_shed_repository( self, repository, repo_info_dict ):
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ /dev/null
@@ -1,382 +0,0 @@
-import logging
-import os
-from galaxy import util
-from galaxy import web
-import tool_shed.util.shed_util_common as suc
-from tool_shed.util import common_util
-from tool_shed.util import data_manager_util
-from tool_shed.util import datatype_util
-from tool_shed.util import encoding_util
-from tool_shed.util import hg_util
-from tool_shed.util import repository_dependency_util
-from tool_shed.util import metadata_util
-from tool_shed.util import tool_dependency_util
-from tool_shed.util import tool_util
-
-log = logging.getLogger( __name__ )
-
-def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None,
- repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ):
- """
- Return a dictionary that includes all of the information needed to install a repository into a local
- Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
- for the repository, as well as the defined tool dependencies.
-
- This method is called from Galaxy under four scenarios:
- 1. During the tool shed repository installation process via the tool shed's get_repository_information()
- method. In this case both the received repository and repository_metadata will be objects, but
- tool_dependencies and repository_dependencies will be None.
- 2. When getting updates for an install repository where the updates include newly defined repository
- dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
- method is the caller, and both the received repository and repository_metadata will be objects, but
- tool_dependencies and repository_dependencies will be None.
- 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
- updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
- and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
- definitions for them.
- 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
- available. In this case, this method is reached via the tool shed's get_updated_repository_information()
- method, and both repository and repository_metadata will be objects but tool_dependencies and
- repository_dependencies will be None.
- """
- repo_info_dict = {}
- repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner )
- if app.name == 'tool_shed':
- # We're in the tool shed.
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
- app.security.encode_id( repository.id ),
- changeset_revision )
- if repository_metadata:
- metadata = repository_metadata.metadata
- if metadata:
- tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
- # Get a dictionary of all repositories upon which the contents of the received repository depends.
- repository_dependencies = \
- repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app,
- repository=repository,
- repository_metadata=repository_metadata,
- toolshed_base_url=tool_shed_url,
- key_rd_dicts_to_be_processed=None,
- all_repository_dependencies=None,
- handled_key_rd_dicts=None,
- circular_repository_dependencies=None )
- tool_dependencies = metadata.get( 'tool_dependencies', {} )
- if tool_dependencies:
- new_tool_dependencies = {}
- for dependency_key, requirements_dict in tool_dependencies.items():
- if dependency_key in [ 'set_environment' ]:
- new_set_environment_dict_list = []
- for set_environment_dict in requirements_dict:
- set_environment_dict[ 'repository_name' ] = repository_name
- set_environment_dict[ 'repository_owner' ] = repository_owner
- set_environment_dict[ 'changeset_revision' ] = changeset_revision
- new_set_environment_dict_list.append( set_environment_dict )
- new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list
- else:
- requirements_dict[ 'repository_name' ] = repository_name
- requirements_dict[ 'repository_owner' ] = repository_owner
- requirements_dict[ 'changeset_revision' ] = changeset_revision
- new_tool_dependencies[ dependency_key ] = requirements_dict
- tool_dependencies = new_tool_dependencies
- # Cast unicode to string, with the exception of description, since it is free text and can contain special characters.
- repo_info_dict[ str( repository.name ) ] = ( repository.description,
- str( repository_clone_url ),
- str( changeset_revision ),
- str( ctx_rev ),
- str( repository_owner ),
- repository_dependencies,
- tool_dependencies )
- return repo_info_dict
-
-def get_prior_install_required_dict( trans, tsr_ids, repo_info_dicts ):
- """
- Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received list of tsr_ids
- and whose associated repository must be installed prior to the repository associated with the tsr_id key.
- """
- # Initialize the dictionary.
- prior_install_required_dict = {}
- for tsr_id in tsr_ids:
- prior_install_required_dict[ tsr_id ] = []
- # Inspect the repository dependencies for each repository about to be installed and populate the dictionary.
- for repo_info_dict in repo_info_dicts:
- repository, repository_dependencies = suc.get_repository_and_repository_dependencies_from_repo_info_dict( trans.app, repo_info_dict )
- if repository:
- encoded_repository_id = trans.security.encode_id( repository.id )
- if encoded_repository_id in tsr_ids:
- # We've located the database table record for one of the repositories we're about to install, so find out if it has any repository
- # dependencies that require prior installation.
- prior_install_ids = suc.get_repository_ids_requiring_prior_import_or_install( trans.app, tsr_ids, repository_dependencies )
- prior_install_required_dict[ encoded_repository_id ] = prior_install_ids
- return prior_install_required_dict
-
-def get_repo_info_dict( trans, repository_id, changeset_revision ):
- repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
- repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
- repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
- repository_id,
- changeset_revision )
- if not repository_metadata:
- # The received changeset_revision is no longer installable, so get the next changeset_revision
- # in the repository's changelog. This generally occurs only with repositories of type
- # repository_suite_definition or tool_dependency_definition.
- next_downloadable_changeset_revision = \
- suc.get_next_downloadable_changeset_revision( repository,repo, changeset_revision )
- if next_downloadable_changeset_revision:
- repository_metadata = \
- suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, next_downloadable_changeset_revision )
- if repository_metadata:
- # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
- # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
- # returned repo_info_dict.
- metadata = repository_metadata.metadata
- if 'tools' in metadata:
- includes_tools = True
- else:
- includes_tools = False
- includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
- repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
- repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
- has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
- suc.get_repository_dependency_types( repository_dependencies )
- if 'tool_dependencies' in metadata:
- includes_tool_dependencies = True
- else:
- includes_tool_dependencies = False
- else:
- # Here's where we may have to handle enhancements to the callers. See above comment.
- includes_tools = False
- has_repository_dependencies = False
- has_repository_dependencies_only_if_compiling_contained_td = False
- includes_tool_dependencies = False
- includes_tools_for_display_in_tool_panel = False
- ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
- repo_info_dict = create_repo_info_dict( app=trans.app,
- repository_clone_url=repository_clone_url,
- changeset_revision=changeset_revision,
- ctx_rev=str( ctx.rev() ),
- repository_owner=repository.user.username,
- repository_name=repository.name,
- repository=repository,
- repository_metadata=repository_metadata,
- tool_dependencies=None,
- repository_dependencies=None )
- return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
- has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
-
-def get_tool_shed_repository_ids( as_string=False, **kwd ):
- tsrid = kwd.get( 'tool_shed_repository_id', None )
- tsridslist = util.listify( kwd.get( 'tool_shed_repository_ids', None ) )
- if not tsridslist:
- tsridslist = util.listify( kwd.get( 'id', None ) )
- if tsridslist:
- if tsrid and tsrid not in tsridslist:
- tsridslist.append( tsrid )
- if as_string:
- return ','.join( tsridslist )
- return tsridslist
- else:
- tsridslist = util.listify( kwd.get( 'ordered_tsr_ids', None ) )
- if as_string:
- return ','.join( tsridslist )
- return tsridslist
- if as_string:
- ''
- return []
-
-def get_update_to_changeset_revision_and_ctx_rev( app, repository ):
- """Return the changeset revision hash to which the repository can be updated."""
- changeset_revision_dict = {}
- tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
- params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ),
- str( repository.owner ),
- str( repository.installed_changeset_revision ) )
- url = common_util.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev%s' % params )
- try:
- encoded_update_dict = common_util.tool_shed_get( app, tool_shed_url, url )
- if encoded_update_dict:
- update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
- includes_data_managers = update_dict.get( 'includes_data_managers', False )
- includes_datatypes = update_dict.get( 'includes_datatypes', False )
- includes_tools = update_dict.get( 'includes_tools', False )
- includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False )
- includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False )
- includes_workflows = update_dict.get( 'includes_workflows', False )
- has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False )
- has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
- changeset_revision = update_dict.get( 'changeset_revision', None )
- ctx_rev = update_dict.get( 'ctx_rev', None )
- changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers
- changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes
- changeset_revision_dict[ 'includes_tools' ] = includes_tools
- changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel
- changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies
- changeset_revision_dict[ 'includes_workflows' ] = includes_workflows
- changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
- changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td
- changeset_revision_dict[ 'changeset_revision' ] = changeset_revision
- changeset_revision_dict[ 'ctx_rev' ] = ctx_rev
- except Exception, e:
- log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) )
- changeset_revision_dict[ 'includes_data_managers' ] = False
- changeset_revision_dict[ 'includes_datatypes' ] = False
- changeset_revision_dict[ 'includes_tools' ] = False
- changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False
- changeset_revision_dict[ 'includes_tool_dependencies' ] = False
- changeset_revision_dict[ 'includes_workflows' ] = False
- changeset_revision_dict[ 'has_repository_dependencies' ] = False
- changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False
- changeset_revision_dict[ 'changeset_revision' ] = None
- changeset_revision_dict[ 'ctx_rev' ] = None
- return changeset_revision_dict
-
-def handle_repository_contents( app, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir,
- tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False ):
- """
- Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy
- (never the tool shed) when an administrator is installing a new repository or reinstalling an uninstalled repository.
- """
- install_model = app.install_model
- shed_config_dict = app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf )
- metadata_dict, invalid_file_tups = \
- metadata_util.generate_metadata_for_changeset_revision( app=app,
- repository=tool_shed_repository,
- changeset_revision=tool_shed_repository.changeset_revision,
- repository_clone_url=repository_clone_url,
- shed_config_dict=shed_config_dict,
- relative_install_dir=relative_install_dir,
- repository_files_dir=None,
- resetting_all_metadata_on_repository=False,
- updating_installed_repository=False,
- persist=True )
- tool_shed_repository.metadata = metadata_dict
- # Update the tool_shed_repository.tool_shed_status column in the database.
- tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( app, tool_shed_repository )
- if tool_shed_status_dict:
- tool_shed_repository.tool_shed_status = tool_shed_status_dict
- install_model.context.add( tool_shed_repository )
- install_model.context.flush()
- if 'tool_dependencies' in metadata_dict and not reinstalling:
- tool_dependencies = tool_dependency_util.create_tool_dependency_objects( app,
- tool_shed_repository,
- relative_install_dir,
- set_status=True )
- if 'sample_files' in metadata_dict:
- sample_files = metadata_dict.get( 'sample_files', [] )
- tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
- tool_data_table_conf_filename, tool_data_table_elems = \
- tool_util.install_tool_data_tables( app, tool_shed_repository, tool_index_sample_files )
- if tool_data_table_elems:
- app.tool_data_tables.add_new_entries_from_config_file( tool_data_table_conf_filename,
- None,
- app.config.shed_tool_data_table_config,
- persist=True )
- if 'tools' in metadata_dict:
- tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section )
- sample_files = metadata_dict.get( 'sample_files', [] )
- tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
- tool_util.copy_sample_files( app, tool_index_sample_files, tool_path=tool_path )
- sample_files_copied = [ str( s ) for s in tool_index_sample_files ]
- repository_tools_tups = suc.get_repository_tools_tups( app, metadata_dict )
- if repository_tools_tups:
- # Handle missing data table entries for tool parameters that are dynamically generated select lists.
- repository_tools_tups = tool_util.handle_missing_data_table_entry( app,
- relative_install_dir,
- tool_path,
- repository_tools_tups )
- # Handle missing index files for tool parameters that are dynamically generated select lists.
