diff --git a/client/galaxy/scripts/mvc/collection/base-creator.js b/client/galaxy/scripts/mvc/collection/base-creator.js index 23cbb66d228..2a1f7ea446f 100644 --- a/client/galaxy/scripts/mvc/collection/base-creator.js +++ b/client/galaxy/scripts/mvc/collection/base-creator.js @@ -93,8 +93,8 @@ var CollectionCreatorMixin = { } }, - _setUpCommonSettings : function( ) { - this.hideOriginals = false; + _setUpCommonSettings : function( attributes ) { + this.hideOriginals = attributes.defaultHideSourceItems || false; }, /** render the footer, completion controls, and cancel controls */ diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js index 22173880b06..59560e1440e 100644 --- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js @@ -195,7 +195,7 @@ var ListCollectionCreator = Backbone.View.extend( BASE_MVC.LoggableMixin ).exten /** unordered, original list - cache to allow reversal */ creator.initialElements = attributes.elements || []; - this._setUpCommonSettings(); + this._setUpCommonSettings( attributes ); this._instanceSetUp(); this._elementsSetUp(); this._setUpBehaviors(); @@ -948,9 +948,10 @@ var listCollectionCreatorModal = function _listCollectionCreatorModal( elements, /** Use a modal to create a list collection, then add it to the given history contents. * @returns {Deferred} resolved when the collection is added to the history. */ -function createListCollection( contents ){ +function createListCollection( contents, defaultHideSourceItems ){ var elements = contents.toJSON(), promise = listCollectionCreatorModal( elements, { + defaultHideSourceItems: defaultHideSourceItems, creationFn : function( elements, name, hideSourceItems ){ elements = elements.map( function( element ){ return { diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js index 0dcf1313fb0..884f9a51180 100644 --- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js @@ -259,7 +259,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** Used for blocking UI events during ajax/operations (don't post twice) */ this.blocking = false; - this._setUpCommonSettings(); + this._setUpCommonSettings( attributes ); this._setUpBehaviors(); this._dataSetUp(); }, @@ -1642,11 +1642,12 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datas //============================================================================= -function createListOfPairsCollection( collection ){ +function createListOfPairsCollection( collection, defaultHideSourceItems ){ var elements = collection.toJSON(); //TODO: validate elements return pairedCollectionCreatorModal( elements, { - historyId : collection.historyId + historyId : collection.historyId, + defaultHideSourceItems: defaultHideSourceItems }); } diff --git a/client/galaxy/scripts/mvc/collection/pair-collection-creator.js b/client/galaxy/scripts/mvc/collection/pair-collection-creator.js index 17b90b35fbb..51231e2831d 100644 --- a/client/galaxy/scripts/mvc/collection/pair-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/pair-collection-creator.js @@ -230,9 +230,10 @@ var pairCollectionCreatorModal = function _pairCollectionCreatorModal( elements, /** Use a modal to create a pair collection, then add it to the given history contents. * @returns {Deferred} resolved when the collection is added to the history. */ -function createPairCollection( contents ){ +function createPairCollection( contents, defaultHideSourceItems ){ var elements = contents.toJSON(), promise = pairCollectionCreatorModal( elements, { + defaultHideSourceItems: defaultHideSourceItems, creationFn : function( elements, name, hideSourceItems ){ elements = [ { name: "forward", src: "hda", id: elements[0].id }, diff --git a/client/galaxy/scripts/mvc/history/history-view-edit.js b/client/galaxy/scripts/mvc/history/history-view-edit.js index 0432f62334c..ceb984b23f7 100644 --- a/client/galaxy/scripts/mvc/history/history-view-edit.js +++ b/client/galaxy/scripts/mvc/history/history-view-edit.js @@ -295,9 +295,10 @@ var HistoryViewEdit = _super.extend( ]; }, - buildCollection : function( collectionType, selection ) { + buildCollection : function( collectionType, selection, hideSourceItems ) { var panel = this; var selection = selection || panel.getSelectedModels(); + var hideSourceItems = hideSourceItems || false; var createFunc; if( collectionType == "list" ) { createFunc = LIST_COLLECTION_CREATOR.createListCollection; @@ -308,7 +309,7 @@ var HistoryViewEdit = _super.extend( } else { console.warn( "Unknown collectionType encountered " + collectionType ); } - createFunc( selection ).done( function() { panel.model.refresh() } ); + createFunc( selection, hideSourceItems ).done( function() { panel.model.refresh() } ); }, // ------------------------------------------------------------------------ sub-views diff --git