From 040f82a615489aea00040a1e232de5194c6e85d7 Mon Sep 17 00:00:00 2001 From: carlfeberhard Date: Wed, 30 Mar 2016 16:25:16 -0400 Subject: [PATCH] Corrections to search and order change in history/view_multiple - Load initial histories using ajax instead of bootstrapping. - Fix rendering after order change. - Fix 'none found' message when searching datasets. - Correct fetch filters when including deleted histories. --- .../mvc/base/controlled-fetch-collection.js | 25 ++++++- .../scripts/mvc/dataset/dataset-model.js | 1 + .../scripts/mvc/history/history-contents.js | 15 +++- .../scripts/mvc/history/history-model.js | 17 +++-- .../scripts/mvc/history/history-view.js | 15 ++-- .../galaxy/scripts/mvc/history/multi-panel.js | 68 +++++++++---------- .../webapps/galaxy/api/history_contents.py | 5 +- .../webapps/galaxy/controllers/history.py | 28 +------- .../base/controlled-fetch-collection.js.map | 2 +- static/maps/mvc/dataset/dataset-model.js.map | 2 +- .../maps/mvc/history/history-contents.js.map | 2 +- static/maps/mvc/history/history-model.js.map | 2 +- static/maps/mvc/history/history-view.js.map | 2 +- static/maps/mvc/history/multi-panel.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 12 ++-- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js.map | 2 +- .../mvc/base/controlled-fetch-collection.js | 2 +- static/scripts/mvc/dataset/dataset-model.js | 2 +- .../scripts/mvc/history/history-contents.js | 2 +- static/scripts/mvc/history/history-model.js | 2 +- static/scripts/mvc/history/history-view.js | 2 +- static/scripts/mvc/history/multi-panel.js | 2 +- .../webapps/galaxy/history/view_multiple.mako | 16 +++-- 24 files changed, 123 insertions(+), 107 deletions(-) diff --git a/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js b/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js index a93df048ce8..0da345b736e 100644 --- a/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js +++ b/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js @@ -115,6 +115,12 @@ var ControlledFetchCollection = Backbone.Collection.extend({ return filterMap; }, + /** override to reset allFetched flag to false */ + reset : function( models, options ){ + this.allFetched = false; + return Backbone.Collection.prototype.reset.call( this, models, options ); + }, + // ........................................................................ order order : null, @@ -133,7 +139,8 @@ var ControlledFetchCollection = Backbone.Collection.extend({ options = options || {}; var collection = this; var comparator = collection.comparators[ order ]; - if( _.isUndefined( comparator ) ){ return; } + if( _.isUndefined( comparator ) ){ throw new Error( 'unknown order: ' + order ); } + // if( _.isUndefined( comparator ) ){ return; } if( comparator === collection.comparator ){ return; } var oldOrder = collection.order; @@ -210,12 +217,26 @@ var PaginatedCollection = ControlledFetchCollection.extend({ // anything less than a full page means we got all there is to get if( !limit || numFetched < limit ){ collection.allFetched = true; - collection.trigger( 'all-fetched', collection ); + collection.trigger( 'all-fetched', this ); } } ); }, + fetchAll : function( options ){ + // whitelist options to prevent allowing limit/offset/filters + // (use vanilla fetch instead) + options = options || {}; + var self = this; + options = _.pick( options, 'silent' ); +//TODO: this doesn't work + options.filters = {}; + return self.fetch( options ).done( function( fetchData ){ + console.log( 'triggering:...' ); + self.allFetched = true; + self.trigger( 'all-fetched', self ); + }); + }, }); diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js index 433890406aa..1bd0897d4d3 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-model.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js @@ -156,6 +156,7 @@ var DatasetAssociation = Backbone.Model if( parsed.update_time ){ parsed.update_time = new Date( parsed.update_time ); } + console.log( 'dataset-model.parsed:', parsed ); return parsed; }, diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js index 883fd28013a..ac2d15dd44a 100644 --- a/client/galaxy/scripts/mvc/history/history-contents.js +++ b/client/galaxy/scripts/mvc/history/history-contents.js @@ -95,7 +95,7 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ return _.first( this.filter( function( content ){ return content.get( 'hid' ) === hid; }) ); }, - /** return true if any contents don't have details */ + /** return true if all