- repository_tools_tups, sample_files_copied = \
- tool_util.handle_missing_index_file( app,
- tool_path,
- sample_files,
- repository_tools_tups,
- sample_files_copied )
- # Copy remaining sample files included in the repository to the ~/tool-data directory of the
- # local Galaxy instance.
- tool_util.copy_sample_files( app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied )
- tool_util.add_to_tool_panel( app=app,
- repository_name=tool_shed_repository.name,
- repository_clone_url=repository_clone_url,
- changeset_revision=tool_shed_repository.installed_changeset_revision,
- repository_tools_tups=repository_tools_tups,
- owner=tool_shed_repository.owner,
- shed_tool_conf=shed_tool_conf,
- tool_panel_dict=tool_panel_dict,
- new_install=True )
- if 'data_manager' in metadata_dict:
- new_data_managers = data_manager_util.install_data_managers( app,
- app.config.shed_data_manager_config_file,
- metadata_dict,
- shed_config_dict,
- relative_install_dir,
- tool_shed_repository,
- repository_tools_tups )
- if 'datatypes' in metadata_dict:
- tool_shed_repository.status = install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
- if not tool_shed_repository.includes_datatypes:
- tool_shed_repository.includes_datatypes = True
- install_model.context.add( tool_shed_repository )
- install_model.context.flush()
- files_dir = relative_install_dir
- if shed_config_dict.get( 'tool_path' ):
- files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir )
- datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir )
- # Load data types required by tools.
- converter_path, display_path = \
- datatype_util.alter_config_and_load_prorietary_datatypes( app, datatypes_config, files_dir, override=False )
- if converter_path or display_path:
- # Create a dictionary of tool shed repository related information.
- repository_dict = \
- datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed,
- name=tool_shed_repository.name,
- owner=tool_shed_repository.owner,
- installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
- tool_dicts=metadata_dict.get( 'tools', [] ),
- converter_path=converter_path,
- display_path=display_path )
- if converter_path:
- # Load proprietary datatype converters
- app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=repository_dict )
- if display_path:
- # Load proprietary datatype display applications
- app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
-
-def handle_tool_shed_repositories( app, installation_dict, using_api=False ):
- # The following installation_dict entries are all required.
- install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ]
- new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ]
- no_changes_checked = installation_dict[ 'no_changes_checked' ]
- repo_info_dicts = installation_dict[ 'repo_info_dicts' ]
- tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ]
- tool_path = installation_dict[ 'tool_path' ]
- tool_shed_url = installation_dict[ 'tool_shed_url' ]
- created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
- repository_dependency_util.create_repository_dependency_objects( app=app,
- tool_path=tool_path,
- tool_shed_url=tool_shed_url,
- repo_info_dicts=repo_info_dicts,
- install_repository_dependencies=install_repository_dependencies,
- no_changes_checked=no_changes_checked,
- tool_panel_section_id=tool_panel_section_id,
- new_tool_panel_section_label=new_tool_panel_section_label )
- return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts
-
-def update_repository_record( app, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ):
- """
- Update a tool_shed_repository database record with new information retrieved from the
- Tool Shed. This happens when updating an installed repository to a new changeset revision.
- """
- repository.metadata = updated_metadata_dict
- # Update the repository.changeset_revision column in the database.
- repository.changeset_revision = updated_changeset_revision
- repository.ctx_rev = updated_ctx_rev
- # Update the repository.tool_shed_status column in the database.
- tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( app, repository )
- if tool_shed_status_dict:
- repository.tool_shed_status = tool_shed_status_dict
- else:
- repository.tool_shed_status = None
- app.install_model.context.add( repository )
- app.install_model.context.flush()
- app.install_model.context.refresh( repository )
- return repository
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/tool_migration_manager.py
--- a/lib/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py
@@ -111,11 +111,11 @@
created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name,
changeset_revision,
repository_dependencies_dict )
- # Order the repositories for proper installation. This process is similar to the process used when installing tool
- # shed repositories (i.e., the order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/
- # repository_util), but does not handle managing tool panel sections and other components since repository dependency
- # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
- # dependency that contains a tool.
+ # Order the repositories for proper installation. This process is similar to the
+ # process used when installing tool shed repositories, but does not handle managing
+ # tool panel sections and other components since repository dependency definitions
+ # contained in tool shed repositories with migrated tools must never define a relationship
+ # to a repository dependency that contains a tool.
ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories,
repository_dependencies_dict )
@@ -585,11 +585,10 @@
in the list of repositories about to be installed, then they are not considered. Repository dependency
definitions that contain circular dependencies should not result in an infinite loop, but obviously prior
installation will not be handled for one or more of the repositories that require prior installation. This
- process is similar to the process used when installing tool shed repositories (i.e., the
- order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/repository_util), but does not
- handle managing tool panel sections and other components since repository dependency definitions contained
- in tool shed repositories with migrated tools must never define a relationship to a repository dependency
- that contains a tool.
+ process is similar to the process used when installing tool shed repositories, but does not handle managing
+ tool panel sections and other components since repository dependency definitions contained in tool shed
+ repositories with migrated tools must never define a relationship to a repository dependency that contains
+ a tool.
"""
ordered_tool_shed_repositories = []
ordered_tsr_ids = []
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/update_repository_manager.py
--- a/lib/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/update_repository_manager.py
@@ -4,6 +4,8 @@
import logging
import threading
import tool_shed.util.shed_util_common as suc
+from tool_shed.util import common_util
+from tool_shed.util import encoding_util
log = logging.getLogger( __name__ )
@@ -20,6 +22,52 @@
self.restarter.start()
self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
+ def get_update_to_changeset_revision_and_ctx_rev( self, repository ):
+ """Return the changeset revision hash to which the repository can be updated."""
+ changeset_revision_dict = {}
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, str( repository.tool_shed ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ),
+ str( repository.owner ),
+ str( repository.installed_changeset_revision ) )
+ url = common_util.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev%s' % params )
+ try:
+ encoded_update_dict = common_util.tool_shed_get( self.app, tool_shed_url, url )
+ if encoded_update_dict:
+ update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
+ includes_data_managers = update_dict.get( 'includes_data_managers', False )
+ includes_datatypes = update_dict.get( 'includes_datatypes', False )
+ includes_tools = update_dict.get( 'includes_tools', False )
+ includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False )
+ includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False )
+ includes_workflows = update_dict.get( 'includes_workflows', False )
+ has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False )
+ has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
+ changeset_revision = update_dict.get( 'changeset_revision', None )
+ ctx_rev = update_dict.get( 'ctx_rev', None )
+ changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers
+ changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes
+ changeset_revision_dict[ 'includes_tools' ] = includes_tools
+ changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel
+ changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies
+ changeset_revision_dict[ 'includes_workflows' ] = includes_workflows
+ changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
+ changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td
+ changeset_revision_dict[ 'changeset_revision' ] = changeset_revision
+ changeset_revision_dict[ 'ctx_rev' ] = ctx_rev
+ except Exception, e:
+ log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) )
+ changeset_revision_dict[ 'includes_data_managers' ] = False
+ changeset_revision_dict[ 'includes_datatypes' ] = False
+ changeset_revision_dict[ 'includes_tools' ] = False
+ changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False
+ changeset_revision_dict[ 'includes_tool_dependencies' ] = False
+ changeset_revision_dict[ 'includes_workflows' ] = False
+ changeset_revision_dict[ 'has_repository_dependencies' ] = False
+ changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False
+ changeset_revision_dict[ 'changeset_revision' ] = None
+ changeset_revision_dict[ 'ctx_rev' ] = None
+ return changeset_revision_dict
+
def __restarter( self ):
log.info( 'Update repository manager restarter starting up...' )
while self.running:
@@ -48,6 +96,26 @@
self.running = False
self.sleeper.wake()
+ def update_repository_record( self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ):
+ """
+ Update a tool_shed_repository database record with new information retrieved from the
+ Tool Shed. This happens when updating an installed repository to a new changeset revision.
+ """
+ repository.metadata = updated_metadata_dict
+ # Update the repository.changeset_revision column in the database.
+ repository.changeset_revision = updated_changeset_revision
+ repository.ctx_rev = updated_ctx_rev
+ # Update the repository.tool_shed_status column in the database.
+ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
+ if tool_shed_status_dict:
+ repository.tool_shed_status = tool_shed_status_dict
+ else:
+ repository.tool_shed_status = None
+ self.app.install_model.context.add( repository )
+ self.app.install_model.context.flush()
+ self.app.install_model.context.refresh( repository )
+ return repository
+
class Sleeper( object ):
"""
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -1,12 +1,11 @@
import copy
+import json
import logging
import os
import urllib
import urllib2
from galaxy import util
from galaxy import web
-from galaxy.util import json
-from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY
import tool_shed.util.shed_util_common as suc
from tool_shed.util import common_util
from tool_shed.util import container_util
@@ -15,7 +14,6 @@
from tool_shed.util import datatype_util
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
-from tool_shed.util import xml_util
log = logging.getLogger( __name__ )
@@ -452,7 +450,7 @@
response = urllib2.urlopen( request ).read()
if response:
try:
- required_repo_info_dict = json.from_json_string( response )
+ required_repo_info_dict = json.loads( response )
except Exception, e:
log.exception( e )
return all_repo_info_dicts
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -1,7 +1,8 @@
+import json
import logging
import os
import urllib2
-from galaxy.util import json
+from galaxy import util
from galaxy.util.odict import odict
from galaxy.web import url_for
from tool_shed.util import encoding_util
@@ -109,12 +110,12 @@
tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
return url_join( tool_shed_url, 'repos', str( repository.owner ), str( repository.name ) )
-def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
+def generate_clone_url_for_repository_in_tool_shed( user, repository ):
"""Generate the URL for cloning a repository that is in the tool shed."""
base_url = url_for( '/', qualified=True ).rstrip( '/' )
- if trans and trans.user:
+ if user:
protocol, base = base_url.split( '://' )
- username = '%s@' % trans.user.username
+ username = '%s@' % user.username
return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name )
else:
return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name )
@@ -156,7 +157,7 @@
print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) )
if tool_shed_accessible:
if len( raw_text ) > 2:
- encoded_text = json.from_json_string( raw_text )
+ encoded_text = json.loads( raw_text )
repository_dependencies_dict = encoding_util.tool_shed_decode( encoded_text )
return tool_shed_accessible, repository_dependencies_dict
@@ -194,6 +195,27 @@
tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type ) )
return tool_shed_accessible, tool_dependencies
+def get_tool_shed_repository_ids( as_string=False, **kwd ):
+ tsrid = kwd.get( 'tool_shed_repository_id', None )
+ tsridslist = util.listify( kwd.get( 'tool_shed_repository_ids', None ) )
+ if not tsridslist:
+ tsridslist = util.listify( kwd.get( 'id', None ) )
+ if tsridslist is not None:
+ if tsrid is not None and tsrid not in tsridslist:
+ tsridslist.append( tsrid )
+ if as_string:
+ return ','.join( tsridslist )
+ return tsridslist
+ else:
+ tsridslist = util.listify( kwd.get( 'ordered_tsr_ids', None ) )
+ if tsridslist is not None:
+ if as_string:
+ return ','.join( tsridslist )
+ return tsridslist
+ if as_string:
+ ''
+ return []
+
def get_tool_shed_url_from_tool_shed_registry( app, tool_shed ):
"""
The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/export_util.py
--- a/lib/tool_shed/util/export_util.py
+++ b/lib/tool_shed/util/export_util.py
@@ -256,7 +256,7 @@
repo_info_dict = {}
# Cast unicode to string.
repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),
- common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ),
+ common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ),
str( changeset_revision ),
str( ctx.rev() ),
str( repository.user.username ),
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -1776,7 +1776,7 @@
log.debug( "Resetting all metadata on repository: %s" % repository.name )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
- repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
# The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop
# completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list.
changeset_revisions = []
@@ -1955,7 +1955,7 @@
message = ''
status = 'done'
encoded_id = trans.security.encode_id( repository.id )
- repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/repository_maintenance_util.py
--- a/lib/tool_shed/util/repository_maintenance_util.py
+++ b/lib/tool_shed/util/repository_maintenance_util.py
@@ -3,9 +3,12 @@
import os
import re
import tool_shed.util.shed_util_common as suc
+from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import import_util
+from tool_shed.util import repository_dependency_util
from galaxy import util
+from galaxy import web
from galaxy.web.form_builder import build_select_field
from galaxy.webapps.tool_shed.model import directory_hash_id
@@ -53,6 +56,79 @@
fp.write( 'hgext.purge=' )
fp.close()
+def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None,
+ repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ):
+ """
+ Return a dictionary that includes all of the information needed to install a repository into a local
+ Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
+ for the repository, as well as the defined tool dependencies.