a/client/galaxy/scripts/mvc/upload/collection/collection-row.js b/client/galaxy/scripts/mvc/upload/collection/collection-row.js new file mode 100644 index 00000000000..30e70beac6b --- /dev/null +++ b/client/galaxy/scripts/mvc/upload/collection/collection-row.js @@ -0,0 +1,163 @@ +/** Renders the collection uploader rows */ +define( [ 'utils/utils', 'mvc/upload/upload-model', 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', 'mvc/ui/ui-select' ], +function( Utils, UploadModel, UploadSettings, Popover, Select ) { + return Backbone.View.extend({ + /** Dictionary of upload states and associated icons */ + status_classes : { + init : 'upload-icon-button fa fa-trash-o', + queued : 'upload-icon fa fa-spinner fa-spin', + running : 'upload-icon fa fa-spinner fa-spin', + success : 'upload-icon-button fa fa-check', + error : 'upload-icon-button fa fa-exclamation-triangle' + }, + + initialize: function( app, options ) { + var self = this; + this.app = app; + this.model = options.model; + this.setElement( this._template( options.model ) ); + this.$mode = this.$( '.upload-mode' ); + this.$title = this.$( '.upload-title-extended' ); + this.$text = this.$( '.upload-text' ); + this.$size = this.$( '.upload-size' ); + this.$info_text = this.$( '.upload-info-text' ); + this.$info_progress = this.$( '.upload-info-progress' ); + this.$text_content = this.$( '.upload-text-content' ); + this.$symbol = this.$( '.upload-symbol' ); + this.$progress_bar = this.$( '.upload-progress-bar' ); + this.$percentage = this.$( '.upload-percentage' ); + + // append popup to settings icon + this.settings = new Popover.View({ + title : 'Upload configuration', + container : this.$( '.upload-settings' ), + placement : 'bottom' + }); + + // identify default genome and extension values + var default_genome = this.app.select_genome.value(); + var default_extension = this.app.select_extension.value(); + + // handle click event + this.$symbol.on('click', function() { self._removeRow(); }); + + // handle text editing event + this.$text_content.on( 'change input', function( e ) { + self.model.set( { 'url_paste': $( e.target ).val(), + 'file_size': $( e.target ).val().length } ); + }); + + // model events + this.listenTo( this.model, 'change:percentage', function() { self._refreshPercentage() } ); + this.listenTo( this.model, 'change:status', function() { self._refreshStatus() } ); + this.listenTo( this.model, 'change:info', function() { self._refreshInfo() } ); + this.listenTo( this.model, 'change:file_size', function() { self._refreshFileSize() } ); + this.listenTo( this.model, 'remove', function() { self.remove() } ); + this.app.collection.on('reset', function() { self.remove() } ); + }, + + render: function() { + var options = this.model.attributes; + this.$title.html( _.escape( options.file_name ) ); + this.$size.html( Utils.bytesToString ( options.file_size ) ); + this.$mode.removeClass().addClass( 'upload-mode' ).addClass( 'text-primary' ); + if ( options.file_mode == 'new' ) { + this.$text.css( { 'width' : this.$el.width() - 16 + 'px', 'top' : this.$el.height() - 8 + 'px' } ).show(); + this.$el.height( this.$el.height() - 8 + this.$text.height() + 16 ); + this.$mode.addClass( 'fa fa-edit' ); + } else if ( options.file_mode == 'local' ) { + this.$mode.addClass( 'fa fa-laptop' ); + } else if ( options.file_mode == 'ftp' ) { + this.$mode.addClass( 'fa fa-folder-open-o' ); + } + }, + + /** Refresh info text */ + _refreshInfo: function() { + var info = this.model.get( 'info' ); + if ( info ) { + this.$info_text.html( 'Failed: ' + info ).show(); + } else { + this.$info_text.hide(); + } + }, + + /** Refresh percentage status */ + _refreshPercentage : function() { + var percentage = parseInt( this.model.get( 'percentage' ) ); + this.$progress_bar.css( { width : percentage + '%' } ); + this.$percentage.html( percentage != 100 ? percentage + '%' : 'Adding to history...' ); + }, + + /** Refresh status */ + _refreshStatus : function() { + var status = this.model.get( 'status' ); + this.$symbol.removeClass().addClass( 'upload-symbol' ).addClass( this.status_classes[ status ] ); + this.model.set( 'enabled', status == 'init' ); + var enabled = this.model.get( 'enabled' ); + this.$text_content.attr( 'disabled', !enabled ); + if ( status == 'success' ) { + this.$el.addClass( 'success' ); + this.$percentage.html( '100%' ); + } + if ( status == 'error' ) { + this.$el.addClass( 'danger' ); + this.$info_progress.hide(); + } + }, + + /** Refresh file size */ + _refreshFileSize: function() { + this.$size.html( Utils.bytesToString ( this.model.get( 'file_size' ) ) ); + }, + + /** Remove row */ + _removeRow: function() { + if ( [ 'init', 'success', 'error' ].indexOf( this.model.get( 'status' ) ) !== -1 ) { + this.app.collection.remove( this.model ); + } + }, + + /** Attach file info popup */ + _showSettings : function() { + if ( !this.settings.visible ) { + this.settings.empty(); + this.settings.append( ( new UploadSettings( this ) ).$el ); + this.settings.show(); + } else { + this.settings.hide(); + } + }, + + /** View template */ + _template: function( options ) { + return '' + + '' + + '
