Merge branch 'collections' into dev

client/GruntFile.js

@@ -11,7 +11,7 @@ module.exports = function(grunt) {
 
         uglify: {
             target : {
-                files: [{ 
+                files: [{
                     expand : true,
                     cwd : SRC_SYMLINK,
                     src : '**/*.js',
@@ -45,7 +45,7 @@ module.exports = function(grunt) {
                     if_return : true,
                     join_vars : true,
                     cascade : true,
-                    drop_console : true
+                    // drop_console : true
                 }
             }
         },

client/galaxy/scripts/mvc/collection/collection-li.js

@@ -24,8 +24,9 @@ var DCListItemView = FoldoutListItemView.extend(
 
     /** override to add linkTarget */
     initialize : function( attributes ){
-        FoldoutListItemView.prototype.initialize.call( this, attributes );
         this.linkTarget = attributes.linkTarget || '_blank';
+        this.hasUser = attributes.hasUser;
+        FoldoutListItemView.prototype.initialize.call( this, attributes );
     },
 
     // ......................................................................... rendering
@@ -51,7 +52,8 @@ var DCListItemView = FoldoutListItemView.extend(
     _getFoldoutPanelOptions : function(){
         var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call( this );
         return _.extend( options, {
-            linkTarget : this.linkTarget
+            linkTarget  : this.linkTarget,
+            hasUser     : this.hasUser
         });
     },
 

client/galaxy/scripts/mvc/collection/collection-panel.js

@@ -37,7 +37,6 @@ var CollectionPanel = _super.extend(
         this.linkTarget = attributes.linkTarget || '_blank';
 
         this.hasUser = attributes.hasUser;
-
         /**  */
         this.panelStack = [];
         /**  */

client/galaxy/scripts/mvc/history/history-panel-edit-current.js

@@ -270,7 +270,8 @@ var CurrentHistoryPanel = _super.extend(
         this.annotationEditor.on( 'hiddenUntilActivated:shown hiddenUntilActivated:hidden',
             function( annotationEditor ){
                 panel.preferences.set( 'annotationEditorShown', annotationEditor.hidden );
-            });
+            }
+        );
     },
 
     /** Override to scroll to cached position (in prefs) after swapping */
@@ -303,7 +304,6 @@ var CurrentHistoryPanel = _super.extend(
 
     /** Override to remove any drill down panels */
     addItemView : function( model, collection, options ){
-console.debug( 'addItemView:', model, collection );
         var view = _super.prototype.addItemView.call( this, model, collection, options );
         if( !view ){ return view; }
         if( this.panelStack.length ){ return this._collapseDrilldownPanel(); }

client/galaxy/scripts/mvc/history/history-panel.js

@@ -404,7 +404,7 @@ var HistoryPanel = _super.extend(
         return this.showDeleted;
     },
 
-    /** Handle the user toggling the deleted visibility by:
+    /** Handle the user toggling the hidden visibility by:
      *      (1) storing the new value in the persistent storage
      *      (2) re-rendering the history
      * @returns {Boolean} new show_hidden setting

client/galaxy/scripts/mvc/list/list-item.js

@@ -380,7 +380,7 @@ ListItemView.prototype.templates = (function(){
  *  _renderDetails does the work of creating this.details: a sub-view that shows the nested list
  */
 var FoldoutListItemView = ListItemView.extend({
-    
+
     /** If 'foldout': show the sub-panel inside the expanded item
      *  If 'drilldown': only fire events and handle by pub-sub
      *      (allow the panel containing this item to attach it, hide itself, etc.)

client/galaxy/scripts/mvc/list/list-panel.js

@@ -364,11 +364,11 @@ var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(
         if( panel.views.length ){
             panel._attachItems( $whereTo );
             panel.$emptyMessage( $whereTo ).hide();
-            
+
         } else {
             panel._renderEmptyMessage( $whereTo ).show();
         }
-        
+
         return panel.views;
     },
 