contents have details */ haveDetails : function(){ return this.all( function( content ){ return content.hasDetails(); }); }, @@ -330,6 +330,7 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ /** copy an existing, accessible hda into this collection */ copy : function( json ){ + // TODO: somehow showhorn all this into 'save' var id, type, contentType; if( _.isString( json ) ){ id = json; @@ -351,7 +352,7 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ type : type }) .done( function( response ){ - collection.add([ response ]); + collection.add([ response ], { parse: true }); }) .fail( function( error, status, message ){ collection.trigger( 'error', collection, xhr, {}, @@ -386,6 +387,16 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ }, // ........................................................................ searching + /** return true if all contents have the searchable attributes */ + haveSearchDetails : function(){ + return this.allFetched && this.all( function( content ){ + // null (which is a valid returned annotation value) + // will return false when using content.has( 'annotation' ) + //TODO: a bit hacky - formalize + return _.has( content.attributes, 'annotation' ); + }); + }, + /** return a new collection of contents whose attributes contain the substring matchesWhat */ matches : function( matchesWhat ){ return this.filter( function( content ){ diff --git a/client/galaxy/scripts/mvc/history/history-model.js b/client/galaxy/scripts/mvc/history/history-model.js index e9366345e46..f535850b97f 100644 --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -300,9 +300,10 @@ var History = Backbone.Model if( !allDatasets ){ postData.all_datasets = false; } + postData.view = 'current'; - var history = this, - copy = jQuery.post( this.urlRoot, postData ); + var history = this; + var copy = jQuery.post( this.urlRoot, postData ); // if current - queue to setAsCurrent before firing 'copied' if( current ){ return copy.then( function( response ){ @@ -352,7 +353,6 @@ var HistoryCollection = _collectionSuper.extend( BASE_MVC.LoggableMixin ).extend /** @type {Number} limit used for each subsequent fetch */ limitPerFetch : 10, - initialize : function( models, options ){ options = options || {}; this.log( 'HistoryCollection.initialize', models, options ); @@ -412,6 +412,10 @@ var HistoryCollection = _collectionSuper.extend( BASE_MVC.LoggableMixin ).extend if( !this.includeDeleted ){ filters.deleted = false; filters.purged = false; + } else { + // force API to return both deleted and non + //TODO: when the API is updated, remove this + filters.deleted = null; } return _.defaults( superFilters, filters ); }, @@ -462,16 +466,11 @@ var HistoryCollection = _collectionSuper.extend( BASE_MVC.LoggableMixin ).extend return this; }, - // /** override to reset allFetched flag to false */ - // reset : function( models, options ){ - // this.allFetched = false; - // return _collectionSuper.prototype.reset.call( this, models, options ); - // }, - toString: function toString(){ return 'HistoryCollection(' + this.length + ',current:' + this.currentHistoryId + ')'; } }); +window.HistoryCollection = HistoryCollection; //============================================================================== diff --git a/client/galaxy/scripts/mvc/history/history-view.js b/client/galaxy/scripts/mvc/history/history-view.js index 14fdacba658..605a8d9c349 100644 --- a/client/galaxy/scripts/mvc/history/history-view.js +++ b/client/galaxy/scripts/mvc/history/history-view.js @@ -106,28 +106,31 @@ var HistoryView = _super.extend( }, // ------------------------------------------------------------------------ inf. scrolling + /** @type {Number} ms to debounce scroll handler for infinite scrolling */ + INFINITE_SCROLL_DEBOUNCE_MS : 40, + /** @type {Number} number of px (or less) from the bottom the scrollbar should be before fetching */ + INFINITE_SCROLL_FETCH_THRESHOLD_PX : 128, + /** override to track the scroll container for this view */ _setUpBehaviors : function( $where ){ - var DEBOUNCED_MS = 40, - self = this, + var self = this, $newRender = _super.prototype._setUpBehaviors.call( this, $where ); // this needs to be handled outside the events hash since we're accessing the scollContainer // (rebind and debounce the method so we can cache for any later removal) - self.scrollHandler = _.debounce( _.bind( this.scrollHandler, self ), DEBOUNCED_MS ); + self.scrollHandler = _.debounce( _.bind( this.scrollHandler, self ), self.INFINITE_SCROLL_DEBOUNCE_MS ); self.