' + + '
' + + '
' + + '
' + + '
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
' + + '',"
","
"].join("")}});return{CitationView:n,CitationListView:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(o,a,r){n=[i(42),i(33),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.FoldoutListItemView,l=e.ListItemView,c=s.extend({className:s.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,s.prototype.initialize.call(this,e)},_setUpListeners:function(){s.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(e,t){o.has(e.changed,"deleted")?this.render():o.has(e.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var e=s.prototype._getFoldoutPanelOptions.call(this);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCListItemView("+e+")"}});c.prototype.templates=function(){var e=o.extend({},s.prototype.templates.warnings,{error:i.wrapTemplate(["<% if( model.error ){ %>",'
',n("There was an error getting the data for this collection"),": <%- model.error %>","
","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'
',n("This collection has been deleted and removed from disk"),"
","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',n("This collection has been deleted"),"
","<% } %>"])}),t=i.wrapTemplate(['
','
','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection"),a=i.wrapTemplate(['
','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',n("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',n("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',n("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',n("a list of <%- countText %>dataset lists"),"<% } %>","
"],"collection");return o.extend({},s.prototype.templates,{warnings:e,titleBar:t,subtitle:a})}();var d=l.extend({className:l.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),l.prototype.initialize.call(this,e)},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCEListItemView("+e+")"}});d.prototype.templates=function(){var e=i.wrapTemplate(['
','
','<%- element.element_identifier %>',"
",'
',"
"],"element");return o.extend({},l.prototype.templates,{titleBar:e})}();var h=t.DatasetListItemView.extend({className:t.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),t.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):r.when()},toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+e+")"}});h.prototype.templates=function(){var e=i.wrapTemplate(['
','','
','<%- element.element_identifier %>',"
","
"],"element");return o.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(e){c.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(71),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return o.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",a.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=a.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),c=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:o.extend({},e.DatasetAssociation.prototype.defaults,n.defaults),constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),n.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){var e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),d=l.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=a.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=a.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),g=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),f=l.extend({model:g,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=f.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),w=f.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(42),i(12),i(21),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var c="dataset",d=e.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),d.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t,i){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):o.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return d.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===t.NOT_VIEWABLE||e===t.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(e===t.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(e===t.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),e.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===t.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var e=d.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=r('