+
+ This method is called from Galaxy under four scenarios:
+ 1. During the tool shed repository installation process via the tool shed's get_repository_information()
+ method. In this case both the received repository and repository_metadata will be objects, but
+ tool_dependencies and repository_dependencies will be None.
+ 2. When getting updates for an install repository where the updates include newly defined repository
+ dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
+ method is the caller, and both the received repository and repository_metadata will be objects, but
+ tool_dependencies and repository_dependencies will be None.
+ 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
+ updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
+ and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
+ definitions for them.
+ 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
+ available. In this case, this method is reached via the tool shed's get_updated_repository_information()
+ method, and both repository and repository_metadata will be objects but tool_dependencies and
+ repository_dependencies will be None.
+ """
+ repo_info_dict = {}
+ repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner )
+ if app.name == 'tool_shed':
+ # We're in the tool shed.
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
+ app.security.encode_id( repository.id ),
+ changeset_revision )
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
+ # Get a dictionary of all repositories upon which the contents of the received repository depends.
+ repository_dependencies = \
+ repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app,
+ repository=repository,
+ repository_metadata=repository_metadata,
+ toolshed_base_url=tool_shed_url,
+ key_rd_dicts_to_be_processed=None,
+ all_repository_dependencies=None,
+ handled_key_rd_dicts=None,
+ circular_repository_dependencies=None )
+ tool_dependencies = metadata.get( 'tool_dependencies', {} )
+ if tool_dependencies:
+ new_tool_dependencies = {}
+ for dependency_key, requirements_dict in tool_dependencies.items():
+ if dependency_key in [ 'set_environment' ]:
+ new_set_environment_dict_list = []
+ for set_environment_dict in requirements_dict:
+ set_environment_dict[ 'repository_name' ] = repository_name
+ set_environment_dict[ 'repository_owner' ] = repository_owner
+ set_environment_dict[ 'changeset_revision' ] = changeset_revision
+ new_set_environment_dict_list.append( set_environment_dict )
+ new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list
+ else:
+ requirements_dict[ 'repository_name' ] = repository_name
+ requirements_dict[ 'repository_owner' ] = repository_owner
+ requirements_dict[ 'changeset_revision' ] = changeset_revision
+ new_tool_dependencies[ dependency_key ] = requirements_dict
+ tool_dependencies = new_tool_dependencies
+ # Cast unicode to string, with the exception of description, since it is free text and can contain special characters.
+ repo_info_dict[ str( repository.name ) ] = ( repository.description,
+ str( repository_clone_url ),
+ str( changeset_revision ),
+ str( ctx_rev ),
+ str( repository_owner ),
+ repository_dependencies,
+ tool_dependencies )
+ return repo_info_dict
+
def create_repository( trans, name, type, description, long_description, user_id, category_ids=[] ):
# Add the repository record to the database.
repository = trans.app.model.Repository( name=name,
@@ -182,6 +258,62 @@
import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
return import_results_tups
+def get_repo_info_dict( app, user, repository_id, changeset_revision ):
+ repository = suc.get_repository_in_tool_shed( app, repository_id )
+ repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository )
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
+ repository_id,
+ changeset_revision )
+ if not repository_metadata:
+ # The received changeset_revision is no longer installable, so get the next changeset_revision
+ # in the repository's changelog. This generally occurs only with repositories of type
+ # repository_suite_definition or tool_dependency_definition.
+ next_downloadable_changeset_revision = \
+ suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
+ if next_downloadable_changeset_revision:
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
+ repository_id,
+ next_downloadable_changeset_revision )
+ if repository_metadata:
+ # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
+ # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
+ # returned repo_info_dict.
+ metadata = repository_metadata.metadata
+ if 'tools' in metadata:
+ includes_tools = True
+ else:
+ includes_tools = False
+ includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
+ repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
+ repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+ has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
+ suc.get_repository_dependency_types( repository_dependencies )
+ if 'tool_dependencies' in metadata:
+ includes_tool_dependencies = True
+ else:
+ includes_tool_dependencies = False
+ else:
+ # Here's where we may have to handle enhancements to the callers. See above comment.
+ includes_tools = False
+ has_repository_dependencies = False
+ has_repository_dependencies_only_if_compiling_contained_td = False
+ includes_tool_dependencies = False
+ includes_tools_for_display_in_tool_panel = False
+ ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
+ repo_info_dict = create_repo_info_dict( app=app,
+ repository_clone_url=repository_clone_url,
+ changeset_revision=changeset_revision,
+ ctx_rev=str( ctx.rev() ),
+ repository_owner=repository.user.username,
+ repository_name=repository.name,
+ repository=repository,
+ repository_metadata=repository_metadata,
+ tool_dependencies=None,
+ repository_dependencies=None )
+ return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
+ has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
+
def get_repository_admin_role_name( repository_name, repository_owner ):
return '%s_%s_admin' % ( str( repository_name ), str( repository_owner ) )
diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -216,7 +216,7 @@
<%def name="render_clone_str( repository )"><%
from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed
- clone_str = generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ clone_str = generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
%>
hg clone <a href="${clone_str}">${clone_str}</a></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: For standardization and clarity, rename Galaxy's UpdateManager to be UpdateRepositoryManager.
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/95937a7e51f2/
Changeset: 95937a7e51f2
User: greg
Date: 2014-06-17 17:24:33
Summary: For standardization and clarity, rename Galaxy's UpdateManager to be UpdateRepositoryManager.
Affected #: 4 files
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -82,10 +82,10 @@
self.data_managers = DataManagers( self )
# If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories.
if self.config.get_bool( 'enable_tool_shed_check', False ):
- from tool_shed.galaxy_install import update_manager
- self.update_manager = update_manager.UpdateManager( self )
+ from tool_shed.galaxy_install import update_repository_manager
+ self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self )
else:
- self.update_manager = None
+ self.update_repository_manager = None
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
@@ -159,8 +159,8 @@
self.object_store.shutdown()
if self.heartbeat:
self.heartbeat.shutdown()
- if self.update_manager:
- self.update_manager.shutdown()
+ if self.update_repository_manager is not None:
+ self.update_repository_manager.shutdown()
if self.control_worker:
self.control_worker.shutdown()
try:
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -887,7 +887,7 @@
"""Handle a request from a local Galaxy instance."""
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- # If the request originated with the UpdateManager, it will not include a galaxy_url.
+ # If the request originated with the UpdateRepositoryManager, it will not include a galaxy_url.
galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/tool_shed/galaxy_install/update_manager.py
--- a/lib/tool_shed/galaxy_install/update_manager.py
+++ /dev/null
@@ -1,67 +0,0 @@
-"""
-Determine if installed tool shed repositories have updates available in their respective tool sheds.
-"""
-import logging
-import threading
-from galaxy.util import string_as_bool
-import tool_shed.util.shed_util_common as suc
-from tool_shed.util import common_util
-from galaxy.model.orm import and_
-
-log = logging.getLogger( __name__ )
-
-
-class UpdateManager( object ):
-
- def __init__( self, app ):
- self.app = app
- self.context = self.app.install_model.context
- # Ideally only one Galaxy server process should be able to check for repository updates.
- self.running = True
- self.sleeper = Sleeper()
- self.restarter = threading.Thread( target=self.__restarter )
- self.restarter.start()
- self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
-
- def __restarter( self ):
- log.info( 'Update manager restarter starting up...' )
- while self.running:
- # Make a call to the tool shed for each installed repository to get the latest status information in the tool shed for the
- # repository. This information includes items like newer installable repository revisions, current revision updates, whether
- # the repository revision is the latest installable revision, and whether the repository has been deprecated in the tool shed.
- for repository in self.context.query( self.app.install_model.ToolShedRepository ) \
- .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ):
- tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
- if tool_shed_status_dict:
- if tool_shed_status_dict != repository.tool_shed_status:
- repository.tool_shed_status = tool_shed_status_dict
- self.context.flush()
- else:
- # The received tool_shed_status_dict is an empty dictionary, so coerce to None.
- tool_shed_status_dict = None
- if tool_shed_status_dict != repository.tool_shed_status:
- repository.tool_shed_status = tool_shed_status_dict
- self.context.flush()
- self.sleeper.sleep( self.seconds_to_sleep )
- log.info( 'Update manager restarter shutting down...' )
-
- def shutdown( self ):
- self.running = False
- self.sleeper.wake()
-
-
-class Sleeper( object ):
- """Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method is called (from a different thread)."""
-
- def __init__( self ):
- self.condition = threading.Condition()
-
- def sleep( self, seconds ):
- self.condition.acquire()
- self.condition.wait( seconds )
- self.condition.release()
-
- def wake( self ):
- self.condition.acquire()
- self.condition.notify()
- self.condition.release()
diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/tool_shed/galaxy_install/update_repository_manager.py
--- /dev/null
+++ b/lib/tool_shed/galaxy_install/update_repository_manager.py
@@ -0,0 +1,69 @@
+"""
+Determine if installed tool shed repositories have updates available in their respective tool sheds.
+"""
+import logging
+import threading
+import tool_shed.util.shed_util_common as suc
+
+log = logging.getLogger( __name__ )
+
+
+class UpdateRepositoryManager( object ):
+
+ def __init__( self, app ):
+ self.app = app
+ self.context = self.app.install_model.context
+ # Ideally only one Galaxy server process should be able to check for repository updates.
+ self.running = True
+ self.sleeper = Sleeper()
+ self.restarter = threading.Thread( target=self.__restarter )
+ self.restarter.start()
+ self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
+
+ def __restarter( self ):
+ log.info( 'Update repository manager restarter starting up...' )
+ while self.running:
+ # Make a call to the Tool Shed for each installed repository to get the latest
+ # status information in the Tool Shed for the repository. This information includes
+ # items like newer installable repository revisions, current revision updates, whether
+ # the repository revision is the latest installable revision, and whether the repository
+ # has been deprecated in the Tool Shed.