$scrollContainer( $where ).on( 'scroll', self.scrollHandler ); return self; }, /** */ scrollHandler : function( ev ){ - var FETCH_MORE_PX_THRESHOLD = 128; var self = this; var pxToBottom = self._scrollDistanceToBottom(); // if the scrollbar is past the trigger point, we're not already fetching, - // AND we're not displaying some panel OVER this one + // AND we're not displaying some panel OVER this one: fetch more contents // note: is( :visible ) won't work here - it's still visible when this is covered with other panels - if( pxToBottom < FETCH_MORE_PX_THRESHOLD && !self._fetching && _.isEmpty( self.panelStack ) ){ + if( pxToBottom < self.INFINITE_SCROLL_FETCH_THRESHOLD_PX && !self._fetching && _.isEmpty( self.panelStack ) ){ self.listenToOnce( self.model.contents, 'sync', self.bulkAppendItemViews ); // TODO: gotta be a better way than a _fetching flag self._fetching = true; diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js index c7c238de5ce..fc6241e0bca 100644 --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -53,7 +53,7 @@ var HistoryInnerView = HISTORY_VIEW_EDIT.HistoryViewEdit.extend({ if( empty ){ return $emptyMsg.empty().append( self.emptyMsg ).show(); - } else if( self.searchFor && self.model.contents.haveDetails() ){ + } else if( self.searchFor && self.model.contents.haveSearchDetails() && !self.views.length ){ return $emptyMsg.empty().append( self.noneFoundMsg ).show(); } return $(); @@ -364,16 +364,15 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ * @fires 'new-collection' when set with this view as the arg */ setCollection : function setCollection( collection ){ + // console.log( 'setCollection:', collection ); this.stopListening( this.collection ); this.collection = collection || new HISTORY_MODEL.HistoryCollection(); this.setUpCollectionListeners(); - // this.collection.sort({ silent : true }); this.createColumns(); this.hdaQueue.clear(); - // multipanel.addModels( collection, { silent: true }); this.trigger( 'new-collection', this ); return this; }, @@ -382,12 +381,13 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ * @fires 'new-collection' when set with this view as the arg */ addModels : function addModels( models, collection, options ){ - console.log( 'addModels:', models, collection, options ); + // console.log( 'addModels:', models, collection, options ); options = options || {}; var multipanel = this; models = _.isArray( models )? models : [ models ]; models.forEach( function( model ){ multipanel.addColumn( model, false ); + // if this is from a fetch, sort will be called and it will call render }); return this; }, @@ -416,6 +416,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ }, _postFetchAll : function( fetchData ){ + console.log( '_postFetchAll' ); this.$( '.histories-loading-indicator' ).remove(); // when new histories is fetched and the indicator is not required, // the panel will jump slightly left - totally aesthetic but jarring @@ -428,16 +429,14 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ /** Re-render and set currentHistoryId to reflect a new current history */ setCurrentHistory : function setCurrentHistory( history ){ - // console.log( 'setCurrentHistory:', history ); + this.log( 'setCurrentHistory:', history ); var oldCurrentColumn = _.findWhere( this.columnMap, { currentHistory: true }); if( oldCurrentColumn ){ oldCurrentColumn.currentHistory = false; oldCurrentColumn.$el.height( '' ); } - // console.log( ' :', oldCurrentColumn ); var newCurrentColumn = this.columnMap[ this.collection.currentHistoryId ]; - // console.log( ' :', newCurrentColumn ); newCurrentColumn.currentHistory = true; this.collection.sort(); this._recalcFirstColumnHeight(); @@ -516,7 +515,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ /** add a new column for history and render all columns if render is true */ addColumn : function add( history, render ){ - //this.debug( 'adding column for:', history ); + // console.debug( 'adding column for:', history, render ); render = render !