'),i=e.model.toJSON();return l.each(e.templates.detailMessages,function(n){t.append(r(n(i,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case t.NOT_VIEWABLE:return[];case t.OK:case t.FAILED_METADATA:case t.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:l.isEmpty(this.model.get("meta_files"))?r(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return r(['
','','',"",'","
"].join("\n"))},events:l.extend(l.clone(d.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetListItemView("+e+")"}});return h.prototype.templates=function(){var e=l.extend({},d.prototype.templates.warnings,{failed_metadata:n.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
',s("An error occurred setting the metadata for this dataset"),"
","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'
',s("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'
',s("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',s("This dataset has been deleted"),"
","<% } %>"])}),i=n.wrapTemplate(['
','
','
','
','
',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'
','
','
',"<% if( dataset.peek ){ %>",'
<%= dataset.peek %>
',"<% } %>","<% } %>","
"],"dataset"),o=n.wrapTemplate(['
','
',s("You do not have permission to view this dataset"),"
","
"],"dataset"),a={};a[t.OK]=a[t.FAILED_METADATA]=n.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
','<%- dataset.misc_blurb %>',"
","<% } %>","<% if( dataset.file_ext ){ %>",'
','",'<%- dataset.file_ext %>',"
","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
','",'',"<%- dataset.metadata_dbkey %>","","
","<% } %>","<% if( dataset.misc_info ){ %>",'
','<%- dataset.misc_info %>',"
","<% } %>"],"dataset"),a[t.NEW]=n.wrapTemplate(["
",s("This is a new dataset and not all of its data are available yet"),"
"],"dataset"),a[t.NOT_VIEWABLE]=n.wrapTemplate(["
",s("You do not have permission to view this dataset"),"
"],"dataset"),a[t.DISCARDED]=n.wrapTemplate(["
",s("The job creating this dataset was cancelled before completion"),"
"],"dataset"),a[t.QUEUED]=n.wrapTemplate(["
",s("This job is waiting to run"),"
"],"dataset"),a[t.RUNNING]=n.wrapTemplate(["
",s("This job is currently running"),"
"],"dataset"),a[t.UPLOAD]=n.wrapTemplate(["
",s("This dataset is currently uploading"),"
"],"dataset"),a[t.SETTING_METADATA]=n.wrapTemplate(["
",s("Metadata is being auto-detected"),"
"],"dataset"),a[t.PAUSED]=n.wrapTemplate(["
",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
"],"dataset"),a[t.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","
<%- dataset.misc_blurb %>
","<% } %>",'',s("An error occurred with this dataset"),":",'
<%- dataset.misc_info %>
'],"dataset"),a[t.EMPTY]=n.wrapTemplate(["
",s("No data"),": <%- dataset.misc_blurb %>
"],"dataset"),a.unknown=n.wrapTemplate(['
Error: unknown dataset state: "<%- dataset.state %>"
'],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'
',s("The job creating this dataset has been resubmitted"),"
","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:e,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4)],s=function(e){var t=o.Model.extend({initialize:function(e){this.app=e},checksum:function(){var e="",t=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=t.app.field_list[i];n&&(e+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),e},create:function(){function e(e,t,i){n.flat_dict[e]=t,o[e]=i,n.app.element_list[t]&&n.app.element_list[t].$el.attr("tour_id",e)}function t(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);g!=-1&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(e,t){return e-t});var a=0;for(var f in h)t(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();e(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);v!=-1&&t(c,o[l.id+"-section-"+v]);break;case"section":t(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),e(c,l.id,m),l.payload))for(var y in l.payload)e(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},t("",s),o},match:function(e){return this.flat_dict&&this.flat_dict[e]},matchCase:function(e,t){return i(e,t)},matchModel:function(e,t){var i=this;n(e.inputs,function(e,n){i.flat_dict[n]&&t(e,i.flat_dict[n])})},matchResponse:function(e){function t(e,s){if("string"==typeof s){var o=n.flat_dict[e];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==e){var l="|";s instanceof Array&&(l="_"),r=e+l+r}t(r,s[a])}}var i={},n=this;return t("",e),i},_iterate:function(e,t){var i=this,n=a(e).children();n.each(function(){var e=this,n=a(e).attr("id");if(a(e).hasClass("section-row")){var s=i.app.input_list[n];t[n]=s&&{input:s}||{},i._iterate(e,t[n])}else i._iterate(e,t)})}}),i=function(e,t){"boolean"==e.test_param.type&&(t="true"==t?e.test_param.truevalue||"true":e.test_param.falsevalue||"false");for(var i in e.cases)if(e.cases[i].value==t)return i;return-1},n=function(e,t,s,o){o=a.extend(!0,{},o),r.each(e,function(e){e&&e.type&&e.name&&(o[e.name]=e)});for(var l in e){var c=e[l];c.name=c.name||l;var d=s?s+"|"+c.name:c.name;switch(c.type){case"repeat":r.each(c.cache,function(e,i){n(e,t,d+"_"+i,o)});break;case"conditional":if(c.test_param){t(c.test_param,d+"|"+c.test_param.name,o);var h=i(c,c.test_param.value);h!