From d995301098e7daef2d7e1bc6bfccfc759933482d Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Tue, 19 Aug 2014 15:01:57 -0400 Subject: [PATCH] ToolForm: Add data selector, dynamic column selector and checkboxes, extends json content for basic parameters --- .../visualizations/charts/static/build-app.js | 2 +- .../charts/static/library/ui-table-form.js | 2 +- .../charts/static/views/types.js | 2 +- lib/galaxy/tools/parameters/basic.py | 14 + static/scripts/mvc/tools/tools-datasets.js | 46 +++ static/scripts/mvc/tools/tools-form.js | 268 +++++++++++++----- static/scripts/mvc/tools/tools-template.js | 19 ++ static/scripts/mvc/ui/ui-checkbox.js | 91 ++++++ static/scripts/mvc/ui/ui-misc.js | 89 +----- static/scripts/mvc/ui/ui-radiobutton.js | 93 ++++++ .../packed/mvc/tools/tools-datasets.js | 1 + static/scripts/packed/mvc/tools/tools-form.js | 2 +- .../packed/mvc/tools/tools-template.js | 1 + static/scripts/packed/mvc/ui/ui-checkbox.js | 1 + static/scripts/packed/mvc/ui/ui-misc.js | 2 +- .../scripts/packed/mvc/ui/ui-radiobutton.js | 1 + templates/webapps/galaxy/tool_form.api.mako | 43 ++- 17 files changed, 505 insertions(+), 172 deletions(-) create mode 100644 static/scripts/mvc/tools/tools-datasets.js create mode 100644 static/scripts/mvc/tools/tools-template.js create mode 100644 static/scripts/mvc/ui/ui-checkbox.js create mode 100644 static/scripts/mvc/ui/ui-radiobutton.js create mode 100644 static/scripts/packed/mvc/tools/tools-datasets.js create mode 100644 static/scripts/packed/mvc/tools/tools-template.js create mode 100644 static/scripts/packed/mvc/ui/ui-checkbox.js create mode 100644 static/scripts/packed/mvc/ui/ui-radiobutton.js diff --git a/config/plugins/visualizations/charts/static/build-app.js b/config/plugins/visualizations/charts/static/build-app.js index 65b143ca3c4..ee6426065df 100644 --- 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=$('
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  • '},_template:function(e){var t="";e.title&&(t="width: auto;");var n='",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return''}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'
     '+e.title+"
    "}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='
    ';return e.title?n+='
     '+''+e.title+""+"
    ":n+='',n+="
    ",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("
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    '}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'
    '+'"+"
    "+"
    "}}),h=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''}}),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''}}),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='
    ';for(key in e.data){var n=e.data[key];t+='"}return t+="
    ",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),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
    '},_templateContainer:function(e,t){return'
    '+'"}})}),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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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){this.app.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'
    '},_template_tab_new:function(e){return'
  • '+e.title_new+""+"
    • "},_template_tab:function(e){var t='
  • '+''+''+e.title+"";return e.ondel&&(t+=''),t+="
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    '+""+''+"
    "+""+e.content+""+"
    "}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$("
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    ");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("
    ");u.append(s.$el),n.info&&u.append('
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    "},_template_item:function(e){return'
    '+''+'
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o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$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.app.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=[];o1)while(op||r>d||d3.event.relatedTarget&&d3.event.relatedTarget.ownerSVGElement===undefined||a){if(l&&d3.event.relatedTarget&&d3.event.relatedTarget.ownerSVGElement===undefined&&d3.event.relatedTarget.className.match(t.nvPointerEventsClass))return;u.elementMouseout({mouseX:n,mouseY:r}),c.renderGuideLine(null);return}var f=s.invert(n);u.elementMousemove({mouseX:n,mouseY:r,pointXValue:f}),d3.event.type==="dblclick"&&u.elementDblclick({mouseX:n,mouseY:r,pointXValue:f})}var 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s&&s>0&&(u=Math.floor(u/s)*s),e.tooltip.calcTooltipPosition([t,u],r,i,h),w}var t=null,n=null,r="w",i=50,s=25,o=null,u=null,a=null,f=null,l={left:null,top:null},c=!0,h="nvtooltip-"+Math.floor(Math.random()*1e5),p="nv-pointer-events-none",d=function(e,t){return e},v=function(e){return e},m=function(e){if(t!=null)return t;if(e==null)return"";var n=d3.select(document.createElement("table")),r=n.selectAll("thead").data([e]).enter().append("thead");r.append("tr").append("td").attr("colspan",3).append("strong").classed("x-value",!0).html(v(e.value));var i=n.selectAll("tbody").data([e]).enter().append("tbody"),s=i.selectAll("tr").data(function(e){return e.series}).enter().append("tr").classed("highlight",function(e){return e.highlight});s.append("td").classed("legend-color-guide",!0).append("div").style("background-color",function(e){return e.color}),s.append("td").classed("key",!0).html(function(e){return e.key}),s.append("td").classed("value",!0).html(function(e,t){return d(e.value,t)}),s.selectAll("td").each(function(e){if(e.highlight){var t=d3.scale.linear().domain([0,1]).range(["#fff",e.color]),n=.6;d3.select(this).style("border-bottom-color",t(n)).style("border-top-color",t(n))}});var o=n.node().outerHTML;return e.footer!==undefined&&(o+="