== undefined? render : true; var newColumn = this.createColumn( history ); this.columnMap[ history.id ] = newColumn; @@ -553,7 +552,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ multipanel._recalcFirstColumnHeight(); } - //TODO: to freeColumn (where Columns have freePanel) + //TODO: to freeColumn (where Columns have freePanel) multipanel.stopListening( column.panel ); multipanel.stopListening( column ); delete multipanel.columnMap[ column.model.id ]; @@ -580,7 +579,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ multipanel._dropData = null; multipanel.currentColumnDropTargetOff(); }, - 'droptarget:drop': function( ev, data, panel ){ + 'droptarget:drop': function( ev, data, panel ){ //note: bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ return panel.model.contents.isCopyable( json ); @@ -657,12 +656,12 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ /** Render the columns and panels */ renderColumns : function renderColumns( speed ){ - speed = speed !== undefined? speed: this.fxSpeed; - //this.log( 'renderColumns:', speed ); + speed = _.isNumber( speed )? speed: this.fxSpeed; + // console.log( 'renderColumns:', speed ); // render columns and track the total number rendered, firing an event when all are rendered var multipanel = this, sortedAndFiltered = multipanel.sortedFilteredColumns(); - //this.log( '\t sortedAndFiltered:', sortedAndFiltered ); + // console.log( '\t sortedAndFiltered:', sortedAndFiltered ); // set up width based on collection size var $middle = multipanel.$( '.middle' ).empty() @@ -671,7 +670,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ sortedAndFiltered.forEach( function( column, i ){ column.$el.appendTo( $middle ); column.delegateEvents(); - multipanel.renderColumn( column, speed ); + column.render( speed ); }); if( !multipanel.collection.allFetched ){ $middle.append( multipanel.loadingIndicatorTemplate( multipanel ) ); @@ -700,12 +699,6 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ ); }, - /** Render a single column using the non-blocking setTimeout( 0 ) pattern */ - renderColumn : function( column, speed ){ - speed = speed !== undefined? speed: this.fxSpeed; - return column.render( speed ); - }, - //TODO: combine the following two more sensibly //TODO: could have HistoryContents.haveDetails return false // if column.model.contents.length === 0 && !column.model.get( 'empty' ) then just check that @@ -716,7 +709,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ // console.log( 'queueHdaFetch:', column, column.model.get( 'contents_shown' ) ); // if the history model says it has hdas but none are present, queue an ajax req for them if( column.model.contents.length === 0 && column.model.get( 'contents_shown' ).shown ){ - //this.log( '\t fetch needed:', column ); + // console.log( 'fetch needed: ' + column ); var ids = _.values( column.panel.storage.get( 'expandedIds' ) ).join(); var fetchOptions = ids? { details : ids } : {}; // this uses a 'named' queue so that duplicate requests are ignored @@ -739,7 +732,9 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ this.hdaQueue.add({ name : column.model.id, fn : function(){ - return column.model.contents.fetch({ details: 'all' }); + return column.model.contents.progressivelyFetchDetails() + .done( function(){ column.panel._renderEmptyMessage(); }); + // return column.model.contents.fetch({ details: 'all' }); } }); // the queue is re-used, so if it's not processing requests - start it again @@ -821,19 +816,24 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ // set the sort order text also multipanel.$( '.current-order' ).text( multipanel.orderDescriptions[ orderKey ] ); multipanel.toggleOptionsPopover(); - - // set the order and re-fetch using the new order + // set the order and re-fetch using the new order, saving the current history as the first collection.setOrder( orderKey ); - collection.reset( collection.slice( 0, 1 ), { silent : true }); - multipanel.setCollection( collection ); - collection.fetchFirst(); - multipanel.once( 'columns-rendered', multipanel._scrollLeft, this ); + var currentHistoryModel = collection.slice( 0, 1 ); + collection.fetchFirst().done( function(){ + collection.unshift( currentHistoryModel, { silent: true }); + multipanel.createColumns(); + // need to clear this or previously fetched contents won't refetch now (bc of named queue) + multipanel.hdaQueue.clear(); + multipanel.render(); + }); + multipanel.once( 'columns-rendered', multipanel._scrollLeft ); //TODO: check allFetched and do not reset if so - just sort instead }, /** scroll the column container right or left */ _scrollLeft : function( val ){ - this.$( '.outer-middle' ).scrollLeft( val || 0 ); + val = _.isNumber( val )? val : 0; + this.$( '.outer-middle' ).scrollLeft( val ); }, /** Set up any view plugins */ @@ -849,20 +849,20 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ onfirstsearch : function( searchFor ){ multipanel.