=-1?n(c.cases[h].inputs,t,d,o):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+d+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+d+".");break;case"section":n(c.inputs,t,d,o);break;default:t(c,d,o)}}};return{Manager:t,visitInputs:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(i,o,a){n=[],s=function(){return i.View.extend({initialize:function(e,t){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=t&&t.field||new i.View,this.model=t&&t.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(t),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,e.trigger&&e.trigger("change"),s.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){o(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&e.indexOf("("+t+")")==-1&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(a.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return o("
").addClass("ui-form-element").append(o("
").addClass("ui-form-error ui-error").append(o("").addClass("fa fa-arrow-down")).append(o("").addClass("ui-form-error-text"))).append(o("
").addClass("ui-form-title").append(o("
").addClass("ui-form-collapsible").append(o("").addClass("ui-form-collapsible-icon")).append(o("").addClass("ui-form-collapsible-text"))).append(o("").addClass("ui-form-title-text"))).append(o("
").addClass("ui-form-field").append(o("").addClass("ui-form-info")).append(o("
").addClass("ui-form-backdrop"))).append(o("
").addClass("ui-form-preview"))}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(47),i(49),i(48),i(45)],s=function(e,t,i,n,s,l){return o.Model.extend({types:{text:"_fieldText",password:"_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",ftpfile:"_fieldFtp"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new i.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var i=e.data;i||(i=[],a.each(e.options,function(e){i.push({label:e[0],value:e[1]})}));var n=t.Select;switch(e.display){case"checkboxes":n=t.Checkbox;break;case"radio":n=t.Radio;break;case"radiobutton":n=t.RadioButton}return new n.View({id:"field-"+e.id,data:i,error_text:e.error_text||"No options available",multiple:e.multiple,optional:e.optional,onchange:e.onchange,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new t.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(i){if(i.options&&i.data)if(i.area=i.multiple,e.isEmpty(i.value))i.value=null;else if(r.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}return new t.Input({id:"field-"+i.id,type:i.type,area:i.area,readonly:i.readonly,placeholder:i.placeholder,datalist:i.datalist,onchange:i.onchange})},_fieldSlider:function(e){return new t.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new t.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new t.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new l({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new n.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new s.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7)], -s=function(e,t,i){var n=o.View.extend({initialize:function(t){this.list={},this.options=e.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new i.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",floating:"clear",cls:"ui-button-icon form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(a("
").append(this.$list=a("
")).append(a("
").append(this.button_new.$el)))},size:function(){return r.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var n=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),s=new t.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:n}});s.append(e.$el),s.$el.addClass("section-row").hide(),this.list[e.id]=s,this.$list.append(s.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){return this.list[e]?(this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(e){e.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(4),i(7),i(9),i(37),i(35),i(36)],s=function(e,t,i,n,s,c){var d=o.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new c,this.setElement(a("