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s=parseInt(i.offsetHeight),o=parseInt(i.offsetWidth),u=e.utils.windowSize().width,a=e.utils.windowSize().height,f=window.pageYOffset,l=window.pageXOffset,c,h;a=window.innerWidth>=document.body.scrollWidth?a:a-16,u=window.innerHeight>=document.body.scrollHeight?u:u-16,n=n||"s",r=r||20;var p=function(t){return e.tooltip.findTotalOffsetTop(t,h)},d=function(t){return e.tooltip.findTotalOffsetLeft(t,c)};switch(n){case"e":c=t[0]-o-r,h=t[1]-s/2;var v=d(i),m=p(i);vl?t[0]+r:l-v+c),mf+a&&(h=f+a-m+h-s);break;case"w":c=t[0]+r,h=t[1]-s/2;var v=d(i),m=p(i);v+o>u&&(c=t[0]-o-r),mf+a&&(h=f+a-m+h-s);break;case"n":c=t[0]-o/2-5,h=t[1]+r;var v=d(i),m=p(i);vu&&(c=c-o/2+5),m+s>f+a&&(h=f+a-m+h-s);break;case"s":c=t[0]-o/2,h=t[1]-s-r;var v=d(i),m=p(i);vu&&(c=c-o/2+5),f>m&&(h=f);break;case"none":c=t[0],h=t[1]-r;var v=d(i),m=p(i)}return i.style.left=c+"px",i.style.top=h+"px",i.style.opacity=1,i.style.position="absolute",i},e.tooltip.cleanup=function(){var 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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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    "}}),d=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.$el.val()},_template:function(e){return''}}),v=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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''}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r,Checkbox:n,Searchbox:p,Select:t,Textarea:v}}),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
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This chart type does not support SVG/PDF 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,u=$("");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'
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  • '+e.title_new+""+"
    • "},_template_tab:function(e){var t='
  • '+''+''+e.title+"";return e.ondel&&(t+=''),t+="
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    '+""+''+"
    "+""+e.content+""+"
    "}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("
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    ");u.append(s.$el),n.info&&u.append('
    '+n.info+"
    "),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add(''+n.title+"","25%"),this.table.add(u))}else this.table.add('
    '+n.title+":
    "),this.table.add($("
    "));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$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","mvc/ui/ui-misc"],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=$('
    ');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({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=$('
    ');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u=''+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'
    '+"• "+e.title+"
    "},_template_item:function(e){return'
    '+''+'
    '+e.title+"
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o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$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.app.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 --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_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_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",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=[];o1)while(op||r>d||d3.event.relatedTarget&&d3.event.relatedTarget.ownerSVGElement===undefined||a){if(l&&d3.event.relatedTarget&&d3.event.relatedTarget.ownerSVGElement===undefined&&d3.event.relatedTarget.className.match(t.nvPointerEventsClass))return;u.elementMouseout({mouseX:n,mouseY:r}),c.renderGuideLine(null);return}var f=s.invert(n);u.elementMousemove({mouseX:n,mouseY:r,pointXValue:f}),d3.event.type==="dblclick"&&u.elementDblclick({mouseX:n,mouseY:r,pointXValue:f})}var 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e.left!="undefined"?e.left:i.left,c):i},c.width=function(e){return arguments.length?(n=e,c):n},c.height=function(e){return arguments.length?(r=e,c):r},c.xScale=function(e){return arguments.length?(s=e,c):s},c.showGuideLine=function(e){return arguments.length?(a=e,c):a},c.svgContainer=function(e){return arguments.length?(f=e,c):f},c},e.interactiveBisect=function(e,t,n){if(!e instanceof Array)return null;typeof n!="function"&&(n=function(e,t){return e.x});var r=d3.bisector(n).left,i=d3.max([0,r(e,t)-1]),s=n(e[i],i);typeof s=="undefined"&&(s=i);if(s===t)return i;var o=d3.min([i+1,e.length-1]),u=n(e[o],o);return typeof u=="undefined"&&(u=o),Math.abs(u-t)>=Math.abs(s-t)?i:o},e.nearestValueIndex=function(e,t,n){var r=Infinity,i=null;return e.forEach(function(e,s){var o=Math.abs(t-e);o<=r&&oT.height?0:x}v.top=Math.abs(x-S.top),v.left=Math.abs(E.left-S.left)}t+=a.offsetLeft+v.left-2*a.scrollLeft,u+=a.offsetTop+v.top-2*a.scrollTop}return s&&s>0&&(u=Math.floor(u/s)*s),e.tooltip.calcTooltipPosition([t,u],r,i,h),w}var t=null,n=null,r="w",i=50,s=25,o=null,u=null,a=null,f=null,l={left:null,top:null},c=!0,h="nvtooltip-"+Math.floor(Math.random()*1e5),p="nv-pointer-events-none",d=function(e,t){return e},v=function(e){return e},m=function(e){if(t!=null)return t;if(e==null)return"";var n=d3.select(document.createElement("table")),r=n.selectAll("thead").data([e]).enter().append("thead");r.append("tr").append("td").attr("colspan",3).append("strong").classed("x-value",!0).html(v(e.value));var i=n.selectAll("tbody").data([e]).enter().append("tbody"),s=i.selectAll("tr").data(function(e){return e.series}).enter().append("tr").classed("highlight",function(e){return e.highlight});s.append("td").classed("legend-color-guide",!0).append("div").style("background-color",function(e){return e.color}),s.append("td").classed("key",!0).html(function(e){return e.key}),s.append("td").classed("value",!0).html(function(e,t){return d(e.value,t)}),s.selectAll("td").each(function(e){if(e.highlight){var t=d3.scale.linear().domain([0,1]).range(["#fff",e.color]),n=.6;d3.select(this).style("border-bottom-color",t(n)).style("border-top-color",t(n))}});var o=n.node().outerHTML;return e.footer!==undefined&&(o+="