$( '#search-histories' ).searchInput( 'toggle-loading' ); multipanel.renderInfo( _l( 'loading all histories for search' ) ); - multipanel.collection.fetch() + multipanel.collection.fetchAll() .done( function(){ multipanel.$( '#search-histories' ).searchInput( 'toggle-loading' ); multipanel.renderInfo( '' ); }); }, - onsearch : function( searchFor ){ + onsearch : function( searchFor ){ multipanel.historySearch = searchFor; multipanel.filters = [ function(){ return this.model.matchesAll( multipanel.historySearch ); }]; multipanel.renderColumns( 0 ); }, - onclear : function( searchFor ){ + onclear : function( searchFor ){ multipanel.historySearch = null; //TODO: remove specifically not just reset multipanel.filters = []; @@ -894,13 +894,13 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ multipanel.$( '#search-datasets' ).searchInput( 'toggle-loading' ); }); }, - onsearch : function( searchFor ){ + onsearch : function( searchFor ){ multipanel.datasetSearch = searchFor; multipanel.sortedFilteredColumns().forEach( function( column ){ column.panel.searchItems( searchFor ); }); }, - onclear : function( searchFor ){ + onclear : function( searchFor ){ multipanel.datasetSearch = null; multipanel.sortedFilteredColumns().forEach( function( column ){ column.panel.clearSearch(); diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index cee8663c5c5..4ebef0c64cd 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -261,9 +261,6 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar self.history_manager.error_unless_accessible( original.history, trans.user, current_history=trans.history ) hda = self.hda_manager.copy( original, history=history ) - # data_copy = original.copy( copy_children=True ) - # hda = history.add_dataset( data_copy ) - trans.sa_session.flush() if not hda: return None @@ -305,7 +302,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar for ld in traverse( folder ): hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) hda_dict = self.hda_serializer.serialize_to_view( hda, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) rval.append( hda_dict ) else: message = "Invalid 'source' parameter in request %s" % source diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index f9bb32b2cd3..fe4009a3cf3 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -638,39 +638,17 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI user_is_owner=user_is_owner, history_is_current=history_is_current, show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) - # @web.require_login( "use more than one Galaxy history" ) + @web.require_login( "use more than one Galaxy history" ) @web.expose def view_multiple( self, trans, include_deleted_histories=False, order='update_time', limit=10 ): """ """ - if not trans.user: - log_in_url = url_for( controller="user", action="login", use_panels=True ) - log_in_link = "log in" % ( log_in_url ) - register_url = url_for( controller="user", action="create", use_panels=True ) - register_link = "register" % ( register_url ) - return trans.show_error_message( "You need to %s or %s to use multiple histories" - % ( log_in_link, register_link ), use_panels=True ) - + current_history_id = trans.security.encode_id( trans.history.id ) # TODO: allow specifying user_id for admin? include_deleted_histories = galaxy.util.string_as_bool( include_deleted_histories ) - order_by = self.history_manager.parse_order_by( order, default='update_time' ) limit = parse_int( limit, min_val=1, default=10, allow_none=True) - deleted_filter = None - if not include_deleted_histories: - deleted_filter = [ model.History.deleted == false(), model.History.purged == false() ] - - current_history = trans.get_history() - histories = [ current_history ] - histories += self.history_manager.by_user( trans.user, filters=deleted_filter, limit=limit, order_by=order_by ) - - history_dictionaries = [] - for history in histories: - history_dictionary = self.history_serializer.serialize_to_view( history, - view='current', user=trans.user, trans=trans ) - history_dictionaries.append( history_dictionary ) - - return trans.fill_template_mako( "history/view_multiple.mako", histories=history_dictionaries, + return trans.fill_template_mako( "history/view_multiple.mako", current_history_id=current_history_id, include_deleted_histories=include_deleted_histories, order=order, limit=limit ) @web.expose diff --git a/static/maps/mvc/base/controlled-fetch-collection.js.map b/static/maps/mvc/base/controlled-fetch-collection.js.map index 10523b5ccbe..3943cdf53a8 100644 --- a/static/maps/mvc/base/controlled-fetch-collection.js.map +++ b/static/maps/mvc/base/controlled-fetch-collection.js.map @@ -1 +1 @@ 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"},requirements:function(t){var e="This tool requires ";for(var i in t.requirements){var n=t.requirements[i];e+=n.name,n.version&&(e+=" (Version "+n.version+")"),ihere for more information.'