+ for repository in self.context.query( self.app.install_model.ToolShedRepository ) \
+ .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ):
+ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
+ if tool_shed_status_dict:
+ if tool_shed_status_dict != repository.tool_shed_status:
+ repository.tool_shed_status = tool_shed_status_dict
+ self.context.flush()
+ else:
+ # The received tool_shed_status_dict is an empty dictionary, so coerce to None.
+ tool_shed_status_dict = None
+ if tool_shed_status_dict != repository.tool_shed_status:
+ repository.tool_shed_status = tool_shed_status_dict
+ self.context.flush()
+ self.sleeper.sleep( self.seconds_to_sleep )
+ log.info( 'Update repository manager restarter shutting down...' )
+
+ def shutdown( self ):
+ self.running = False
+ self.sleeper.wake()
+
+
+class Sleeper( object ):
+ """
+ Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method
+ is called (from a different thread).
+ """
+
+ def __init__( self ):
+ self.condition = threading.Condition()
+
+ def sleep( self, seconds ):
+ self.condition.acquire()
+ self.condition.wait( seconds )
+ self.condition.release()
+
+ def wake( self ):
+ self.condition.acquire()
+ self.condition.notify()
+ self.condition.release()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Instantiate the Tool Shed's various tool dependency recipe classes with app so it doesn't have to be passed to functions.
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fa69b6d3cafd/
Changeset: fa69b6d3cafd
User: greg
Date: 2014-06-17 17:00:49
Summary: Instantiate the Tool Shed's various tool dependency recipe classes with app so it doesn't have to be passed to functions.
Affected #: 7 files
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -58,9 +58,10 @@
actions = actions_dict.get( 'actions', None )
filtered_actions = []
env_file_builder = EnvFileBuilder( install_dir )
- install_environment = InstallEnvironment( tool_shed_repository_install_dir=tool_shed_repository_install_dir,
+ install_environment = InstallEnvironment( app=self.app,
+ tool_shed_repository_install_dir=tool_shed_repository_install_dir,
install_dir=install_dir )
- step_manager = StepManager()
+ step_manager = StepManager( self.app )
if actions:
with install_environment.make_tmp_dir() as work_dir:
with lcd( work_dir ):
@@ -76,8 +77,7 @@
# tool_dependency status in this stage because it should not have been changed based on a
# download.
tool_dependency, filtered_actions, dir = \
- step_manager.execute_step( app=self.app,
- tool_dependency=tool_dependency,
+ step_manager.execute_step( tool_dependency=tool_dependency,
package_name=package_name,
actions=actions,
action_type=action_type,
@@ -102,8 +102,7 @@
with lcd( current_dir ):
action_type, action_dict = action_tup
tool_dependency, tmp_filtered_actions, tmp_dir = \
- step_manager.execute_step( app=self.app,
- tool_dependency=tool_dependency,
+ step_manager.execute_step( tool_dependency=tool_dependency,
package_name=package_name,
actions=actions,
action_type=action_type,
@@ -154,7 +153,7 @@
"""
attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ]
installed_packages = []
- tag_manager = TagManager()
+ tag_manager = TagManager( self.app )
# Parse the tool_dependencies.xml config.
tree, error_message = xml_util.parse_xml( tool_dependencies_config )
if tree is None:
@@ -192,8 +191,7 @@
# If the tool_dependency.type is 'set_environment', then the call to process_tag_set() will
# handle everything - no additional installation is necessary.
tool_dependency, proceed_with_install, action_elem_tuples = \
- tag_manager.process_tag_set( self.app,
- tool_shed_repository,
+ tag_manager.process_tag_set( tool_shed_repository,
tool_dependency,
elem,
name,
@@ -250,9 +248,9 @@
elems = [ action_elem ]
else:
elems = []
- step_manager = StepManager()
+ step_manager = StepManager( self.app )
tool_shed_repository_install_dir = self.get_tool_shed_repository_install_dir( tool_shed_repository )
- install_environment = InstallEnvironment( tool_shed_repository_install_dir, install_dir )
+ install_environment = InstallEnvironment( self.app, tool_shed_repository_install_dir, install_dir )
for action_elem in elems:
# Make sure to skip all comments, since they are now included in the XML tree.
if action_elem.tag != 'action':
@@ -260,8 +258,7 @@
action_dict = {}
action_type = action_elem.get( 'type', None )
if action_type is not None:
- action_dict = step_manager.prepare_step( app=self.app,
- tool_dependency=tool_dependency,
+ action_dict = step_manager.prepare_step( tool_dependency=tool_dependency,
action_type=action_type,
action_elem=action_elem,
action_dict=action_dict,
@@ -287,7 +284,7 @@
Install a tool dependency package defined by the XML element elem. The value of tool_dependencies is
a partial or full list of ToolDependency records associated with the tool_shed_repository.
"""
- tag_manager = TagManager()
+ tag_manager = TagManager( self.app )
# The value of package_name should match the value of the "package" type in the tool config's
# <requirements> tag set, but it's not required.
package_name = elem.get( 'name', None )
@@ -300,8 +297,7 @@
if tool_dependency is not None:
for package_elem in elem:
tool_dependency, proceed_with_install, actions_elem_tuples = \
- tag_manager.process_tag_set( self.app,
- tool_shed_repository,
+ tag_manager.process_tag_set( tool_shed_repository,
tool_dependency,
package_elem,
package_name,
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
@@ -17,7 +17,7 @@
return_code = self.file_append( env_entry, env_file, make_executable=make_executable )
self.return_code = self.return_code or return_code
return self.return_code
-
+
@staticmethod
def create_or_update_env_shell_file( install_dir, env_var_dict ):
env_var_action = env_var_dict[ 'action' ]
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
@@ -35,12 +35,13 @@
"""Object describing the environment built up as part of the process of building and installing a package."""
- def __init__( self, tool_shed_repository_install_dir, install_dir ):
+ def __init__( self, app, tool_shed_repository_install_dir, install_dir ):
"""
The value of the received tool_shed_repository_install_dir is the root installation directory
of the repository containing the tool dependency, and the value of the received install_dir is
the root installation directory of the tool dependency.
"""
+ self.app = app
self.env_shell_file_paths = []
self.install_dir = install_dir
self.tool_shed_repository_install_dir = tool_shed_repository_install_dir
@@ -122,9 +123,9 @@
log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) )
return env_vars
- def handle_command( self, app, tool_dependency, cmd, return_output=False ):
+ def handle_command( self, tool_dependency, cmd, return_output=False ):
"""Handle a command and log the results."""
- context = app.install_model.context
+ context = self.app.install_model.context
command = str( cmd )
output = self.handle_complex_command( command )
self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) )
@@ -137,7 +138,7 @@
print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY )
stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if output.return_code not in [ 0 ]:
- tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR
+ tool_dependency.status = self.app.install_model.ToolDependency.installation_status.ERROR
if stderr:
tool_dependency.error_message = unicodify( stderr )
elif stdout:
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
@@ -9,18 +9,18 @@
class StepManager( object ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.step_handlers_by_type = self.load_step_handlers()
def get_step_handler_by_type( self, type ):
return self.step_handlers_by_type.get( type, None )
- def execute_step( self, app, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions,
+ def execute_step( self, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions,
env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ):
if actions:
step_handler = self.get_step_handler_by_type( action_type )
- tool_dependency, filtered_actions, dir = step_handler.execute_step( app=app,
- tool_dependency=tool_dependency,
+ tool_dependency, filtered_actions, dir = step_handler.execute_step( tool_dependency=tool_dependency,
package_name=package_name,
actions=actions,
action_dict=action_dict,
@@ -35,39 +35,38 @@
return tool_dependency, filtered_actions, dir
def load_step_handlers( self ):
- step_handlers_by_type = dict( assert_directory_executable=step_handler.AssertDirectoryExecutable(),
- assert_directory_exists=step_handler.AssertDirectoryExists(),
- assert_file_executable=step_handler.AssertFileExecutable(),
- assert_file_exists=step_handler.AssertFileExists(),
- autoconf=step_handler.Autoconf(),
- change_directory=step_handler.ChangeDirectory(),
- chmod=step_handler.Chmod(),
- download_binary=step_handler.DownloadBinary(),
- download_by_url=step_handler.DownloadByUrl(),
- download_file=step_handler.DownloadFile(),
- make_directory=step_handler.MakeDirectory(),
- make_install=step_handler.MakeInstall(),
- move_directory_files=step_handler.MoveDirectoryFiles(),
- move_file=step_handler.MoveFile(),
- set_environment=step_handler.SetEnvironment(),
- set_environment_for_install=step_handler.SetEnvironmentForInstall(),
- setup_perl_environment=step_handler.SetupPerlEnvironment(),
- setup_r_environment=step_handler.SetupREnvironment(),
- setup_ruby_environment=step_handler.SetupRubyEnvironment(),
- setup_virtualenv=step_handler.SetupVirtualEnv(),
- shell_command=step_handler.ShellCommand(),
- template_command=step_handler.TemplateCommand() )
+ step_handlers_by_type = dict( assert_directory_executable=step_handler.AssertDirectoryExecutable( self.app ),
+ assert_directory_exists=step_handler.AssertDirectoryExists( self.app ),
+ assert_file_executable=step_handler.AssertFileExecutable( self.app ),
+ assert_file_exists=step_handler.AssertFileExists( self.app ),
+ autoconf=step_handler.Autoconf( self.app ),
+ change_directory=step_handler.ChangeDirectory( self.app ),
+ chmod=step_handler.Chmod( self.app ),
+ download_binary=step_handler.DownloadBinary( self.app ),
+ download_by_url=step_handler.DownloadByUrl( self.app ),
+ download_file=step_handler.DownloadFile( self.app ),
+ make_directory=step_handler.MakeDirectory( self.app ),
+ make_install=step_handler.MakeInstall( self.app ),
+ move_directory_files=step_handler.MoveDirectoryFiles( self.app ),
+ move_file=step_handler.MoveFile( self.app ),
+ set_environment=step_handler.SetEnvironment( self.app ),
+ set_environment_for_install=step_handler.SetEnvironmentForInstall( self.app ),
+ setup_perl_environment=step_handler.SetupPerlEnvironment( self.app ),
+ setup_r_environment=step_handler.SetupREnvironment( self.app ),
+ setup_ruby_environment=step_handler.SetupRubyEnvironment( self.app ),
+ setup_virtualenv=step_handler.SetupVirtualEnv( self.app ),
+ shell_command=step_handler.ShellCommand( self.app ),
+ template_command=step_handler.TemplateCommand( self.app ) )
return step_handlers_by_type
- def prepare_step( self, app, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download ):
"""
Prepare the recipe step for later execution. This generally alters the received action_dict
with new information needed during this step's execution.