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e=="function"&&(d=e),w):d},w.headerFormatter=function(e){return arguments.length?(typeof e=="function"&&(v=e),w):v},w.id=function(){return h},w},e.tooltip.show=function(t,n,r,i,s,o){var u=document.createElement("div");u.className="nvtooltip "+(o?o:"xy-tooltip");var a=s;if(!s||s.tagName.match(/g|svg/i))a=document.getElementsByTagName("body")[0];u.style.left=0,u.style.top=0,u.style.opacity=0,u.innerHTML=n,a.appendChild(u),s&&(t[0]=t[0]-s.scrollLeft,t[1]=t[1]-s.scrollTop),e.tooltip.calcTooltipPosition(t,r,i,u)},e.tooltip.findFirstNonSVGParent=function(e){while(e.tagName.match(/^g|svg$/i)!==null)e=e.parentNode;return e},e.tooltip.findTotalOffsetTop=function(e,t){var n=t;do isNaN(e.offsetTop)||(n+=e.offsetTop);while(e=e.offsetParent);return n},e.tooltip.findTotalOffsetLeft=function(e,t){var n=t;do isNaN(e.offsetLeft)||(n+=e.offsetLeft);while(e=e.offsetParent);return n},e.tooltip.calcTooltipPosition=function(t,n,r,i){var s=parseInt(i.offsetHeight),o=parseInt(i.offsetWidth),u=e.utils.windowSize().width,a=e.utils.windowSize().height,f=window.pageYOffset,l=window.pageXOffset,c,h;a=window.innerWidth>=document.body.scrollWidth?a:a-16,u=window.innerHeight>=document.body.scrollHeight?u:u-16,n=n||"s",r=r||20;var p=function(t){return e.tooltip.findTotalOffsetTop(t,h)},d=function(t){return e.tooltip.findTotalOffsetLeft(t,c)};switch(n){case"e":c=t[0]-o-r,h=t[1]-s/2;var v=d(i),m=p(i);vl?t[0]+r:l-v+c),mf+a&&(h=f+a-m+h-s);break;case"w":c=t[0]+r,h=t[1]-s/2;var v=d(i),m=p(i);v+o>u&&(c=t[0]-o-r),mf+a&&(h=f+a-m+h-s);break;case"n":c=t[0]-o/2-5,h=t[1]+r;var v=d(i),m=p(i);vu&&(c=c-o/2+5),m+s>f+a&&(h=f+a-m+h-s);break;case"s":c=t[0]-o/2,h=t[1]-s-r;var v=d(i),m=p(i);vu&&(c=c-o/2+5),f>m&&(h=f);break;case"none":c=t[0],h=t[1]-r;var v=d(i),m=p(i)}return i.style.left=c+"px",i.style.top=h+"px",i.style.opacity=1,i.style.position="absolute",i},e.tooltip.cleanup=function(){var 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Array]"?function(e,n){return e.color||t[n%t.length]}:t:e.utils.defaultColor()},e.utils.defaultColor=function(){var e=d3.scale.category20().range();return function(t,n){return t.color||e[n%e.length]}},e.utils.customTheme=function(e,t,n){t=t||function(e){return e.key},n=n||d3.scale.category20().range();var r=n.length;return function(i,s){var o=t(i);return r||(r=n.length),typeof e[o]!="undefined"?typeof e[o]=="function"?e[o]():e[o]:n[--r]}},e.utils.pjax=function(t,n){function r(r){d3.html(r,function(r){var i=d3.select(n).node();i.parentNode.replaceChild(d3.select(r).select(n).node(),i),e.utils.pjax(t,n)})}d3.selectAll(t).on("click",function(){history.pushState(this.href,this.textContent,this.href),r(this.href),d3.event.preventDefault()}),d3.select(window).on("popstate",function(){d3.event.state&&r(d3.event.state)})},e.utils.calcApproxTextWidth=function(e){if(typeof e.style=="function"&&typeof e.text=="function"){var 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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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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"

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\ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/library/ui-table-form.js b/config/plugins/visualizations/charts/static/library/ui-table-form.js index ca66e47f5fe..03ef15eb4c3 100644 --- a/config/plugins/visualizations/charts/static/library/ui-table-form.js +++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js @@ -88,7 +88,7 @@ var View = Backbone.View.extend({ break; // radiobox field case 'radiobutton' : - field = new Ui.RadioButton({ + field = new Ui.RadioButton.View({ id : 'field-' + id, data : settings_def.data, value : model.get(id), diff --git a/config/plugins/visualizations/charts/static/views/types.js b/config/plugins/visualizations/charts/static/views/types.js index 6fa3b0f4440..dceb9d648f4 100644 --- a/config/plugins/visualizations/charts/static/views/types.js +++ b/config/plugins/visualizations/charts/static/views/types.js @@ -35,7 +35,7 @@ return Backbone.View.extend({ $el.append(Utils.wrap((new Ui.Label({ title : 'How many data points would you like to analyze?'})).$el)); // construct chart type subset selection buttons - this.library = new Ui.RadioButton({ + this.library = new Ui.RadioButton.View({ data : [ { label: 'Few (<500)', value: 'small' }, { label: 'Some (<10k)', value: 'medium' }, { label: 'Many (>10k)', value: 'large' }], diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index ffdbb11de41..2509c5fee82 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -991,6 +991,8 @@ class SelectToolParameter( ToolParameter ): # Found selected option. value = option[1] d[ 'value' ] = value + + d[ 'display' ] = self.display return d @@ -1230,6 +1232,8 @@ class ColumnListParameter( SelectToolParameter ): def need_late_validation( self, trans, context ): if super( ColumnListParameter, self ).need_late_validation( trans, context ): return True + if self.data_ref not in context: + return False # Get the selected dataset if selected dataset = context[ self.data_ref ] if dataset: @@ -1242,6 +1246,16 @@ class ColumnListParameter( SelectToolParameter ): # No late validation return False + def to_dict( self, trans, view='collection', value_mapper=None ): + # call parent to_dict + d = super( ColumnListParameter, self ).to_dict( trans ) + + # add data reference + d[ 'data_ref' ] = self.data_ref + + # return + return d + class DrillDownSelectToolParameter( SelectToolParameter ): """ diff --git a/static/scripts/mvc/tools/tools-datasets.js b/static/scripts/mvc/tools/tools-datasets.js new file mode 100644 index 00000000000..90e9c50073c --- /dev/null +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -0,0 +1,46 @@ +define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ + return Backbone.Model.extend({ + // initialize + initialize: function(options) { + // create history contents container + this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({}); + + // identify current history id + this.currHistoryContents.historyId = "f597429621d6eb2b";//Galaxy.currHistoryPanel.model.id; + + // make request + var self = this; + var xhr = this.currHistoryContents.fetchAllDetails() + .done( function(){ + // log request success + console.debug('tools-datasets::initialize() - Completed.'); + + // callback + options.success && options.success(); + }) + .fail( function(){ + // log request failure + console.debug('tools-datasets::initialize() - Ajax request failed.'); + }); + }, + + // filter datasets by data type + filterType: function(filter_type) { + // return matched datasets + return this.currHistoryContents.filter( function( content ){ + // link details + var history_content_type = content.get( 'history_content_type' ); + var data_type = content.get( 'data_type'); + + // apply filter + return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === ''); + }); + }, + + // filter datasets by id + filter: function(filter_id) { + // return matched datasets + return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); + } + }); +}); \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form.js b/static/scripts/mvc/tools/tools-form.js index ab77955b16e..e7652a714a7 100644 --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -1,4 +1,8 @@ -define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], function(Tools, Portlet, Table, Ui) { +define(['mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', + 'mvc/citation/citation-model', 'mvc/citation/citation-view', + 'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-datasets'], + function(Portlet, Table, Ui, CitationModel, CitationView, + Tools, ToolTemplate, ToolDatasets) { // create tool model var Model = Backbone.Model.extend({ @@ -17,14 +21,31 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], // link this var self = this; + // link options + this.options = options; + // load tool model this.model = new Model({ id : options.id }); + // initialize datasets + this.datasets = new ToolDatasets({ + success: function() { + self._initializeToolForm(); + } + }); + }, + + // initialize tool form + _initializeToolForm: function() { // fetch model and render form + var self = this; this.model.fetch({ success: function() { + // inputs + self.inputs = self.model.get('inputs'); + // create portlet self.portlet = new Portlet.View({ icon : 'fa-wrench', @@ -41,15 +62,35 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], } }); - // table + // create table self.table = new Table.View(); - // add message + // create message self.message = new Ui.Message(); self.portlet.append(self.message.$el); - // append portlet + // append form $(self.main_el).append(self.portlet.$el); + + // append help + if (self.options.help != '') { + $(self.main_el).append(ToolTemplate.help(self.options.help)); + } + + // append citations + if (self.options.citations) { + // append html + $(self.main_el).append(ToolTemplate.citations()); + + // fetch citations + var citations = new CitationModel.ToolCitationCollection(); + citations.tool_id = self.options.id; + var citation_list_view = new CitationView.CitationListView({ collection: citations } ); + citation_list_view.render(); + citations.fetch(); + } + + // configure portlet and form table self.setElement(self.portlet.content()); self.portlet.append(self.table.$el); self.render(); @@ -59,9 +100,6 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], // update render: function() { - // inputs - var settings = this.model.get('inputs'); - // reset table this.table.delAll(); @@ -72,8 +110,8 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], var data = new Backbone.Model(); // load settings elements into table - for (var id in settings) { - this._add(settings[id], data); + for (var id in this.inputs) { + this._add(this.inputs[id], data); } // trigger change @@ -83,53 +121,55 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], }, // add table row - _add: function(settings_def, data) { + _add: function(inputs_def, data) { // link this var self = this; // get id - var id = settings_def.name; - - // log - console.debug(settings_def); + var id = inputs_def.name; // field wrapper var field = null; - + console.log(inputs_def); // create select field - var type = settings_def.type; + var type = inputs_def.type; switch(type) { // text input field case 'text' : - field = this.field_text(settings_def, data); + field = this.field_text(inputs_def, data); break; // select field case 'select' : - field = this.field_select(settings_def, data); + field = this.field_select(inputs_def, data); break; // radiobox field case 'radiobutton' : - field = this.field_radio(settings_def, data); + field = this.field_radio(inputs_def, data); break; // dataset case 'data': - field = this.field_select(settings_def, data); + field = this.field_data(inputs_def, data); break; - // slider input field + // dataset column + case 'data_column': + field = this.field_column(inputs_def, data); + break; + + // text area field case 'textarea' : - field = this.field_textarea(settings_def, data); + field = this.field_textarea(inputs_def, data); break; // default default: field = new Ui.Input({ id : 'field-' + id, - placeholder : settings_def.placeholder, - type : settings_def.type, + placeholder : inputs_def.placeholder, + type : inputs_def.type, onchange : function() { data.set(id, field.value()); } @@ -138,7 +178,7 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], // set value if (!data.get(id)) { - data.set(id, settings_def.value); + data.set(id, inputs_def.value); } field.value(data.get(id)); @@ -148,31 +188,26 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], // combine field and info var $input = $('
    '); $input.append(field.$el); - if (settings_def.info) { - $input.append('
    ' + settings_def.info + '
    '); + if (inputs_def.info) { + $input.append('
    ' + inputs_def.info + '
    '); } // add row to table - if (this.options.style == 'bold') { - this.table.add(new Ui.Label({title: settings_def.title, cls: 'form-label'}).$el); - this.table.add($input); - } else { - this.table.add('' + settings_def.label + '', '25%'); - this.table.add($input); - } - + this.table.add('' + inputs_def.label + '', '25%'); + this.table.add($input); + // add to table this.table.append(id); // show/hide - if (settings_def.hide) { + if (inputs_def.hide) { this.table.get(id).hide(); } }, // text input field - field_text : function(settings_def, data) { - var id = settings_def.name; + field_text : function(inputs_def, data) { + var id = inputs_def.name; return new Ui.Input({ id : 'field-' + id, value : data.get(id), @@ -183,8 +218,8 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], }, // text area - field_textarea : function(settings_def, data) { - var id = settings_def.name; + field_textarea : function(inputs_def, data) { + var id = inputs_def.name; return new Ui.Textarea({ id : 'field-' + id, onchange : function() { @@ -193,12 +228,89 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], }); }, - // select field - field_select : function (settings_def, data) { + // data input field + field_data : function(inputs_def, data) { + // link this + var self = this; + + // get element id + var id = inputs_def.name; + + // get datasets + var datasets = this.datasets.filterType(); + // configure options fields var options = []; - for (var i in settings_def.options) { - var option = settings_def.options[i]; + for (var i in datasets) { + options.push({ + label: datasets[i].get('name'), + value: datasets[i].get('id') + }); + } + + // find referenced columns + var column_list = _.where(this.inputs, { + data_ref : id, + type : 'data_column' + }); + + // select field + return new Ui.Select.View({ + id : 'field-' + id, + data : options, + value : options[0].value, + onchange : function(value) { + // update value + data.set(id, value); + + // find selected dataset + var dataset = self.datasets.filter(value); + + // check dataset + if (dataset && column_list.length > 0) { + // log selection + console.debug('tool-form::field_data() - Selected dataset ' + value + '.'); + + // get meta data + var meta = dataset.get('metadata_column_types'); + + // check meta data + if (!meta) { + console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.'); + } + + // load column options + var columns = []; + for (var key in meta) { + // add to selection + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } + + // update referenced columns + for (var i in column_list) { + var column_field = self.list[column_list[i].name] + if (column_field) { + column_field.update(columns); + column_field.value(column_field.first()); + } + } + } else { + // log failure + console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.'); + } + } + }); + }, + + // select field + field_column : function (inputs_def, data) { + // configure options fields + var options = []; + for (var i in inputs_def.options) { + var option = inputs_def.options[i]; options.push({ label: option[0], value: option[1] @@ -206,56 +318,56 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], } // select field - var id = settings_def.name; + var id = inputs_def.name; return new Ui.Select.View({ id : 'field-' + id, data : options, value : data.get(id), onchange : function(value) { - // set new value data.set(id, value); - - // find selected dictionary - var dict = _.findWhere(options, {value: value}); - if (dict && dict.operations) { - var operations = dict.operations; - for (var i in operations.show) { - var target = operations.show[i]; - self.table.get(target).show(); - } - for (var i in operations.hide) { - var target = operations.hide[i]; - self.table.get(target).hide(); - } - } + } + }); + }, + + // select field + field_select : function (inputs_def, data) { + // configure options fields + var options = []; + for (var i in inputs_def.options) { + var option = inputs_def.options[i]; + options.push({ + label: option[0], + value: option[1] + }); + } + + // identify display type + var SelectClass = Ui.Select; + if (inputs_def.display == 'checkboxes') { + SelectClass = Ui.Checkbox; + } + + // select field + var id = inputs_def.name; + return new SelectClass.View({ + id : 'field-' + id, + data : options, + value : data.get(id), + onchange : function(value) { + data.set(id, value); } }); }, // radio