}}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(9),i(7)],s=function(t,e,i){var n=o.View.extend({initialize:function(t){var n=this;this.options=t,this.name=t.name||"element",this.multiple=t.multiple||!1,this.message=new i.Message,this.portlet=new e.View({cls:"ui-portlet-section"}),this.select=new i.Select.View({optional:t.optional}),this.button=new i.ButtonIcon({icon:"fa fa-sign-in",floating:"left",tooltip:"Insert new "+this.name,onclick:function(){n.add({id:n.select.value(),name:n.select.text()})}}),this.setElement(this._template(t)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(t){if(void 0!==t){if(this.portlet.empty(),a.isArray(t))for(var e in t){var i=t[e],n=null,s=null;"string"!=a.type(i)?(n=i.id,s=i.name):n=s=i,null!=n&&this.add({id:n,name:s})}this._refresh()}var o=[];return this.$(".ui-list-id").each(function(){o.push({id:a(this).prop("id"),name:a(this).find(".ui-list-name").html()})}),0==o.length?null:o},add:function(e){var i=this;if(0===this.$('[id="'+e.id+'"]').length)if(t.validate(e.id)){var n=a(this._templateRow({id:e.id,name:e.name}));n.on("click",function(){n.remove(),i._refresh()}),n.on("mouseover",function(){n.addClass("portlet-highlight")}),n.on("mouseout",function(){n.removeClass("portlet-highlight")}),this.portlet.append(n),this._refresh()}else this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(t){this.select.update(t)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(t){return'
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'},_template_tab_new:function(t){return'
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this.ERRORS_},this.parse=function(t){for(var e=0;en;n++){var l=i[n],c=!1;"\\"==l&&a-1>n?l=i[++n]:"{"!=l&&"}"!=l||(c=!0),c||(r+=l)}t.Fields[e]=r}if("string"==t.ObjectType)for(var e in t.Fields)this.MACROS_[e]=t.Fields[e];else this.CALLBACK_(t)},this.processCharacter_=function(t){if(this.CHAR_++,this.CHAR_IN_LINE_++,"\n"==t&&(this.LINE_++,this.CHAR_IN_LINE_=1),this.SKIPTILLEOL_)return void("\n"==t&&(this.SKIPTILLEOL_=!1));if(this.SKIPCOMMENT_&&"%"==t)return void(this.SKIPTILLEOL_=!0);if(!this.SKIPWS_||!/\s/.test(t)){this.SKIPWS_=!1,this.SKIPCOMMENT_=!1,this.SKIPTILLEOL_=!1;for(var e=!0;e;)switch(e=!1,this.STATE_){case this.STATES_.ENTRY_OR_JUNK:"@"==t&&(this.STATE_=this.STATES_.OBJECT_TYPE,this.DATA_={ObjectType:""}),this.BRACETYPE_=null,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(t))this.DATA_.ObjectType+=t.toLowerCase(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;else{var i=this.DATA_.ObjectType;"comment"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:"string"==i?(this.DATA_.ObjectType=i,this.DATA_.Fields={},this.BRACETYPE_=t,this.BRACECOUNT_=1,this.STATE_=this.STATES_.KV_KEY,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.PARSETMP_={Key:""}):"preamble"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:i in this.ENTRY_TYPES_?(this.DATA_.ObjectType="entry",this.DATA_.EntryType=i,this.DATA_.EntryKey="",this.STATE_=this.STATES_.ENTRY_KEY,e=!0):(this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"'),this.STATE_=this.STATES_.ENTRY_OR_JUNK)}break;case this.STATES_.ENTRY_KEY:if(("{"===t||"("===t)&&null==this.BRACETYPE_){this.BRACETYPE_=t,this.BRACECOUNT_=1,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break}/[,%\s]/.test(t)?this.DATA_.EntryKey.length<1?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0):null==this.BRACETYPE_?(this.error_("No opening brace for object."),this.STATE_=this.STATES_.ENTRY_OR_JUNK):(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,e=!0,this.STATE_=this.STATES_.KV_KEY,this.PARSETMP_.Key="",this.DATA_.Fields={}):(this.DATA_.EntryKey+=t,this.SKIPWS_=!1,this.SKIPCOMMENT_=!1);break;case this.STATES_.KV_KEY:if("}"==t&&"{"==this.BRACETYPE_||")"==t&&"("==this.BRACETYPE_){this.processEntry_(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}/[\-A-Za-z:]/.test(t)?(this.PARSETMP_.Key+=t,this.SKIPWS_=!1,this.SKIPCOMMENT_=!1):this.PARSETMP_.Key.length<1?