"""
if action_elem is not None:
step_handler = self.get_step_handler_by_type( action_type )
- action_dict = step_handler.prepare_step( app=app,
- tool_dependency=tool_dependency,
+ action_dict = step_handler.prepare_step( tool_dependency=tool_dependency,
action_elem=action_elem,
action_dict=action_dict,
install_environment=install_environment,
@@ -76,18 +75,18 @@
class TagManager( object ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.tag_handlers = self.load_tag_handlers()
def get_tag_handler_by_tag( self, tag ):
return self.tag_handlers.get( tag, None )
- def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
tag_handler = self.get_tag_handler_by_tag( package_elem.tag )
tool_dependency, proceed_with_install, action_elem_tuples = \
- tag_handler.process_tag_set( app,
- tool_shed_repository,
+ tag_handler.process_tag_set( tool_shed_repository,
tool_dependency,
package_elem,
package_name,
@@ -97,10 +96,10 @@
return tool_dependency, proceed_with_install, action_elem_tuples
def load_tag_handlers( self ):
- tag_handlers = dict( environment_variable=tag_handler.SetEnvironment(),
- install=tag_handler.Install(),
- package=tag_handler.Package(),
- readme=tag_handler.ReadMe(),
- repository=tag_handler.Repository(),
- set_environment=tag_handler.SetEnvironment() )
+ tag_handlers = dict( environment_variable=tag_handler.SetEnvironment( self.app ),
+ install=tag_handler.Install( self.app ),
+ package=tag_handler.Package( self.app ),
+ readme=tag_handler.ReadMe( self.app ),
+ repository=tag_handler.Repository( self.app ),
+ set_environment=tag_handler.SetEnvironment( self.app ) )
return tag_handlers
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -180,17 +180,18 @@
class RecipeStep( object ):
"""Abstract class that defines a standard format for handling recipe steps when installing packages."""
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
raise "Unimplemented Method"
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
raise "Unimplemented Method"
class AssertDirectoryExecutable( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'assert_directory_executable'
def assert_directory_executable( self, full_path ):
@@ -209,7 +210,7 @@
return True
return False
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Make sure a symbolic link or directory on disk exists and is executable, but is not a file.
@@ -221,16 +222,16 @@
else:
full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
if not self.assert_directory_executable( full_path=full_path ):
- status = app.install_model.ToolDependency.installation_status.ERROR
+ status = self.app.install_model.ToolDependency.installation_status.ERROR
error_message = 'The path %s is not a directory or is not executable by the owner.' % str( full_path )
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency,
status=status,
error_message=error_message,
remove_from_disk=False )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="assert_executable">$INSTALL_DIR/mira/my_file</action>
if action_elem.text:
action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -239,7 +240,8 @@
class AssertDirectoryExists( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'assert_directory_exists'
def assert_directory_exists( self, full_path ):
@@ -254,7 +256,7 @@
return True
return False
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Make sure a a symbolic link or directory on disk exists, but is not a file. Since this
@@ -266,16 +268,16 @@
else:
full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
if not self.assert_directory_exists( full_path=full_path ):
- status = app.install_model.ToolDependency.installation_status.ERROR
+ status = self.app.install_model.ToolDependency.installation_status.ERROR
error_message = 'The path %s is not a directory or does not exist.' % str( full_path )
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency,
status=status,
error_message=error_message,
remove_from_disk=False )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="make_directory">$INSTALL_DIR/mira</action>
if action_elem.text:
action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -284,7 +286,8 @@
class AssertFileExecutable( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'assert_file_executable'
def assert_file_executable( self, full_path ):
@@ -303,7 +306,7 @@
return True
return False
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Make sure a symbolic link or file on disk exists and is executable, but is not a directory.
@@ -315,16 +318,16 @@
else:
full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
if not self.assert_file_executable( full_path=full_path ):
- status = app.install_model.ToolDependency.installation_status.ERROR
+ status = self.app.install_model.ToolDependency.installation_status.ERROR
error_message = 'The path %s is not a file or is not executable by the owner.' % str( full_path )
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency,
status=status,
error_message=error_message,
remove_from_disk=False )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="assert_executable">$INSTALL_DIR/mira/my_file</action>
if action_elem.text:
action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -333,7 +336,8 @@
class AssertFileExists( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'assert_file_exists'
def assert_file_exists( self, full_path ):
@@ -349,7 +353,7 @@
return True
return False
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Make sure a symbolic link or file on disk exists, but is not a directory. Since this
@@ -361,16 +365,16 @@
else:
full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
if not self.assert_file_exists( full_path=full_path ):
- status = app.install_model.ToolDependency.installation_status.ERROR
+ status = self.app.install_model.ToolDependency.installation_status.ERROR
error_message = 'The path %s is not a file or does not exist.' % str( full_path )
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency,
status=status,
error_message=error_message,
remove_from_disk=False )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="assert_on_path">$INSTALL_DIR/mira/my_file</action>
if action_elem.text:
action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -379,10 +383,11 @@
class Autoconf( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'autoconf'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Handle configure, make and make install in a shell, allowing for configuration options. Since this
@@ -396,15 +401,14 @@
else:
pre_cmd = './configure --prefix=$INSTALL_DIR %s && make && make install' % configure_opts
cmd = install_environment.build_command( basic_util.evaluate_template( pre_cmd, install_environment ) )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
# The caller should check the status of the returned tool_dependency since this function
# does nothing with the return_code.
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# Handle configure, make and make install allow providing configuration options
if action_elem.text:
configure_opts = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -414,10 +418,11 @@
class ChangeDirectory( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'change_directory'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Change the working directory in a shell. Since this class is not used in the initial download stage,
@@ -436,7 +441,7 @@
dir = current_dir
return tool_dependency, None, dir
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="change_directory">PHYLIP-3.6b</action>
if action_elem.text:
action_dict[ 'directory' ] = action_elem.text
@@ -445,10 +450,11 @@
class Chmod( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'chmod'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Change the mode setting for certain files in the installation environment. Since this class is not
@@ -462,7 +468,7 @@
log.debug( 'Invalid file %s specified, ignoring %s action.', target_file, action_type )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# Change the read, write, and execute bits on a file.
# <action type="chmod">
# <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file>
@@ -492,7 +498,8 @@
class DownloadBinary( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'download_binary'
def download_binary( self, url, work_dir ):
@@ -510,7 +517,7 @@
filtered_actions.append( action )
return filtered_actions
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Download a binary file. If the value of initial_download is True, the recipe steps will be
@@ -561,7 +568,7 @@
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
platform_info_dict = tool_dependency_util.get_platform_info_dict()
platform_info_dict[ 'name' ] = str( tool_dependency.name )
platform_info_dict[ 'version' ] = str( tool_dependency.version )
@@ -584,10 +591,11 @@
class DownloadByUrl( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'download_by_url'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Download a file via HTTP. If the value of initial_download is True, the recipe steps will be
@@ -622,7 +630,7 @@
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="download_by_url">
# http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…
# </action>
@@ -638,10 +646,11 @@
class DownloadFile( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'download_file'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Download a file. If the value of initial_download is True, the recipe steps will be
@@ -667,7 +676,7 @@
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action>
if action_elem.text:
action_dict[ 'url' ] = action_elem.text
@@ -680,10 +689,11 @@
class MakeDirectory( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'make_directory'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Make a directory on disk. Since this class is not used in the initial download stage, no recipe step
@@ -700,7 +710,7 @@
if not os.path.exists( full_path ):
os.makedirs( full_path )
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="make_directory">$INSTALL_DIR/lib/python</action>
if action_elem.text:
action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -709,10 +719,11 @@
class MakeInstall( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'make_install'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Execute a make_install command in a shell. Since this class is not used in the initial download stage,
@@ -722,15 +733,14 @@
with settings( warn_only=True ):
make_opts = action_dict.get( 'make_opts', '' )
cmd = install_environment.build_command( 'make %s && make install' % make_opts )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
# The caller should check the status of the returned tool_dependency since this function
# does nothing with the return_code.
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# make; make install; allow providing make options
if action_elem.text:
make_opts = basic_util.evaluate_template( action_elem.text, install_environment )
@@ -740,10 +750,11 @@
class MoveDirectoryFiles( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'move_directory_files'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Move a directory of files. Since this class is not used in the initial download stage, no recipe step
@@ -774,7 +785,7 @@
for source_file, destination_file in regular_files:
shutil.move( source_file, destination_file )
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="move_directory_files">
# <source_directory>bin</source_directory>
# <destination_directory>$INSTALL_DIR/bin</destination_directory>
@@ -788,10 +799,11 @@
class MoveFile( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'move_file'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Move a file on disk. Since this class is not used in the initial download stage, no recipe step
@@ -803,7 +815,7 @@
rename_to=action_dict[ 'rename_to' ] )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="move_file" rename_to="new_file_name">
# <source>misc/some_file</source>
# <destination>$INSTALL_DIR/bin</destination>
@@ -816,10 +828,11 @@
class SetEnvironment( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'set_environment'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Configure an install environment. Since this class is not used in the initial download stage,
@@ -831,8 +844,7 @@
env_var_dicts = action_dict.get( 'environment_variable', [] )
for env_var_dict in env_var_dicts:
# Check for the presence of the $ENV[] key string and populate it if possible.
- env_var_dict = self.handle_environment_variables( app=app,
- install_environment=install_environment,
+ env_var_dict = self.handle_environment_variables( install_environment=install_environment,
tool_dependency=tool_dependency,
env_var_dict=env_var_dict,
set_prior_environment_commands=cmds )
@@ -842,7 +854,7 @@
return_code = env_file_builder.return_code
return tool_dependency, None, None
- def handle_environment_variables( self, app, install_environment, tool_dependency, env_var_dict,
+ def handle_environment_variables( self, install_environment, tool_dependency, env_var_dict,
set_prior_environment_commands ):
"""
This method works with with a combination of three tool dependency definition tag sets, which are defined
@@ -925,8 +937,7 @@
set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) )
command = ' ; '.join( set_prior_environment_commands )
# Run the command and capture the output.
- command_return = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ command_return = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=command,
return_output=True )
# And extract anything labeled with the name of the environment variable we're populating here.
@@ -944,7 +955,7 @@
env_var_dict[ 'value' ] = env_var_value
return env_var_dict
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# This function is only called for set environment actions as defined above, not within a <set_environment> tool
# dependency type. Here is an example of the tag set this function does handle:
# <action type="set_environment">
@@ -955,7 +966,7 @@
# <action type="set_environment">
# <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
# </action>
- env_manager = EnvManager( app )
+ env_manager = EnvManager( self.app )
env_var_dicts = []
for env_elem in action_elem:
if env_elem.tag == 'environment_variable':
@@ -971,10 +982,11 @@
class SetEnvironmentForInstall( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'set_environment_for_install'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Configure an environment for compiling a package. Since this class is not used in the initial
@@ -989,7 +1001,7 @@
install_environment.add_env_shell_file_paths( env_shell_file_paths )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="set_environment_for_install">
# <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056">
# <package name="numpy" version="1.7.1" />
@@ -1002,7 +1014,7 @@
# the current tool dependency package. See the package_matplotlib_1_2 repository in the test tool
# shed for a real-world example.
all_env_shell_file_paths = []
- env_manager = EnvManager( app )
+ env_manager = EnvManager( self.app )
for env_elem in action_elem:
if env_elem.tag == 'repository':
env_shell_file_paths = env_manager.get_env_shell_file_paths( env_elem )
@@ -1014,10 +1026,11 @@
class SetupPerlEnvironment( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'setup_purl_environment'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Initialize the environment for installing Perl packages. The class is called during the initial
@@ -1076,8 +1089,7 @@
return tool_dependency, None, None
with lcd( tmp_work_dir ):
cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
if return_code:
@@ -1089,8 +1101,7 @@
# cpanm should be installed with the parent perl distribution, otherwise this will not work.
cmd += '''cpanm --local-lib=$INSTALL_DIR %s''' % ( perl_package )
cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
if return_code:
@@ -1115,7 +1126,7 @@
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# setup a Perl environment.