@@ -543,7 +543,7 @@ var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(
 
     /** get views based on model.id */
     viewFromModelId : function( id ){
-        for( var i=0; i<this.views.length; i++ ){
+        for( var i = 0; i < this.views.length; i++ ){
             if( this.views[i].model.id === id ){
                 return this.views[i];
             }

static/maps/galaxy.interactive_environments.js.map

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+{"version":3,"file":"galaxy.interactive_environments.js","sources":["../src/galaxy.interactive_environments.js"],"names":["append_notebook","url","clear_main_area","$","append","remove","children","display_spinner","galaxy_root","test_ie_availability","success_callback","request_count","interval","setInterval","ajax","xhrFields","withCredentials","type","timeout","success","console","log","clearInterval","error","toastr","closeButton","timeOut","tapToDismiss"],"mappings":"AAIA,QAASA,iBAAgBC,GACrBC,kBACAC,EAAE,SAASC,OAAO,uHAAwHH,EAAK,eAInJ,QAASC,mBACLC,EAAE,YAAYE,SACdF,EAAE,SAASG,WAAWD,SAG1B,QAASE,mBACDJ,EAAE,SAASC,OAAO,0BAA4BI,YAAc,yGAWpE,QAASC,sBAAqBR,EAAKS,GAC/B,GAAIC,GAAgB,CACpBJ,mBACAK,SAAWC,YAAY,WACnBV,EAAEW,MACEb,IAAKA,EACLc,WACIC,iBAAiB,GAErBC,KAAM,MACNC,QAAS,IACTC,QAAS,WACLC,QAAQC,IAAI,8BACZC,cAAcV,UACdF,KAEJa,MAAO,WACHZ,IACAS,QAAQC,IAAI,WAAaV,GACtBA,EAAgB,KACfW,cAAcV,UACdV,kBACAsB,OAAOD,MACH,sDACA,SACCE,aAAe,EAAMC,QAAW,IAAOC,cAAgB,SAKzE"}

static/maps/libs/toastr.js.map

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static/maps/mvc/collection/collection-li.js.map

@@ -1 +1 @@
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static/maps/mvc/collection/collection-panel.js.map

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static/maps/mvc/form/form-parameters.js.map

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static/maps/mvc/form/form-repeat.js.map

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static/maps/mvc/form/form-select-content.js.map

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static/maps/mvc/job/job-model.js.map

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static/maps/mvc/tools/tools-form-workflow.js.map

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static/maps/mvc/tools/tools-jobs.js.map

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static/maps/mvc/ui/ui-select.js.map

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static/maps/utils/deferred.js.map

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static/maps/utils/utils.js.map

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static/scripts/galaxy.interactive_environments.js

@@ -1,2 +1,2 @@
-function append_notebook(a){clear_main_area(),$("#main").append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="'+a+'"></iframe>')}function clear_main_area(){$("#spinner").remove(),$("#main").children().remove()}function display_spinner(){$("#main").append('<img id="spinner" src="'+galaxy_root+'/static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">')}function test_ie_availability(a,b){var c=0;display_spinner(),interval=setInterval(function(){$.ajax({url:a,xhrFields:{withCredentials:!0},type:"GET",timeout:500,success:function(){clearInterval(interval),b()},error:function(){c++,c>30&&(clearInterval(interval),clear_main_area(),toastr.error("Could not connect to IE, contact your administrator","Error",{closeButton:!0,timeOut:2e4,tapToDismiss:!1}))}})},1e3)}
+function append_notebook(a){clear_main_area(),$("#main").append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="'+a+'"></iframe>')}function clear_main_area(){$("#spinner").remove(),$("#main").children().remove()}function display_spinner(){$("#main").append('<img id="spinner" src="'+galaxy_root+'/static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">')}function test_ie_availability(a,b){var c=0;display_spinner(),interval=setInterval(function(){$.ajax({url:a,xhrFields:{withCredentials:!0},type:"GET",timeout:500,success:function(){console.log("Connected to IE, returning"),clearInterval(interval),b()},error:function(){c++,console.log("Request "+c),c>30&&(clearInterval(interval),clear_main_area(),toastr.error("Could not connect to IE, contact your administrator","Error",{closeButton:!0,timeOut:2e4,tapToDismiss:!1}))}})},1e3)}
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static/scripts/libs/toastr.js

@@ -1,2 +1,2 @@
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static/scripts/mvc/collection/collection-li.js