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0):(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.EQUALS,e=!0);break;case this.STATES_.EQUALS:if("}"==t&&"{"==this.BRACETYPE_||")"==t&&"("==this.BRACETYPE_){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no 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    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i,n.app.element_list[e]&&n.app.element_list[e].$el.attr("tour_id",t)}function e(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 f=p.indexOf(d);-1!=f&&(f+=d.length,h.push(parseInt(p.substr(f))),u||(u=p.substr(0,f)))}h.sort(function(t,e){return t-e});var a=0;for(var g in h)e(c+"_"+a++,r[u+h[g]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!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),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){return s(t.inputs,this.flat_dict,e)},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='
    ';return e+=t.disabled||void 0===t.collapsible_value?t.label:'
    '+t.label+"
    ",e+='
    ',e+='
    ',t.help&&(e+=t.help),t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")"),e+='
    ',t.collapsible_preview&&(e+='
    '+t.text_value+"
    "),e+="
    "}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(39),i(52),i(51),i(48)],s=function(t,e,i,n,s,l){return o.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",ftpfile:"_fieldFtp"},initialize:function(t,e){this.app=t},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(this.app.incompatible=!0,i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];a.each(t.options,function(t){i.push({label:t[0],value:t[1]})});var n=e.Select;switch(t.display){case"checkboxes":n=e.Checkbox;break;case"radio":n=e.Radio}var s=this;return new n.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){s.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.is_workflow)return this._fieldText(t);var i=this;return new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,onchange:function(){i.app.trigger("change")}})},_fieldText:function(i){if(i.options)if(i.area=i.multiple,t.validate(i.value)){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}}else i.value=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(t){i.onchange?i.onchange(t):o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:function(){i.app.trigger("change")}})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){var i=this;return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){i.app.trigger("change")}})},_fieldColor:function(t){var e=this;return new l({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
    "),this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title_new,tooltip:"Add new "+this.options.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(a("
    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(14),i(7),i(9),i(37),i(35),i(36)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=r.size(t.cache),l=0;ll?t.cache[l]:t.inputs);this.app.options.sustain_repeats&&o.hideOptions();var d=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(d.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("
    ").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(27)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement('
    '),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),"single"!=this.mode&&"multiple"!=this.mode||(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var f in this.list)this.$el.append(this.list[f].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({hid:o.hid,label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.add(n,function(t,e){return e.hid-t.hid})}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),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}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(31),i(76),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=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)}}),d=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)}}),h=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)}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(69),i(74),i(41),i(43),i(6)],s=function(t,e,i,n,s){"use strict";var l=t.PaginatedCollection,c=l.