field - field_radio : function(settings_def, data) { - var id = settings_def.name; + field_radio : function(inputs_def, data) { + var id = inputs_def.name; return new Ui.RadioButton({ id : 'field-' + id, - data : settings_def.data, + data : inputs_def.data, value : data.get(id), onchange : function(value) { - // set new value data.set(id, value); - - // find selected dictionary - var dict = _.findWhere(settings_def.data, {value: value}); - if (dict && dict.operations) { - var operations = dict.operations; - for (var i in operations.show) { - var target = operations.show[i]; - self.table.get(target).show(); - } - for (var i in operations.hide) { - var target = operations.hide[i]; - self.table.get(target).hide(); - } - } } }); } diff --git a/static/scripts/mvc/tools/tools-template.js b/static/scripts/mvc/tools/tools-template.js new file mode 100644 index 00000000000..261fe973426 --- /dev/null +++ b/static/scripts/mvc/tools/tools-template.js @@ -0,0 +1,19 @@ +// dependencies +define([], function() { + +// tool form templates +return { + help: function(content) { + return '
    ' + + '
    ' + + content + + '
    ' + + '
    '; + }, + + citations: function() { + return '
    '; + } +}; + +}); \ No newline at end of file diff --git a/static/scripts/mvc/ui/ui-checkbox.js b/static/scripts/mvc/ui/ui-checkbox.js new file mode 100644 index 00000000000..14527bd1e6b --- /dev/null +++ b/static/scripts/mvc/ui/ui-checkbox.js @@ -0,0 +1,91 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend({ + // options + optionsDefault: { + value : '', + visible : true, + cls : '', + data : [], + id : Utils.uuid() + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // current value + this.current = this.options.value; + + // onchange event handler. fires on user activity. + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + }); + }, + + // value + value : function (new_val) { + // get current value + var before = this.current; + + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.current = new_val; + } + + // check value + var after = this.current; + if (after != before && this.options.onchange) { + this.options.onchange(this.current); + } + + // get and return value + return this.current; + }, + + // get value + _getValue: function() { + var selected = this.$el.find(':checked'); + var value = null; + if (selected.length > 0) { + value = selected.val(); + } + return value; + }, + + // element + _template: function(options) { + var tmpl = '
    '; + for (key in options.data) { + var pair = options.data[key]; + tmpl += '' + pair.label + '
    '; + } + tmpl += '
    '; + return tmpl; + } +}); + +return { + View : View +}; + +}); diff --git a/static/scripts/mvc/ui/ui-misc.js b/static/scripts/mvc/ui/ui-misc.js index be9c83f19a3..a9b85d5f7b1 100644 --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-checkbox', 'mvc/ui/ui-radiobutton', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Checkbox, RadioButton, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -409,90 +409,6 @@ var Textarea = Backbone.View.extend({ } }); -// plugin -var RadioButton = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - visible : true, - cls : '', - data : [], - id : Utils.uuid() - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // set initial value - if (this.options.value) { - this.value(this.options.value); - } - - // current value - this.current = this.options.value; - - // onchange event handler. fires on user activity. - var self = this; - this.$el.find('input').on('change', function() { - self.value(self._getValue()); - }); - }, - - // value - value : function (new_val) { - // get current value - var before = this.current; - - // set new value - if (new_val !== undefined) { - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); - this.current = new_val; - } - - // check value - var after = this.current; - if (after != before && this.options.onchange) { - this.options.onchange(this.current); - } - - // get and return value - return this.current; - }, - - // get value - _getValue: function() { - var selected = this.$el.find(':checked'); - var value = null; - if (selected.length > 0) { - value = selected.val(); - } - return value; - }, - - // element - _template: function(options) { - var tmpl = '
    '; - for (key in options.data) { - var pair = options.data[key]; - tmpl += ''; - } - tmpl += '
    '; - return tmpl; - } -}); // return return { @@ -507,6 +423,7 @@ return { Message : Message, Modal : Modal, RadioButton : RadioButton, + Checkbox : Checkbox, Searchbox : Searchbox, Select : Select, Textarea : Textarea diff --git a/static/scripts/mvc/ui/ui-radiobutton.js b/static/scripts/mvc/ui/ui-radiobutton.js new file mode 100644 index 00000000000..b0a82529414 --- /dev/null +++ b/static/scripts/mvc/ui/ui-radiobutton.js @@ -0,0 +1,93 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend({ + // options + optionsDefault: { + value : '', + visible : true, + cls : '', + data : [], + id : Utils.uuid() + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // current value + this.current = this.options.value; + + // onchange event handler. fires on user activity. + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + }); + }, + + // value + value : function (new_val) { + // get current value + var before = this.current; + + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.current = new_val; + } + + // check value + var after = this.current; + if (after != before && this.options.onchange) { + this.options.onchange(this.current); + } + + // get and return value + return this.current; + }, + + // get value + _getValue: function() { + var selected = this.$el.find(':checked'); + var value = null; + if (selected.length > 0) { + value = selected.val(); + } + return value; + }, + + // element + _template: function(options) { + var tmpl = '