@@ -1,2 +1,2 @@
-define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){e.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank"},_renderSubtitle:function(){var a=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return a.text(d("a list of datasets"));case"paired":return a.text(d("a pair of datasets"));case"list:paired":return a.text(d("a list of paired datasets"))}return a},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget})},$selector:function(){return this.$("> .selector")},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCListItemView("+a+")"}});g.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{titleBar:a})}();var h=f.extend({className:f.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DCEListItemView.initialize:",a),f.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCEListItemView("+a+")"}});h.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},f.prototype.templates,{titleBar:a})}();var i=b.DatasetListItemView.extend({className:b.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DatasetDCEListItemView.initialize:",a),b.DatasetListItemView.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+a+")"}});i.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},b.DatasetListItemView.prototype.templates,{titleBar:a})}();var j=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(a){g.prototype._swapNewRender.call(this,a);var b=this.model.get("state")||"ok";return this.$el.addClass("state-"+b),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
+define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,e.prototype.initialize.call(this,a)},_renderSubtitle:function(){var a=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return a.text(d("a list of datasets"));case"paired":return a.text(d("a pair of datasets"));case"list:paired":return a.text(d("a list of paired datasets"))}return a},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCListItemView("+a+")"}});g.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{titleBar:a})}();var h=f.extend({className:f.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DCEListItemView.initialize:",a),f.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCEListItemView("+a+")"}});h.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},f.prototype.templates,{titleBar:a})}();var i=b.DatasetListItemView.extend({className:b.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DatasetDCEListItemView.initialize:",a),b.DatasetListItemView.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+a+")"}});i.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},b.DatasetListItemView.prototype.templates,{titleBar:a})}();var j=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(a){g.prototype._swapNewRender.call(this,a);var b=this.model.get("state")||"ok";return this.$el.addClass("state-"+b),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
 //# sourceMappingURL=../../../maps/mvc/collection/collection-li.js.map

static/scripts/mvc/form/form-parameters.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(a,b,c,d,e){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a)),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(!this.app.options.is_dynamic)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){c.options&&(c.area=c.multiple,a.validate(c.value)?c.value instanceof Array?c.value=value.toString():(c.value=String(c.value).replace(/[\[\]'"\s]/g,""),c.multiple&&(c.value=c.value.replace(/,/g,"\n"))):c.value="");var d=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){d.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new e({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
+define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(a,b,c,d,e){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(!this.app.options.is_dynamic)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){c.options&&(c.area=c.multiple,a.validate(c.value)?c.value instanceof Array?c.value=value.toString():(c.value=String(c.value).replace(/[\[\]'"\s]/g,""),c.multiple&&(c.value=c.value.replace(/,/g,"\n"))):c.value="");var d=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){d.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new e({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map

static/scripts/mvc/form/form-repeat.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("<div/>");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(a.id&&!this.list[a.id]){this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()}},del:function(a){if(this.list[a]){this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()}},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("<div/>");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(!a.id||this.list[a.id])return void console.debug("form-repeat::add - Duplicate repeat block id.");this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(a){if(!this.list[a])return void console.debug("form-repeat::del - Invalid repeat block id.");this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}});
 //# sourceMappingURL=../../../maps/mvc/form/form-repeat.js.map

static/scripts/mvc/form/form-select-content.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){history={};var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d;var e=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var c=[];for(var d in b){var e=b[d];c.push({label:e.hid+": "+e.name,value:e.id}),history[e.id+"_"+e.src]=e}a.update(c)}}b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:c}});
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){history={};var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d;var e=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var c=[];for(var d in b){var e=b[d];c.push({label:e.hid+": "+e.name,value:e.id}),history[e.id+"_"+e.src]=e}a.update(c)}}b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/form/form-select-content.js.map

static/scripts/mvc/form/form-view.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change")}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message})}})});
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),console.debug("tools-form-base::initialize() - Completed.")}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map

static/scripts/mvc/job/job-model.js

@@ -1,2 +1,2 @@
-define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}});
+define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){console.debug(a,b)},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){console.debug(this);var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}});
 //# sourceMappingURL=../../../maps/mvc/job/job-model.js.map

static/scripts/mvc/tools/tools-form-base.js

@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("<div/>"),this.container=a.container||"body",$(this.container).append(this.$el),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this,d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g)},error:function(a){c.deferred.done(g);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url,c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("<div/>"),this.container=a.container||"body",$(this.container).append(this.$el),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this,d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url,c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map

static/scripts/mvc/tools/tools-form-workflow.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,this.node){this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:!1,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&(a.optional=-1==["data","data_hidden","hidden","repeat","conditional"].indexOf(a.type))}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})}},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={label:"Add Actions: '"+a+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:!1,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&(a.optional=-1==["data","data_hidden","hidden","repeat","conditional"].indexOf(a.type))}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={label:"Add Actions: '"+a+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map

static/scripts/mvc/tools/tools-jobs.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}});
+define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map

static/scripts/mvc/ui/ui-select.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.options.container&&(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple)){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-select.js.map