# <action type="setup_perl_environment">
# <repository name="package_perl_5_18" owner="bgruening">
@@ -1129,7 +1140,7 @@
# with each repository. This will potentially update the value of the 'env_shell_file_paths' entry
# in action_dict.
all_env_shell_file_paths = []
- env_manager = EnvManager( app )
+ env_manager = EnvManager( self.app )
action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths,
action_elem,
action_dict )
@@ -1149,10 +1160,11 @@
class SetupREnvironment( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'setup_r_environment'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Initialize the environment for installing R packages. The class is called during the initial
@@ -1198,8 +1210,7 @@
Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % \
( str( tarball_name ) )
cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
if return_code:
@@ -1219,7 +1230,7 @@
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# setup an R environment.
# <action type="setup_r_environment">
# <repository name="package_r_3_0_1" owner="bgruening">
@@ -1232,7 +1243,7 @@
# associated with each repository. This will potentially update the value of the
# 'env_shell_file_paths' entry in action_dict.
all_env_shell_file_paths = []
- env_manager = EnvManager( app )
+ env_manager = EnvManager( self.app )
action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths,
action_elem,
action_dict )
@@ -1247,10 +1258,11 @@
class SetupRubyEnvironment( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'setup_ruby_environment'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Initialize the environment for installing Ruby packages. The class is called during the initial
@@ -1313,8 +1325,7 @@
cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
gem install %s''' % ( gem )
cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
if return_code:
@@ -1338,7 +1349,7 @@
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# setup a Ruby environment.
# <action type="setup_ruby_environment">
# <repository name="package_ruby_2_0" owner="bgruening">
@@ -1353,7 +1364,7 @@
# associated with each repository. This will potentially update the value of the
# 'env_shell_file_paths' entry in action_dict.
all_env_shell_file_paths = []
- env_manager = EnvManager( app )
+ env_manager = EnvManager( self.app )
action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths,
action_elem,
action_dict )
@@ -1381,10 +1392,11 @@
class SetupVirtualEnv( Download, RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'setup_virtualenv'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Initialize a virtual environment for installing packages. If initial_download is True, the recipe
@@ -1395,8 +1407,8 @@
# This class is not currently used during stage 1 of the installation process, so filter_actions
# are not affected, and dir is not set. Enhancements can easily be made to this function if this
# class is needed in stage 1.
- venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) )
- if not self.install_virtualenv( app, install_environment, venv_src_directory ):
+ venv_src_directory = os.path.abspath( os.path.join( self.app.config.tool_dependency_dir, '__virtualenv_src' ) )
+ if not self.install_virtualenv( install_environment, venv_src_directory ):
log.debug( 'Unable to install virtualenv' )
return tool_dependency, None, None
requirements = action_dict[ 'requirements' ]
@@ -1438,8 +1450,7 @@
else:
install_command = "%s && %s" % ( install_command, line_install_command )
full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command )
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=full_setup_command,
return_output=False )
if return_code:
@@ -1448,7 +1459,7 @@
return tool_dependency, None, None
site_packages_directory, site_packages_directory_list = \
self.__get_site_packages_directory( install_environment,
- app,
+ self.app,
tool_dependency,
python_cmd,
venv_directory )
@@ -1462,7 +1473,7 @@
return_code = env_file_builder.return_code
return tool_dependency, None, None
- def install_virtualenv( self, app, install_environment, venv_dir ):
+ def install_virtualenv( self, install_environment, venv_dir ):
if not os.path.exists( venv_dir ):
with install_environment.make_tmp_dir() as work_dir:
downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1]
@@ -1476,7 +1487,7 @@
shutil.move( full_path_to_dir, venv_dir )
return True
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="setup_virtualenv" />
## Install requirements from file requirements.txt of downloaded bundle - or -
# <action type="setup_virtualenv">tools/requirements.txt</action>
@@ -1511,8 +1522,7 @@
os.path.join( venv_directory, "bin", "python" ),
r"""%s -c 'import os, sys; print os.path.join( sys.prefix, "lib", "python" + sys.version[:3], "site-packages" )'""" % \
os.path.join( venv_directory, "bin", "python" ) ]:
- output = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ output = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=site_packages_command,
return_output=True )
site_packages_directory_list.append( output.stdout )
@@ -1522,10 +1532,11 @@
class ShellCommand( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'shell_command'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Execute a command in a shell. If the value of initial_download is True, the recipe steps will
@@ -1546,15 +1557,14 @@
with settings( warn_only=True ):
# The caller should check the status of the returned tool_dependency since this function
# does nothing with return_code.
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
if initial_download:
return tool_dependency, filtered_actions, dir
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="shell_command">make</action>
action_elem_text = basic_util.evaluate_template( action_elem.text, install_environment )
if action_elem_text:
@@ -1564,10 +1574,11 @@
class TemplateCommand( RecipeStep ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.type = 'template_command'
- def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+ def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
"""
Execute a template command in a shell. If the value of initial_download is True, the recipe steps
@@ -1586,13 +1597,12 @@
cmd = fill_template( '#from fabric.api import env\n%s' % action_dict[ 'command' ], context=env_vars )
# The caller should check the status of the returned tool_dependency since this function
# does nothing with return_code.
- return_code = install_environment.handle_command( app=app,
- tool_dependency=tool_dependency,
+ return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
return_output=False )
return tool_dependency, None, None
- def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
+ def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# Default to Cheetah as it's the first template language supported.
language = action_elem.get( 'language', 'cheetah' ).lower()
if language == 'cheetah':
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -20,24 +20,25 @@
class RecipeTag( object ):
"""Abstract class that defines a standard format for handling recipe tags when installing packages."""
- def process_tag_set( app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
raise "Unimplemented Method"
class Install( RecipeTag ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.tag = 'install'
- def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
# <install version="1.0">
# Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository.
actions_elem_tuples = []
proceed_with_install = False
install_dir = \
- tool_dependency_util.get_tool_dependency_install_dir( app=app,
+ tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
@@ -57,7 +58,7 @@
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, proceed_with_install = \
- tool_dependency_util.sync_database_with_file_system( app,
+ tool_dependency_util.sync_database_with_file_system( self.app,
tool_shed_repository,
package_name,
package_version,
@@ -71,9 +72,9 @@
proceed_with_install = True
if proceed_with_install:
package_install_version = package_elem.get( 'version', '1.0' )
- status = app.install_model.ToolDependency.installation_status.INSTALLING
+ status = self.app.install_model.ToolDependency.installation_status.INSTALLING
tool_dependency = \
- tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_dependency_util.create_or_update_tool_dependency( app=self.app,
tool_shed_repository=tool_shed_repository,
name=package_name,
version=package_version,
@@ -95,7 +96,7 @@
error_message += 'tag set.'
# Since there was an installation error, update the tool dependency status to Error.
# The remove_installation_path option must be left False here.
- tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app,
+ tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app,
tool_dependency,
error_message,
remove_installation_path=False )
@@ -106,29 +107,30 @@
class Package( RecipeTag ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.tag = 'package'
- def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
action_elem_tuples = []
proceed_with_install = False
# Only install the tool_dependency if it is not already installed and it is associated with a database
# record in the received tool_dependencies.
if package_name and package_version:
- dependencies_ignored = not app.toolbox.dependency_manager.uses_tool_shed_dependencies()
+ dependencies_ignored = not self.app.toolbox.dependency_manager.uses_tool_shed_dependencies()
if dependencies_ignored:
attr_tups_of_dependencies_for_install = []
log.debug( "Skipping installation of tool dependency package %s because tool shed dependency resolver not enabled." % \
str( package_name ) )
# Tool dependency resolves have been configured and they do not include the tool shed. Do not install package.
- if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY:
+ if self.app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY:
## TODO: Do something here such as marking it installed or configured externally.
pass
tool_dependency = \
- tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.ERROR,
+ status=self.app.install_model.ToolDependency.installation_status.ERROR,
error_message=None,
remove_from_disk=False )
else:
@@ -142,10 +144,11 @@
class ReadMe( RecipeTag ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.tag = 'readme'
- def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
# Nothing to be done.
action_elem_tuples = []
@@ -155,12 +158,13 @@
class Repository( RecipeTag ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.tag = 'repository'
- def create_temporary_tool_dependencies_config( self, app, tool_shed_url, name, owner, changeset_revision ):
+ def create_temporary_tool_dependencies_config( self, tool_shed_url, name, owner, changeset_revision ):
"""Make a call to the tool shed to get the required repository's tool_dependencies.xml file."""
- tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed_url )
if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed because one or more of the "
message += "following required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
@@ -169,7 +173,7 @@
params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/get_tool_dependencies_config_contents%s' % params )
- text = common_util.tool_shed_get( app, tool_shed_url, url )
+ text = common_util.tool_shed_get( self.app, tool_shed_url, url )
if text:
# Write the contents to a temporary file on disk so it can be reloaded and parsed.
fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-cttdc" )
@@ -185,7 +189,7 @@
raise Exception( message )
return None
- def create_tool_dependency_with_initialized_env_sh_file( self, app, dependent_install_dir, tool_shed_repository,
+ def create_tool_dependency_with_initialized_env_sh_file( self, dependent_install_dir, tool_shed_repository,
required_repository, package_name, package_version, tool_dependencies_config ):
"""
Create or get a tool_dependency record that is defined by the received package_name and package_version.