    '; + for (key in options.data) { + var pair = options.data[key]; + tmpl += ''; + } + tmpl += '
    '; + return tmpl; + } +}); + +return { + View : View +}; + +}); diff --git a/static/scripts/packed/mvc/tools/tools-datasets.js b/static/scripts/packed/mvc/tools/tools-datasets.js new file mode 100644 index 00000000000..57037d2e5a6 --- /dev/null +++ b/static/scripts/packed/mvc/tools/tools-datasets.js @@ -0,0 +1 @@ +define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId="f597429621d6eb2b";var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){return this.currHistoryContents.filter(function(c){var d=c.get("history_content_type");var e=c.get("data_type");return d==="dataset"})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/tools/tools-form.js b/static/scripts/packed/mvc/tools/tools-form.js index 733f83040df..6837c1cd9ac 100644 --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1 +1 @@ -define(["mvc/tools","mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc"],function(b,c,a,f){var e=Backbone.Model.extend({initialize:function(g){this.url=galaxy_config.root+"api/tools/"+g.id+"?io_details=true"}});var d=Backbone.View.extend({main_el:"body",initialize:function(h){var g=this;this.model=new e({id:h.id});this.model.fetch({success:function(){g.portlet=new c.View({icon:"fa-wrench",title:""+g.model.get("name")+" "+g.model.get("description"),buttons:{execute:new f.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});g.table=new a.View();g.message=new f.Message();g.portlet.append(g.message.$el);$(g.main_el).append(g.portlet.$el);g.setElement(g.portlet.content());g.portlet.append(g.table.$el);g.render()}})},render:function(){var g=this.model.get("inputs");this.table.delAll();this.list=[];var h=new Backbone.Model();for(var i in g){this._add(g[i],h)}for(var i in this.list){this.list[i].trigger("change")}},_add:function(g,j){var h=this;var m=g.name;console.debug(g);var k=null;var i=g.type;switch(i){case"text":k=this.field_text(g,j);break;case"select":k=this.field_select(g,j);break;case"radiobutton":k=this.field_radio(g,j);break;case"data":k=this.field_select(g,j);break;case"textarea":k=this.field_textarea(g,j);break;default:k=new f.Input({id:"field-"+m,placeholder:g.placeholder,type:g.type,onchange:function(){j.set(m,k.value())}})}if(!j.get(m)){j.set(m,g.value)}k.value(j.get(m));this.list[m]=k;var l=$("
    ");l.append(k.$el);if(g.info){l.append('
    '+g.info+"
    ")}if(this.options.style=="bold"){this.table.add(new f.Label({title:g.title,cls:"form-label"}).$el);this.table.add(l)}else{this.table.add(''+g.label+"","25%");this.table.add(l)}this.table.append(m);if(g.hide){this.table.get(m).hide()}},field_text:function(g,h){var i=g.name;return new f.Input({id:"field-"+i,value:h.get(i),onchange:function(j){h.set(i,j)}})},field_textarea:function(g,h){var i=g.name;return new f.Textarea({id:"field-"+i,onchange:function(){h.set(i,field.value())}})},field_select:function(g,l){var h=[];for(var j in g.options){var k=g.options[j];h.push({label:k[0],value:k[1]})}var m=g.name;return new f.Select.View({id:"field-"+m,data:h,value:l.get(m),onchange:function(p){l.set(m,p);var r=_.findWhere(h,{value:p});if(r&&r.operations){var n=r.operations;for(var o in n.show){var q=n.show[o];self.table.get(q).show()}for(var o in n.hide){var q=n.hide[o];self.table.get(q).hide()}}}})},field_radio:function(g,h){var i=g.name;return new f.RadioButton({id:"field-"+i,data:g.data,value:h.get(i),onchange:function(l){h.set(i,l);var n=_.findWhere(g.data,{value:l});if(n&&n.operations){var j=n.operations;for(var k in j.show){var m=j.show[k];self.table.get(m).show()}for(var k in j.hide){var m=j.hide[k];self.table.get(m).hide()}}}})}});return{View:d}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:""+k.model.get("name")+" "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.list=[];var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.list){this.list[l].trigger("change")}},_add:function(l,n){var k=this;var q=l.name;var o=null;console.log(l);var m=l.type;switch(m){case"text":o=this.field_text(l,n);break;case"select":o=this.field_select(l,n);break;case"radiobutton":o=this.field_radio(l,n);break;case"data":o=this.field_data(l,n);break;case"data_column":o=this.field_column(l,n);break;case"textarea":o=this.field_textarea(l,n);break;default:o=new j.Input({id:"field-"+q,placeholder:l.placeholder,type:l.type,onchange:function(){n.set(q,o.value())}})}if(!n.get(q)){n.set(q,l.value)}o.value(n.get(q));this.list[q]=o;var p=$("
    ");p.append(o.$el);if(l.info){p.append('
    '+l.info+"
    ")}this.table.add(''+l.label+"","25%");this.table.add(p);this.table.append(q);if(l.hide){this.table.get(q).hide()}},field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},field_data:function(n,q){var l=this;var r=n.name;var p=this.datasets.filterType();var m=[];for(var o in p){m.push({label:p[o].get("name"),value:p[o].get("id")})}var k=_.where(this.inputs,{data_ref:r,type:"data_column"});return new j.Select.View({id:"field-"+r,data:m,value:m[0].value,onchange:function(w){q.set(r,w);var y=l.datasets.filter(w);if(y&&k.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in k){var s=l.list[k[t].name];if(s){s.update(v);s.value(s.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/tools/tools-template.js b/static/scripts/packed/mvc/tools/tools-template.js new file mode 100644 index 00000000000..ba7fe6ebdb2 --- /dev/null +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -0,0 +1 @@ +define([],function(){return{help:function(a){return'