")),this.render()},render:function(){var e=this;this.$el.empty(),r.each(this.inputs,function(t){e.add(t)})},add:function(t){var i=l.extend(!0,{},t);switch(i.id=t.id=e.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var s in e.cases){var o=e.cases[s],a=t.$("#"+e.id+"-section-"+s),r=!1;for(var l in o.inputs)if(!o.inputs[l].hidden){r=!0;break}s==n&&r?a.fadeIn("fast"):a.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new d(this.app,{inputs:e.cases[n].inputs});this._append(s.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+o++,s=new d(i.app,{inputs:t});a.add({id:n,$el:s.$el,ondel:function(){a.del(n),i.app.trigger("change")}})}for(var i=this,o=0,a=new n.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),l=r.size(e.cache),c=0;c").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var o=new s(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=o,this._append(o.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});return{View:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o){n=[i(32),i(75),i(5)],s=function(e,t,i){"use strict";function n(e){return function(t,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",t=t||{},t.type="dataset_collection"),e.call(this,t,i)}}var s=t.HistoryContentMixin,a=e.ListDatasetCollection,r=e.PairDatasetCollection,l=e.ListPairedDatasetCollection,c=e.ListOfListsDatasetCollection,d=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(a.prototype.save),toString:function(){return"History"+a.prototype.toString.call(this)}}),h=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(r.prototype.save),toString:function(){return"History"+r.prototype.toString.call(this)}}),u=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(l.prototype.save),toString:function(){return"History"+l.prototype.toString.call(this)}}),p=c.extend(s).extend({defaults:o.extend(o.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(66),i(73),i(39),i(41),i(6),i(132)],s=function(e,t,i,n,s,l){"use strict";var c=e.PaginatedCollection,d=c.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(e,n){if("dataset"===e.history_content_type)return new t.HistoryDatasetAssociation(e,n);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new i.HistoryListDatasetCollection(e,n);case"paired":return new i.HistoryPairDatasetCollection(e,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(e,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(e,n)}var s="Unknown collection_type: "+e.collection_type;return console.warn(s,e),{validationError:s}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){t=t||{},c.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},setHistoryId:function(e){this.historyId=e,this._setUpWebStorage()},_setUpWebStorage:function(e){if(this.historyId)return this.storage=new n.HistoryPrefs({id:n.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:o.extend(o.clone(c.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),hid:s.buildComparator("hid",{ascending:!1}),"hid-asc":s.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(e,t){if(o.isBoolean(e)&&e!==this.includeDeleted){if(this.includeDeleted=e,o.result(t,"silent"))return;this.trigger("include-deleted",e,this)}},setIncludeHidden:function(e,t){if(o.isBoolean(e)&&e!==this.includeHidden){if(this.includeHidden=e,t=t||{},o.result(t,"silent"))return;this.trigger("include-hidden",e,this)}},fetch:function(e){if(e=e||{},this.historyId&&!e.details){var t=n.HistoryPrefs.get(this.historyId).toJSON();o.isEmpty(t.expandedIds)||(e.details=o.values(t.expandedIds).join(","))}return c.prototype.fetch.call(this,e)},_buildFetchData:function(e){return o.extend(c.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=c.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),o.defaults(t,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{deleted:!0,purged:void 0}),e.remove=!1,t.trigger("fetching-deleted",t),t.fetch(e).always(function(){t.trigger("fetching-deleted-done",t)})},fetchHidden:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{visible:!1}),e.remove=!1,t.trigger("fetching-hidden",t),t.fetch(e).always(function(){t.trigger("fetching-hidden-done",t)})},fetchAllDetails:function(e){e=e||{};var t={details:"all"};return e.data=o.extend(e.data||{},t),this.fetch(e)},fetchCollectionCounts:function(e){return e=e||{},e.keys=["type_id","element_count"].join(","),e.filters=o.extend(e.filters||{},{history_content_type:"dataset_collection"}),e.remove=!1,this.fetch(e)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var o=i.get(t[n]);return o?e.concat(o):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(e,t,i){return i=i||this.models,new l.AjaxQueue(i.slice().reverse().map(function(i,n){var s=o.isString(e)?i[e]:e;return function(){return s.apply(i,t)}})).deferred},progressivelyFetchDetails:function(e){function i(t){t=t||0;var a=o.extend(o.clone(e),{view:"summary",keys:c,limit:r,offset:t,reset:0===t,remove:!1});o.defer(function(){s.fetch.call(s,a).fail(n.reject).done(function(e){n.notify(e,r,t),e.length!==r?(s.allFetched=!0,n.resolve(e,r,t)):i(t+r)})})}e=e||{};var n=a.Deferred(),s=this,r=e.limitPerCall||s.limitPerProgressiveFetch,l=t.HistoryDatasetAssociation.prototype.searchAttributes,c=l.join(",");return i(),n},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return o.isObject(e)&&e.id&&o.contains(t,e.model_class)},copy:function(e){var t,i,n;o.isString(e)?(t=e,n="hda",i="dataset"):(t=e.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[e.