static/scripts/utils/deferred.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})});
+define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,console.debug("Deferred:register() - Register "+b),b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,console.debug("Deferred:done() - Unregister "+a),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})});
 //# sourceMappingURL=../../maps/utils/deferred.js.map

static/scripts/utils/utils.js

@@ -1,2 +1,2 @@
-define(["libs/underscore"],function(a){function b(a,c){for(var d in a){var e=a[d];e&&"object"==typeof e&&(c(e),b(e,c))}}function c(a){return $("<div/>").text(a).html()}function d(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__","None",null,void 0].indexOf(a[b])>-1)return!1;return!0}function e(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function f(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?a.success&&a.success(top.__utils__get__[a.url]):g({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function g(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function h(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function i(a){$('link[href^="'+a+'"]').length||$('<link href="'+galaxy_config.root+a+'" rel="stylesheet">').appendTo("head")}function j(b,c){return b?a.defaults(b,c):c}function k(a,b){var c="";if(a>=1e11)a/=1e11,c="TB";else if(a>=1e8)a/=1e8,c="GB";else if(a>=1e5)a/=1e5,c="MB";else if(a>=100)a/=100,c="KB";else{if(!(a>0))return"<strong>-</strong>";a=10*a,c="b"}var d=Math.round(a)/10;return b?d+" "+c:"<strong>"+d+"</strong> "+c}function l(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function m(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes(),d=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c;return d}return{cssLoadFile:i,cssGetAttribute:h,get:f,merge:j,bytesToString:k,uid:l,time:m,request:g,sanitize:c,textify:e,validate:d,deepeach:b}});
+define(["libs/underscore"],function(a){function b(a,c){for(var d in a){var e=a[d];e&&"object"==typeof e&&(c(e),b(e,c))}}function c(a){return $("<div/>").text(a).html()}function d(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__","None",null,void 0].indexOf(a[b])>-1)return!1;return!0}function e(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function f(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):g({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function g(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function h(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function i(a){$('link[href^="'+a+'"]').length||$('<link href="'+galaxy_config.root+a+'" rel="stylesheet">').appendTo("head")}function j(b,c){return b?a.defaults(b,c):c}function k(a,b){var c="";if(a>=1e11)a/=1e11,c="TB";else if(a>=1e8)a/=1e8,c="GB";else if(a>=1e5)a/=1e5,c="MB";else if(a>=100)a/=100,c="KB";else{if(!(a>0))return"<strong>-</strong>";a=10*a,c="b"}var d=Math.round(a)/10;return b?d+" "+c:"<strong>"+d+"</strong> "+c}function l(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function m(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes(),d=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c;return d}return{cssLoadFile:i,cssGetAttribute:h,get:f,merge:j,bytesToString:k,uid:l,time:m,request:g,sanitize:c,textify:e,validate:d,deepeach:b}});
 //# sourceMappingURL=../../maps/utils/utils.js.map