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},limitOnFirstFetch:100,limitPerFetch:50,order:"create_time",initialize:function(t,e){return e=e||{},this.historyId=e.historyId||null,this.model.prototype.idAttribute="type_id",this.includeDeleted=e.includeDeleted||!1,this.includeHidden=e.includeHidden||!1,l.prototype.initialize.call(this,t,e)},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},running:function(){function t(t){return!t.inReadyState()}return new c(this.filter(t))},getByHid:function(t){return o.first(this.filter(function(e){return e.get("hid")===t}))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},visibleAndUndeleted:function(){function t(t){return t.get("visible")&&!t.get("deleted")}return new c(this.filter(t))},setIncludeDeleted:function(t){o.isBoolean(t)&&t!==this.includeDeleted&&(this.includeDeleted=t,this.trigger("change:include-deleted",t,this))},setIncludeHidden:function(t){o.isBoolean(t)&&t!==this.includeHidden&&(this.includeHidden=t,this.trigger("change:include-hidden",t,this))},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var e=n.HistoryPrefs.get(this.historyId).toJSON();t.details=o.values(e.expandedIds).join(",")}return l.prototype.fetch.call(this,t)},_buildFetchData:function(t){return o.extend(l.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:l.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var e=l.prototype._buildFetchFilters.call(this,t)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),o.defaults(e,i)},fetchUpdated:function(t,e){return t&&(e=e||{filters:{}},e.filters={"update_time-ge":t.toISOString(),visible:""}),this.fetch(e).done(function(t){console.log("updated:",t.length,t)})},fetchDeleted:function(t){t=t||{};var e=this;return t.filters=o.extend(t.filters,{ -deleted:!0,purged:void 0}),e.trigger("fetching-deleted",e),e.fetch(t).always(function(){e.trigger("fetching-deleted-done",e)})},fetchHidden:function(t){t=t||{};var e=this;return t.filters=o.extend(t.filters,{visible:!1}),e.trigger("fetching-hidden",e),e.fetch(t).always(function(){e.trigger("fetching-hidden-done",e)})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=o.extend(t.data||{},e),this.fetch(t)},ajaxQueue:function(t,e){var i=a.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},progressivelyFetchDetails:function(t){function i(t,e){return s.notify(t,l,e),!t.length||t.length .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a('
    '),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_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(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=t.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=t.wrapTemplate(['
    ']),o=t.wrapTemplate(['
    ']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(56),i(7),i(40),i(20),i(18),i(29)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("
    ").append(s.help(t));if(t.citations){var i=o("
    "),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(17),i(11),i(19)],s=function(t,e,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(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(t){this.set("value",parseInt(t,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(t){this.set("value",parseFloat(t))}}),u=r.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[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(e){this.set("inputs",new l(t.map(e.inputs,function(t){var e=r.subModelTypes[t.type]||r;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(p.prototype,s);var f=(o.View.extend({}),o.Collection.extend({model:p})),g=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof g?(i=t,i.hide()):t instanceof p&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_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 t=this.attributes.query;if(t.length");if(t.append(S.tool_link(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),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 e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof p){var i=new w({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof g){var n=new b({model:t});n.render(),e.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.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$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(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.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 t=this,e=new C({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof m){var i=new x({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof p){var n=new w({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof g){var s=new b({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$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.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:t.template(['',' ',''].join("")),panel_section:t.template(['
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