    '+a+"
    "},citations:function(){return'
    '}}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/ui/ui-checkbox.js b/static/scripts/packed/mvc/ui/ui-checkbox.js new file mode 100644 index 00000000000..2b2027b1b10 --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-checkbox.js @@ -0,0 +1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='
    ';for(key in d.data){var e=d.data[key];c+=''+e.label+"
    "}c+="
    ";return c}});return{View:b}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/ui/ui-misc.js b/static/scripts/packed/mvc/ui/ui-misc.js index 8ddd86d19e9..81ccfcd4c2f 100644 --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1 +1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,o,m){var c=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(p){return''}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options))},title:function(p){this.$el.html(p)},_template:function(p){return'"},value:function(){return options.title}});var d=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){return'
     '+p.title+"
    "}});var f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick);$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){var q='";return q}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick);$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){var q="";if(p.title){q="width: auto;"}var r='
    ';if(p.title){r+='
     '+p.title+"
    "}else{r+=''}r+="
    ";return r}});var e=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick)},_template:function(p){return'"}});var n=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement("
    ")},update:function(q){this.options=k.merge(q,this.optionsDefault);if(q.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(q.message);this.$el.fadeIn();if(!q.persistent){var p=this;window.setTimeout(function(){if(p.$el.is(":visible")){p.$el.fadeOut()}else{p.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(p){return'
    '}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));var p=this;if(this.options.onclick){this.$el.on("submit",function(s){var r=p.$el.find("#search");p.options.onclick(r.val())})}},_template:function(p){return'
    '}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var p=this;this.$el.on("input",function(){if(p.options.onchange){p.options.onchange(p.$el.val())}})},value:function(p){if(p!==undefined){this.$el.val(p)}return this.$el.val()},_template:function(p){return''}});var h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var p=this;this.$el.on("input",function(){if(p.options.onchange){p.options.onchange(p.$el.val())}})},value:function(p){if(p!==undefined){this.$el.val(p)}return this.$el.val()},_template:function(p){return''}});var l=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:k.uuid()},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var p=this;this.$el.find("input").on("change",function(){p.value(p._getValue())})},value:function(p){var q=this.current;if(p!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+p+'"]').closest("label").addClass("active");this.current=p}var r=this.current;if(r!=q&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var p=this.$el.find(":checked");var q=null;if(p.length>0){q=p.val()}return q},_template:function(q){var p='
    ';for(key in q.data){var r=q.data[key];p+='"}p+="
    ";return p}});return{Anchor:e,Button:f,ButtonIcon:g,ButtonMenu:o,Icon:d,Image:c,Input:i,Label:j,Message:n,Modal:m,RadioButton:l,Searchbox:a,Select:b,Textarea:h}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,e,m,p,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return''}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'
     '+q.title+"
    "}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='
    ';if(q.title){s+='
     '+q.title+"
    "}else{s+=''}s+="
    ";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement("
    ")},update:function(r){this.options=l.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'
    '}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'
    '}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return''}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return''}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Textarea:i}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/ui/ui-radiobutton.js b/static/scripts/packed/mvc/ui/ui-radiobutton.js new file mode 100644 index 00000000000..f901094c14c --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-radiobutton.js @@ -0,0 +1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='
    ';for(key in d.data){var e=d.data[key];c+='"}c+="
    ";return c}});return{View:b}}); \ No newline at end of file diff --git a/templates/webapps/galaxy/tool_form.api.mako b/templates/webapps/galaxy/tool_form.api.mako index e6eeea0d789..7c28e7cf44c 100644 --- a/templates/webapps/galaxy/tool_form.api.mako +++ b/templates/webapps/galaxy/tool_form.api.mako @@ -1,10 +1,47 @@ <%inherit file="/base.mako"/> + +<% + # load tool help + tool_help = '' + if tool.help: + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + endif + + # check if citations exist + tool_citations = False + if tool.citations: + tool_citations = True + + # form configuration + self.form_config = { + 'id' : tool.id, + 'help' : tool_help, + 'citations' : tool_citations + } +%> +${h.js( "libs/bibtex" )} + +%if tool.tool_shed_repository: + <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %> + %if tool_url: +
    + ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: %s' % ( tool_url, tool_url ), 'info' ) } + %endif +%endif