static/style/blue/base.css

@@ -2017,6 +2017,8 @@ div.permissionContainer{padding-left:20px}
 .list-panel .controls>*:not(:empty){margin-bottom:8px}
 .list-panel .controls .name{word-wrap:break-word;font-weight:bold}
 .list-panel .controls .subtitle{color:#777;font-size:90%}.list-panel .controls .subtitle a{color:inherit}
+.list-panel .controls .editable-text{border:solid transparent 1px}
+.list-panel .controls .editable-text:hover{cursor:pointer;border:1px dotted #999999}
 .list-panel .controls .actions{display:inline-block;float:right}.list-panel .controls .actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none}
 .list-panel .controls .actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px}
 .list-panel .controls .actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px}
@@ -2088,31 +2090,27 @@ div.permissionContainer{padding-left:20px}
 .dataset .details .dataset-peek{margin-bottom:8px;width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset .details .dataset-peek th{color:white;background:#5f6990}
 .dataset .details .dataset-peek table,.dataset .details .dataset-peek th,.dataset .details .dataset-peek tr,.dataset .details .dataset-peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px}
 .history-content.dataset .title-bar .title .hid:after,.history-content.dataset-collection .title-bar .title .hid:after{content:':'}
-.history-panel .controls{margin:10px 10px 0px 10px;padding:0px}.history-panel .controls .messages{margin-bottom:0px}.history-panel .controls .messages>*{cursor:pointer}.history-panel .controls .messages>*:last-child{margin-bottom:8px}
-.history-panel .controls .title{margin-bottom:4px}.history-panel .controls .title input{width:100%;margin:-3px 0 -3px -3px;font-weight:bold}
-.history-panel .controls .subtitle:not(:empty){margin-top:-4px;margin-bottom:6px}
-.history-panel .controls .editable-text{border:solid transparent 1px}
-.history-panel .controls .editable-text:hover{cursor:pointer;border:1px dotted #999999}
-.history-panel .controls .history-size{display:inline-block;margin-top:4px;color:black}
-.history-panel .controls .actions{margin-bottom:0px}
-.history-panel .controls .quota-message{display:none;margin:8px 0px 5px 0px}
-.history-panel .controls .tags-display,.history-panel .controls .annotation-display{display:none;margin-bottom:8px}.history-panel .controls .tags-display label,.history-panel .controls .annotation-display label{display:block;margin:0px;padding:0px;font-weight:normal;color:#555}
-.history-panel .controls .tags-display label:after,.history-panel .controls .annotation-display label:after{content:':'}
-.history-panel .controls .tags-display .select2-container{min-width:0px}.history-panel .controls .tags-display .select2-container .select2-choices{border-radius:3px}
-.history-panel .controls .tags-display input{border-radius:3px}
-.history-panel .controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-wrap;overflow:auto}
-.history-panel .controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'}
-.history-panel .controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%}
+.history-panel>.controls{margin:10px 10px 0px 10px;padding:0px}.history-panel>.controls .messages{margin-bottom:0px}.history-panel>.controls .messages>*{cursor:pointer}.history-panel>.controls .messages>*:last-child{margin-bottom:8px}
+.history-panel>.controls .title{margin-bottom:4px}.history-panel>.controls .title input{width:100%;margin:-3px 0 -3px -3px;font-weight:bold}
+.history-panel>.controls .subtitle:not(:empty){margin-top:-4px;margin-bottom:6px}
+.history-panel>.controls .history-size{display:inline-block;margin-top:4px;color:black}
+.history-panel>.controls .actions{margin-bottom:0px}
+.history-panel>.controls .quota-message{display:none;margin:8px 0px 5px 0px}
+.history-panel>.controls .tags-display,.history-panel>.controls .annotation-display{display:none;margin-bottom:8px}.history-panel>.controls .tags-display label,.history-panel>.controls .annotation-display label{display:block;margin:0px;padding:0px;font-weight:normal;color:#555}
+.history-panel>.controls .tags-display label:after,.history-panel>.controls .annotation-display label:after{content:':'}
+.history-panel>.controls .tags-display .select2-container{min-width:0px}.history-panel>.controls .tags-display .select2-container .select2-choices{border-radius:3px}
+.history-panel>.controls .tags-display input{border-radius:3px}
+.history-panel>.controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-wrap;overflow:auto}
+.history-panel>.controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'}
+.history-panel>.controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%}
 .history-panel .list-item.history-content{border-width:1px 0px 0px 0px}.history-panel .list-item.history-content:last-child{border-width:1px 0px 1px 0px}
 .history-panel .empty-message{margin:0px 10px 0px 10px}
 .history-panel .dataset-collection .subtitle{margin-top:2px}
-.history-panel .dataset-collection-panel .controls{padding:0px}
-.history-panel .dataset-collection-panel .list-items{margin-top:0px}
-.annotated-history-panel .controls{margin:0px}.annotated-history-panel .controls .name{font-size:150%;margin-bottom:4px}
-.annotated-history-panel .controls .subtitle{color:black}.annotated-history-panel .controls .subtitle:not(:empty){margin:0px 0px 0px 4px}
-.annotated-history-panel .controls .messages:not(:empty){margin-top:16px}
-.annotated-history-panel .controls .annotation-display{display:block;border:1px solid lightgrey;border-width:1px 0px 0px 0px;padding:4px 0px 4px 0px;margin:4px 4px 0px 4px;white-space:pre-wrap}.annotated-history-panel .controls .annotation-display:empty{display:none}
-.annotated-history-panel .controls .search{padding:16px 0px 0px 0px;margin-bottom:0px}
+.annotated-history-panel>.controls{margin:0px}.annotated-history-panel>.controls .name{font-size:150%;margin-bottom:4px}
+.annotated-history-panel>.controls .subtitle{color:black}.annotated-history-panel>.controls .subtitle:not(:empty){margin:0px 0px 0px 4px}
+.annotated-history-panel>.controls .messages:not(:empty){margin-top:16px}
+.annotated-history-panel>.controls .annotation-display{display:block;border:1px solid lightgrey;border-width:1px 0px 0px 0px;padding:4px 0px 4px 0px;margin:4px 4px 0px 4px;white-space:pre-wrap}.annotated-history-panel>.controls .annotation-display:empty{display:none}
+.annotated-history-panel>.controls .search{padding:16px 0px 0px 0px;margin-bottom:0px}
 .annotated-history-panel table.list-items{width:100%;table-layout:fixed}.annotated-history-panel table.list-items .headers{border-bottom:2px solid grey}
 .annotated-history-panel table.list-items .headers th{padding:8px}
 .annotated-history-panel table.list-items>tbody>tr{cursor:pointer;border-bottom:1px solid grey}.annotated-history-panel table.list-items>tbody>tr>td{margin:0px;padding:0px;vertical-align:top}.annotated-history-panel table.list-items>tbody>tr>td:nth-child(1){width:50%}
@@ -2201,7 +2199,7 @@ pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Cons
 .dataset-collection-panel{margin:0px;padding:0px}.dataset-collection-panel .vertically-spaced{margin-top:4px}
 .dataset-collection-panel .controls{padding:8px}.dataset-collection-panel .controls .navigation{margin-top:4px}.dataset-collection-panel .controls .navigation .back .fa-icon{margin-right:4px;font-size:120%;font-weight:bold;text-decoration:none}
 .dataset-collection-panel .controls .title{margin-top:12px}.dataset-collection-panel .controls .title .name{font-weight:bold}
-.dataset-collection-panel .list-items{margin-top:8px}.dataset-collection-panel .list-items .dataset-collection-element{border-width:1px 0px 0px 0px}.dataset-collection-panel .list-items .dataset-collection-element:last-child{border-bottom-width:1px}
+.dataset-collection-panel .list-items .dataset-collection-element{border-width:1px 0px 0px 0px}.dataset-collection-panel .list-items .dataset-collection-element:last-child{border-bottom-width:1px}
 .job.list-item{border:1px solid #bfbfbf}.job.list-item .title-bar .subtitle{color:grey;font-size:80%}
 .job.list-item>.details{padding:0px}.job.list-item>.details .params{padding:0px 8px 0px 8px}.job.list-item>.details .params .param .prompt,.job.list-item>.details .params .input .prompt{font-size:80%;color:grey}
 .job.list-item>.details .params .param .value,.job.list-item>.details .params .input .value{display:inline-block;font-weight:bold}