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,r=a.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:t,source:n,type:i})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,o,a){s.trigger("error",s,r,{},"Error copying contents",{type:i,id:t,source:n})});return r},createHDCA:function(e,t,i,n,s){var o=this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e});return o.save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return o.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=r.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(o){n=[i(6)],s=function(e){"use strict";var t=e.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(e){return o.result(this.get("expandedIds"),e,!1)},allExpanded:function(){return o.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(e){return o.isUndefined(e)||this.set("show_deleted",e),this.get("show_deleted")},includeHidden:function(e){return o.isUndefined(e)||this.set("show_hidden",e),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return t.storageKeyPrefix+e},get:function(e){return new t({id:t.historyStorageKey(e)})},clearAll:function(e){for(var i in sessionStorage)0===i.indexOf(t.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(e,t){"use strict";var i="list",n=o.View.extend(e.LoggableMixin).extend({_logNamespace:i,initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):a(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}}),s=n.extend(e.mixin(e.SelectableViewMixin,e.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(t){n.prototype.initialize.call(this,t),e.SelectableViewMixin.initialize.call(this,t),e.DraggableViewMixin.initialize.call(this,t),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=n.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return n.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=a('
'),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(a(n(i,e)))}),t},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
','
','
','',"
",'
','
','
',"
"]),i={},n=e.wrapTemplate(['
','','
','<%- element.name %>',"
",'
',"
"],"element"),s=e.wrapTemplate(['
']),o=e.wrapTemplate(['
']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});return c.prototype.templates=function(){var t=e.wrapTemplate(['
',"
"],"collection");return r.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(4),i(54),i(7),i(22),i(17),i(30)],s=function(e,t,i,n,s,r){return n.extend({initialize:function(e){var i=this;this.deferred=new t,n.prototype.initialize.call(this,e),this.model.get("inputs")?this._buildForm(this.model.attributes):this.deferred.execute(function(e){i._buildModel(e,i.model.attributes,!0)}),this.model.get("listen_to_history")&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){i.model.get("onchange")()}),this.$el.on("remove",function(){i.remove()})},remove:function(){var e=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(e),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var t=this;this.model.set(e),this.model.set({title:e.title||""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:!this.model.get("hide_operations")&&this._operations(),onchange:function(){t.deferred.reset(),t.deferred.execute(function(e){t.model.get("postchange")(e,t)})}}),this.model.get("customize")&&this.model.get("customize")(this),this.render(),this.model.get("collapsible")||this.$el.append(o("
").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(t,n,s){var a=this,r=this.model.attributes;r.version=n.version,r.id=n.id;var l="",c={};r.job_id?l=Galaxy.root+"api/jobs/"+r.job_id+"/build_for_rerun":(l=Galaxy.root+"api/tools/"+r.id+"/build",Galaxy.params&&Galaxy.params.tool_id==r.id&&(c=o.extend({},Galaxy.params),r.version&&(c.tool_version=r.version))),e.get({url:l,data:c,success:function(e){return e.display?(a._buildForm(e),!s&&a.message.update({status:"success",message:"Now you are using '"+r.name+"' version "+r.version+", id '"+r.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",e),void t.resolve()):void(window.location=Galaxy.root)},error:function(e,n){var s=e&&e.err_msg||"Uncaught error.";401==n?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+r.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},_operations:function(){var t=this,n=this.model.attributes,s=new i.ButtonMenu({icon:"fa-cubes",title:!n.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!n.sustain_version&&n.versions&&n.versions.length>1)for(var o in n.versions){var a=n.versions[o];a!=n.version&&s.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var e=n.id.replace(n.version,this.version),i=this.version;t.deferred.reset(),t.deferred.execute(function(n){t._buildModel(n,{id:e,version:i})})}})}else s.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!n.narrow&&"Options"||null,tooltip:"View available options"});return n.