@@ -215,7 +219,7 @@
# Check the database to see if we have a record for the required tool dependency (we may not which is ok). If we
# find a record, we need to see if it is in an error state and if so handle it appropriately.
required_tool_dependency = \
- tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app,
+ tool_dependency_util.get_tool_dependency_by_name_version_type_repository( self.app,
required_repository,
required_td_package_name,
required_td_package_version,
@@ -223,29 +227,29 @@
if required_td_package_name == package_name and required_td_package_version == package_version:
# Get or create a database tool_dependency record with which the installed package on disk will be associated.
tool_dependency = \
- tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_dependency_util.create_or_update_tool_dependency( app=self.app,
tool_shed_repository=tool_shed_repository,
name=package_name,
version=package_version,
type='package',
- status=app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
+ status=self.app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
set_status=True )
# Create an env.sh file for the tool_dependency whose first line will source the env.sh file located in
# the path defined by required_tool_dependency_env_file_path. It doesn't matter if the required env.sh
# file currently exists..
required_tool_dependency_env_file_path = \
- tool_dependency_util.get_required_repository_package_env_sh_path( app,
+ tool_dependency_util.get_required_repository_package_env_sh_path( self.app,
package_name,
package_version,
required_repository )
- env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( app ) )
+ env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( self.app ) )
env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path )
return_code = env_file_builder.return_code
if return_code:
error_message = 'Error defining env.sh file for package %s, return_code: %s' % \
( str( package_name ), str( return_code ) )
tool_dependency = \
- tool_dependency_util.handle_tool_dependency_installation_error( app,
+ tool_dependency_util.handle_tool_dependency_installation_error( self.app,
tool_dependency,
error_message,
remove_installation_path=False )
@@ -253,47 +257,47 @@
error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \
( str( required_tool_dependency.name ), str( required_tool_dependency.version ), str( required_tool_dependency.status ) )
tool_dependency = \
- tool_dependency_util.handle_tool_dependency_installation_error( app,
+ tool_dependency_util.handle_tool_dependency_installation_error( self.app,
tool_dependency,
error_message,
remove_installation_path=False )
else:
tool_dependency = \
- tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.INSTALLED )
+ status=self.app.install_model.ToolDependency.installation_status.INSTALLED )
tool_dependencies.append( tool_dependency )
return tool_dependencies
- def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, app, tool_shed_url, name, owner, changeset_revision ):
- sa_session = app.install_model.context
+ def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, tool_shed_url, name, owner, changeset_revision ):
+ sa_session = self.app.install_model.context
# The protocol is not stored, but the port is if it exists.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
- tool_shed_repository = sa_session.query( app.install_model.ToolShedRepository ) \
- .filter( and_( app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
- app.install_model.ToolShedRepository.table.c.name == name,
- app.install_model.ToolShedRepository.table.c.owner == owner,
- app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+ tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \
+ .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
+ self.app.install_model.ToolShedRepository.table.c.name == name,
+ self.app.install_model.ToolShedRepository.table.c.owner == owner,
+ self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
.first()
if tool_shed_repository:
return tool_shed_repository
# The tool_shed_repository must have been updated to a newer changeset revision than the one defined in the repository_dependencies.xml file,
# so call the tool shed to get all appropriate newer changeset revisions.
- text = suc.get_updated_changeset_revisions_from_tool_shed( app, tool_shed_url, name, owner, changeset_revision )
+ text = suc.get_updated_changeset_revisions_from_tool_shed( self.app, tool_shed_url, name, owner, changeset_revision )
if text:
changeset_revisions = listify( text )
for changeset_revision in changeset_revisions:
- tool_shed_repository = sa_session.query( app.install_model.ToolShedRepository ) \
- .filter( and_( app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
- app.install_model.ToolShedRepository.table.c.name == name,
- app.install_model.ToolShedRepository.table.c.owner == owner,
- app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+ tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \
+ .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
+ self.app.install_model.ToolShedRepository.table.c.name == name,
+ self.app.install_model.ToolShedRepository.table.c.owner == owner,
+ self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
.first()
if tool_shed_repository:
return tool_shed_repository
return None
- def handle_complex_repository_dependency_for_package( self, app, elem, package_name, package_version, tool_shed_repository,
+ def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository,
from_tool_migration_manager=False ):
"""
Inspect the repository defined by a complex repository dependency definition and take certain steps to
@@ -310,8 +314,7 @@
required_repository_owner = elem.attrib[ 'owner' ]
default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
required_repository = \
- self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app,
- tool_shed,
+ self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( tool_shed,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
@@ -320,7 +323,7 @@
required_repository_changeset_revision = required_repository.installed_changeset_revision
# Define the installation directory for the required tool dependency package in the required repository.
required_repository_package_install_dir = \
- tool_dependency_util.get_tool_dependency_install_dir( app=app,
+ tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=required_repository_name,
repository_owner=required_repository_owner,
repository_changeset_revision=required_repository_changeset_revision,
@@ -330,7 +333,7 @@
# Define this dependent repository's tool dependency installation directory that will contain
# the env.sh file with a path to the required repository's installed tool dependency package.
dependent_install_dir = \
- tool_dependency_util.get_tool_dependency_install_dir( app=app,
+ tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
@@ -350,7 +353,7 @@
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, can_install_tool_dependency = \
- tool_dependency_util.sync_database_with_file_system( app,
+ tool_dependency_util.sync_database_with_file_system( self.app,
tool_shed_repository,
package_name,
package_version,
@@ -370,7 +373,7 @@
if required_repository.is_deactivated_or_installed:
if not os.path.exists( required_repository_package_install_dir ):
print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir )
- repo_files_dir = required_repository.repo_files_directory( app )
+ repo_files_dir = required_repository.repo_files_directory( self.app )
tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
if tool_dependencies_config:
config_to_use = tool_dependencies_config
@@ -381,7 +384,7 @@
else:
# Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
# should be updated if it's not current.
- text = suc.get_updated_changeset_revisions_from_tool_shed( app=app,
+ text = suc.get_updated_changeset_revisions_from_tool_shed( app=self.app,
tool_shed_url=tool_shed,
name=required_repository_name,
owner=required_repository_owner,
@@ -391,15 +394,13 @@
# The list of changeset revisions is in reverse order, so the newest will be first.
required_repository_changeset_revision = updated_changeset_revisions[ 0 ]
# Make a call to the tool shed to get the required repository's tool_dependencies.xml file.
- tmp_filename = self.create_temporary_tool_dependencies_config( app,
- tool_shed,
+ tmp_filename = self.create_temporary_tool_dependencies_config( tool_shed,
required_repository_name,
required_repository_owner,
required_repository_changeset_revision )
config_to_use = tmp_filename
handled_tool_dependencies = \
- self.create_tool_dependency_with_initialized_env_sh_file( app=app,
- dependent_install_dir=dependent_install_dir,
+ self.create_tool_dependency_with_initialized_env_sh_file( dependent_install_dir=dependent_install_dir,
tool_shed_repository=tool_shed_repository,
required_repository=required_repository,
package_name=package_name,
@@ -412,19 +413,18 @@
raise Exception( message )
return handled_tool_dependencies
- def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
# We have a complex repository dependency definition.
action_elem_tuples = []
proceed_with_install = False
- rd_tool_dependencies = self.handle_complex_repository_dependency_for_package( app,
- package_elem,
+ rd_tool_dependencies = self.handle_complex_repository_dependency_for_package( package_elem,
package_name,
package_version,
tool_shed_repository,
from_tool_migration_manager=from_tool_migration_manager )
for rd_tool_dependency in rd_tool_dependencies:
- if rd_tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR:
+ if rd_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
# We'll log the error here, but continue installing packages since some may not require this dependency.
print "Error installing tool dependency for required repository: %s" % str( rd_tool_dependency.error_message )
return tool_dependency, proceed_with_install, action_elem_tuples
@@ -441,10 +441,11 @@
class SetEnvironment( RecipeTag ):
- def __init__( self ):
+ def __init__( self, app ):
+ self.app = app
self.tag = 'set_environment'
- def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
+ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
# We need to handle two tag sets for package_elem here, this:
# <set_environment version="1.0">
@@ -459,21 +460,21 @@
else:
attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependency_db_records ]
try:
- tool_dependencies = self.set_environment( app, package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install )
+ tool_dependencies = self.set_environment( package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install )
except Exception, e:
error_message = "Error setting environment for tool dependency: %s" % str( e )
log.debug( error_message )
for tool_dependency in tool_dependencies:
- if tool_dependency and tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR:
+ if tool_dependency and tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
# Since there was an installation error, update the tool dependency status to Error. The
# remove_installation_path option must be left False here.
- tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app,
+ tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app,
tool_dependency,
error_message,
remove_installation_path=False )
return tool_dependency, proceed_with_install, action_elem_tuples
- def set_environment( self, app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ):
+ def set_environment( self, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ):
"""
Create a ToolDependency to set an environment variable. This is different from the process used to
set an environment variable that is associated with a package. An example entry in a tool_dependencies.xml
@@ -497,10 +498,10 @@
# <set_environment version="1.0">
# <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" />
# </set_environment>
- env_manager = EnvManager( app )
+ env_manager = EnvManager( self.app )
tool_dependencies = []
env_var_version = elem.get( 'version', '1.0' )
- tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( app ) )
+ tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( self.app ) )
if elem.tag == 'environment_variable':
# <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
elems = [ elem ]
@@ -520,23 +521,24 @@
attr_tup = ( env_var_name, None, 'set_environment' )
if attr_tup in attr_tups_of_dependencies_for_install:
install_dir = \
- tool_dependency_util.get_tool_dependency_install_dir( app=app,
+ tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='set_environment',
tool_dependency_name=env_var_name,
tool_dependency_version=None )
- install_environment = InstallEnvironment( tool_shed_repository_install_dir=tool_shed_repository_install_dir,
+ install_environment = InstallEnvironment( app=self.app,
+ tool_shed_repository_install_dir=tool_shed_repository_install_dir,
install_dir=install_dir )
env_var_dict = env_manager.create_env_var_dict( elem=env_var_elem,
install_environment=install_environment )
if env_var_dict:
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
- status = app.install_model.ToolDependency.installation_status.INSTALLING
+ status = self.app.install_model.ToolDependency.installation_status.INSTALLING
tool_dependency = \
- tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_dependency_util.create_or_update_tool_dependency( app=self.app,
tool_shed_repository=tool_shed_repository,
name=env_var_name,
version=None,
@@ -551,19 +553,19 @@
error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \
( str( tool_dependency.name ), str( return_code ) )
log.debug( error_message )
- status = app.install_model.ToolDependency.installation_status.ERROR
+ status = self.app.install_model.ToolDependency.installation_status.ERROR
tool_dependency = \
- tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message,
remove_from_disk=False )
else:
- if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR,
- app.install_model.ToolDependency.installation_status.INSTALLED ]:
- status = app.install_model.ToolDependency.installation_status.INSTALLED
+ if tool_dependency.status not in [ self.app.install_model.ToolDependency.installation_status.ERROR,
+ self.app.install_model.ToolDependency.installation_status.INSTALLED ]:
+ status = self.app.install_model.ToolDependency.installation_status.INSTALLED
tool_dependency = \
- tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=status,
error_message=None,
@@ -572,9 +574,9 @@
( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) )
else:
error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
- status = app.install_model.ToolDependency.installation_status.ERROR
+ status = self.app.install_model.ToolDependency.installation_status.ERROR
tool_dependency = \
- tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message,
diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -17,8 +17,6 @@
from tool_shed.util import tool_util
from tool_shed.util import xml_util
-from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager
-
log = logging.getLogger( __name__ )
def activate_repository( app, repository ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
commit/galaxy-central: guerler: Charts: Minor fixes, hide tooltip, patch nvd3 library
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ac9a4a915fde/
Changeset: ac9a4a915fde
User: guerler
Date: 2014-06-17 14:36:47
Summary: Charts: Minor fixes, hide tooltip, patch nvd3 library
Affected #: 5 files
diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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(){for(var e in this.queue)if(this.counter==0){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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.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_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,o=$("<svg/>");o.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var u="",a=0;t.find("svg").each(function(){var e=$(this),t=$('<g transform="translate('+a+', 0)">');t.append(e.clone().find("g").first()),o.append(t),a+=i});var u=s.serializeToString(o[0]);window.location.href="data:none/none;base64,"+btoa(u)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}return{createPNG:t,createSVG:s}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG or SVG file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file-o",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,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=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),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)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+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,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),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.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$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.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<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.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div 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t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});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.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var 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title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{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 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return 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arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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(){for(var e in this.queue)if(this.counter==0){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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));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,100),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(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.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_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,o=$("<svg/>");o.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var u="",a=0;t.find("svg").each(function(){var e=$(this),t=$('<g transform="translate('+a+', 0)">');t.append(e.clone().find("g").first()),o.append(t),a+=i});var u=s.serializeToString(o[0]);window.location.href="data:none/none;base64,"+btoa(u)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}return{createPNG:t,createSVG:s}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG or SVG file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file-o",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(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)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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.del(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="ui-table '+e.cls+'">'+"<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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_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({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div 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t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var 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title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{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 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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large"})}),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/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{jqplot_bar:p,nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f,jqplot_line:d,jqplot_scatter:v,jqplot_boxplot:m,others_heatmap:g,others_heatmap_cluster:y}})}),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()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
@@ -21,15 +21,6 @@
$.extend(true, plot_config, {
seriesDefaults: {
renderer : $.jqplot.BarRenderer
- },
- axes: {
- xaxis: {
- pad : 1.2
- },
-
- yaxis: {
- pad : 1.2
- }
}
});
}
diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
@@ -11,27 +11,13 @@
seriesColors: d3.scale.category20().range(),
seriesDefaults: {
renderer : $.jqplot.LineRenderer,
- //lineWidth : 1, // Width of the line in pixels.