static/style/src/less/collections.less

@@ -33,7 +33,7 @@
 
     .controls {
         padding: 8px;
-        
+
         .navigation {
             margin-top: 4px;
             .back {
@@ -54,7 +54,6 @@
         }
     }
     .list-items {
-        margin-top: 8px;
         .dataset-collection-element {
             border-width: 1px 0px 0px 0px;
             &:last-child {

static/style/src/less/history.less

@@ -238,7 +238,7 @@
             .visualizations-dropdown {
                 display: inline-block;
             }
-            
+
             .left {
                 .icon-btn-group();
                 float: left;
@@ -347,7 +347,7 @@
 // ---------------------------------------------------------------------------- history
 .history-panel {
 
-    .controls {
+    & > .controls {
         margin: 10px 10px 0px 10px;
         padding: 0px;
 
@@ -374,14 +374,6 @@
             margin-top: -4px;
             margin-bottom: 6px;
         }
-        .editable-text {
-            border: solid transparent 1px;
-        }
-        .editable-text:hover {
-            cursor: pointer;
-            border: 1px dotted #999999;
-        }
-
         .history-size {
             display: inline-block;
             margin-top: 4px;
@@ -473,20 +465,12 @@
             margin-top: 2px;
         }
     }
-    .dataset-collection-panel {
-        .controls {
-            padding: 0px;
-        }
-        .list-items {
-            margin-top: 0px;
-        }
-    }
 }
 
 
 // ---------------------------------------------------------------------------- annotated-history-panel
 .annotated-history-panel {
-    .controls {
+    & > .controls {
         margin: 0px;
         .name {
             font-size: 150%;

static/style/src/less/list-item.less

@@ -143,6 +143,14 @@
                 color: inherit;
             }
         }
+        .editable-text {
+            border: solid transparent 1px;
+        }
+        .editable-text:hover {
+            cursor: pointer;
+            border: 1px dotted #999999;
+        }
+
         .actions {
             .icon-btn-group();
             float: right;