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",onclick:function(){window.open(n.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",onclick:function(){window.open(n.biostar_url+"/local/search/page/?q="+n.name)}})),r.addMenu({icon:"fa-share",title:"Share",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+n.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&(r.addMenu({icon:"fa-download",title:"Download",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+n.id+"/download"}}),r.addMenu({icon:"fa-refresh",title:"Reload XML",onclick:function(){e.get({url:Galaxy.root+"api/tools/"+n.id+"/reload",success:function(e){t.message.update({persistent:!1,message:"Tool XML has been reloaded.",status:"success"})},error:function(e){t.message.update({persistent:!1,message:e.err_msg,status:"danger"})}})}})),n.requirements&&n.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",onclick:function(){!this.requirements_visible||t.portlet.collapsed?(this.requirements_visible=!0,t.portlet.expand(),t.message.update({persistent:!0,message:t._templateRequirements(n),status:"info"})):(this.requirements_visible=!1,t.message.update({message:""}))}}),n.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",onclick:function(){window.open(n.sharable_url)}}),{menu:r,versions:s}},_footer:function(){var e=this.model.attributes,t=o("
").append(this._templateHelp(e));if(e.citations){var i=o("
"),n=new s.ToolCitationCollection;n.tool_id=e.id;var a=new r.CitationListView({el:i,collection:n});a.render(),n.fetch(),t.append(i)}return t},_templateHelp:function(e){var t=o("
").addClass("ui-form-help").append(e.help);return t.find("a").attr("target","_blank"),t},_templateRequirements:function(e){var t=e.requirements.length;if(t>0){var i="This tool requires ";a.each(e.requirements,function(e,n){i+=e.name+(e.version?" (Version "+e.version+")":"")+(n").attr("target","_blank").attr("href","https://wiki.galaxyproject.org/Tools/Requirements").text("here");return o("").append(i+". Click ").append(n).append(" for more information.")}return"No requirements found."}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(2),i(16),i(11),i(23)],s=function(e,t,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(e){this.set("value",parseFloat(e))}}),u=r.extend({get_samples:function(){return e.map(this.get("options"),function(e){return e[0]})}});r.subModelTypes={integer:d,float:h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(t){this.set("inputs",new l(e.map(t.inputs,function(e){var t=r.subModelTypes[e.type]||r;return new t(e)})))},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return e.inputs=this.get("inputs").map(function(e){return e.toJSON()}),e},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return e.indexOf(t.get("type"))!==-1});t.get("inputs").remove(i)},copy:function(e){var t=new p(this.toJSON());if(e){var i=new o.Collection;t.get("inputs").each(function(e){e.get_samples()&&i.push(e)}),t.set("inputs",i)}return t},apply_search_results:function(t){return e.indexOf(t,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(t){var i=this;e.each(e.keys(t),function(e){i.set_input_value(e,t[e])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(n){var s=e.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new t.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return a.when(r.go()).then(function(e){o.resolve(new i.DatasetCollection(e))}),o}});e.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){e.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var i,n=!0;e.each(this.attributes.elems,function(e){e instanceof f?(i=e,i.hide()):e instanceof p&&e.apply_search_results(t)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});e.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length");e.append(S.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(e),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return e.each(this.model.attributes.elems,function(e){if(e instanceof p){var i=new w({model:e,className:"toolTitle" -});i.render(),t.append(i.$el)}else if(e instanceof f){var n=new b({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),a("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){return this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new C({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof m){var i=new x({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof p){var n=new w({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof f){var s=new b({model:t});s.render(),e.$el.append(s.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=a(this).attr("class").split(/\s+/)[0],n=e.model.get("tools").get(i);e.trigger("tool_link_click",t,n)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:e.template(['',' ',''].join("")),panel_section:e.template(['
','<%- name %>',"
",'