+ //lineWidth : 1, // width of the line in pixels.
shadow : false, // show shadow or not.
showLine : true, // whether to render the line segments or not.
-
- // Show point labels to the right ('e'ast) of each bar.
- // edgeTolerance of -15 allows labels flow outside the grid
- // up to 15 pixels. If they flow out more than that, they
- // will be hidden.
- //pointLabels : { show: true, location: 'e', edgeTolerance: -15 },
- // Rotate the bar shadow as if bar is lit from top right.
- //shadowAngle : 135,
- // Here's where we tell the chart it is oriented horizontally.
rendererOptions: {
shadowDepth : 0,
//barDirection : 'horizontal',
- //barPadding : 5,
- //barMargin : 2,
- //barWidth : Math.max(0.5 / chart.groups.length, 2),
- barWidth : 10,
- //fillToZero : true,
- //stackedValue : true
+ barWidth : 1
},
markerRenderer : $.jqplot.MarkerRenderer,
markerOptions: {
@@ -43,9 +29,9 @@
shadow : false, // wether to draw shadow on marker or not.
shadowAngle : 45, // angle of the shadow. Clockwise from x axis.
shadowOffset : 1, // offset from the line of the shadow,
- shadowDepth : 3, // Number of strokes to make when drawing shadow. Each stroke
+ shadowDepth : 3, // number of strokes to make when drawing shadow. Each stroke
// offset by shadowOffset from the last.
- shadowAlpha : 0.07 // Opacity of the shadow
+ shadowAlpha : 0.07 // opacity of the shadow
}
},
@@ -104,7 +90,7 @@
series: []
};
- // Show the legend and put it outside the grid
+ // show the legend and put it outside the grid
if (chart.settings.get('show_legend') == 'true') {
plot_config.legend = {
renderer : $.jqplot.EnhancedLegendRenderer,
diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
--- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
+++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
@@ -65,7 +65,7 @@
this._makeTickFormat('y');
// add tooltip
- this.tooltip = d3.select('.charts-viewport').append('div')
+ this.tooltip = d3.select('.charts-viewport-container').append('div')
.attr('class', 'charts-tooltip')
.style(this.options.style)
.style('opacity', 0);
@@ -210,12 +210,16 @@
self.tooltip.style('opacity', 0.9);
self.tooltip .html(self._templateTooltip(d))
.style('left', (d3.event.pageX) + 'px')
- .style('top', (d3.event.pageY - 28) + 'px');
+ .style('top', (d3.event.pageY - 20) + 'px');
})
.on('mouseout', function(d) {
self.tooltip.style('opacity', 0);
});
+ // initially hide tooltips
+ this.tooltip.style('opacity', 0);
+
+ // exit
boxes.exit().remove();
},
diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
--- a/config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
+++ b/config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
@@ -11104,10 +11104,10 @@
var pX = getX(point,pointIndex);
var pY = getY(point,pointIndex);
- return [x(pX)+ Math.random() * 1e-7,
- y(pY)+ Math.random() * 1e-7,
+ return [x(pX),
+ y(pY),
groupIndex,
- pointIndex, point]; //temp hack to add noise untill I think of a better way so there are no duplicates
+ pointIndex, point];
})
.filter(function(pointArray, pointIndex) {
return pointActive(pointArray[4], pointIndex); // Issue #237.. move filter to after map, so pointIndex is correct!
@@ -11158,6 +11158,18 @@
[width + 10,-10]
]);
+ // delete duplicates from vertices - essential assumption for d3.geom.voronoi
+ var epsilon = 1e-6; // d3 uses 1e-6 to determine equivalence.
+ vertices = vertices.sort(function(a,b){return ((a[0] - b[0]) || (a[1] - b[1]))});
+ for (var i = 0; i < vertices.length - 1; ) {
+ if ((Math.abs(vertices[i][0] - vertices[i+1][0]) < epsilon) &&
+ (Math.abs(vertices[i][1] - vertices[i+1][1]) < epsilon)) {
+ vertices.splice(i+1, 1);
+ } else {
+ i++;
+ }
+ }
+
var voronoi = d3.geom.voronoi(vertices).map(function(d, i) {
return {
'data': bounds.clip(d),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Update LWR client and synchronized modules through LWR changeset 148132f.
by commits-noreply＠bitbucket.org 17 Jun '14
by commits-noreply＠bitbucket.org 17 Jun '14
17 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/45df9d2018e1/
Changeset: 45df9d2018e1
User: jmchilton
Date: 2014-06-17 06:14:59
Summary: Update LWR client and synchronized modules through LWR changeset 148132f.
Mostly style fixes but also adds ability to configure LWR file staging actions with YAML instead of JSON.
Affected #: 6 files
diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/action_mapper.py
--- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py
+++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py
@@ -11,6 +11,7 @@
from re import escape
import galaxy.util
from galaxy.util.bunch import Bunch
+from .config_util import read_file
from .util import directory_files
from .util import unique_path_prefix
from .transport import get_file
@@ -160,7 +161,7 @@
def __client_to_config(self, client):
action_config_path = client.action_config_path
if action_config_path:
- config = load(open(action_config_path, 'rb'))
+ config = read_file(action_config_path)
else:
config = dict()
config["default_action"] = client.default_file_action
@@ -434,7 +435,7 @@
elif value is REQUIRED_ACTION_KWD:
message_template = "action_type %s requires key word argument %s"
message = message_template % (action_type, key)
- raise Exception( message )
+ raise Exception(message)
self.action_type = action_type
self.action_kwds = action_kwds
path_types_str = config.get('path_types', "*defaults*")
diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 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
@@ -73,7 +73,8 @@
except (IOError, socket.error), exc:
# In testing, errno is None
log.warning('Got %s, will retry: %s', exc.__class__.__name__, exc)
- heartbeat_thread.join()
+ if heartbeat_thread:
+ heartbeat_thread.join()
def heartbeat(self, connection):
log.debug('AMQP heartbeat thread alive')
diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/config_util.py
--- /dev/null
+++ b/lib/galaxy/jobs/runners/lwr_client/config_util.py
@@ -0,0 +1,80 @@
+""" Generic interface for reading YAML/INI/JSON config files into nested dictionaries.
+"""
+
+try:
+ from galaxy import eggs
+ eggs.require('PyYAML')
+except Exception:
+ # If not in Galaxy, ignore this.
+ pass
+try:
+ import yaml
+except ImportError:
+ yaml = None
+try:
+ from ConfigParser import ConfigParser
+except ImportError:
+ from configparser import ConfigParser
+import json
+
+
+CONFIG_TYPE_JSON = "json"
+CONFIG_TYPE_YAML = "yaml"
+CONFIG_TYPE_INI = "ini"
+
+DEFAULT_CONFIG_TYPE = CONFIG_TYPE_YAML
+
+JSON_EXTS = [".json"]
+YAML_EXTS = [".yaml", ".yml"]
+INI_EXTS = [".ini"]
+
+EXT_MAP = {
+ CONFIG_TYPE_JSON: JSON_EXTS,
+ CONFIG_TYPE_YAML: YAML_EXTS,
+ CONFIG_TYPE_INI: INI_EXTS,
+}
+
+
+def read_file(path, type=None, default_type=DEFAULT_CONFIG_TYPE):
+ if path is None:
+ raise ValueError("Undefined path supplied.")
+
+ config_type = __find_type(path, type, default_type)
+ return EXT_READERS[config_type](path)
+
+
+def __find_type(path, explicit_type, default_type):
+ if explicit_type:
+ return explicit_type
+
+ for config_type, config_exts in EXT_MAP.items():
+ for ext in config_exts:
+ if path.endswith(ext):
+ return config_type
+
+ return default_type
+
+
+def __read_yaml(path):
+ if yaml is None:
+ raise ImportError("Attempting to read YAML configuration file - but PyYAML dependency unavailable.")
+
+ with open(path, "rb") as f:
+ return yaml.load(f)
+
+
+def __read_ini(path):
+ config = ConfigParser()
+ config.read(path)
+ return config._sections
+
+
+def __read_json(path):
+ with open(path, "rb") as f:
+ return json.load(f)
+
+EXT_READERS = {
+ CONFIG_TYPE_JSON: __read_json,
+ CONFIG_TYPE_YAML: __read_yaml,
+ CONFIG_TYPE_INI: __read_ini,
+}
diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/transport/curl.py
--- a/lib/galaxy/jobs/runners/lwr_client/transport/curl.py
+++ b/lib/galaxy/jobs/runners/lwr_client/transport/curl.py
@@ -10,7 +10,7 @@
PYCURL_UNAVAILABLE_MESSAGE = \
- "You are attempting to use the Pycurl version of the LWR client by pycurl is unavailable."
+ "You are attempting to use the Pycurl version of the LWR client but pycurl is unavailable."
class PycurlTransport(object):
diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 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
@@ -135,7 +135,7 @@
message_template = "Cannot compute new path for file %s, does not start with %s."
message = message_template % (posix_path, old_base)
raise Exception(message)
- stripped_path = posix_path[ len(old_base): ]
+ stripped_path = posix_path[len(old_base):]
while stripped_path.startswith("/"):
stripped_path = stripped_path[1:]
path_parts = stripped_path.split(self.separator)
diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/util/cli/job/slurm.py
--- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py
@@ -1,4 +1,4 @@
-# A simple CLI runner for slurm that can be used when running Galaxy from a
+# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
try:
@@ -22,6 +22,7 @@
'partition': '-p'
}
+
class Slurm(BaseJobExec):
def __init__(self, **params):
@@ -31,8 +32,8 @@
def job_script_kwargs(self, ofile, efile, job_name):
scriptargs = {'-o': ofile,
- '-e': efile,
- '-J': job_name}
+ '-e': efile,
+ '-J': job_name}
# Map arguments using argmap.
for k, v in self.params.items():
@@ -66,7 +67,7 @@
def parse_status(self, status, job_ids):
# Get status for each job, skipping header.
rval = {}
- for line in status.splitlines()[ 1: ]:
+ for line in status.splitlines()[1:]:
id, state = line.split()
if id in job_ids:
# map job states to Galaxy job states.
@@ -75,7 +76,7 @@
def parse_single_status(self, status, job_id):
status = status.splitlines()
- if len( status ) > 1:
+ if len(status) > 1:
# Job still on cluster and has state.
id, state = status[1].split()
return self._get_job_state(state)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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