' +\n '' +\n '
' +\n '' +\n '![]()
' +\n '' +\n '
' +\n '' +\n '';\n }\n});\n\nreturn {\n View: View\n};\n\n});\n"]}
\ No newline at end of file
+{"version":3,"sources":["layout/masthead.js"],"names":["define","View","Backbone","QuotaMeter","options","extend","initialize","setElement","self","$navbarBrandLink","this","$navbarBrandImage","$navbarBrandTitle","$","$navbarTabs","$quoteMeter","Menu","Collection","collection","empty","model","append","callback","render","$el","m","on","fetch","Galaxy","frame","Scratchbook","user","UserQuotaMeter","el","window","$download_link","target","length","closest","attr","hide","e","preventDefault","get","q","text","logo_url","brand","logo_src","quotaMeter","_template"],"mappings":"aAAAA,QACI,cADJA,cAGI,qBAIJ,4BACA,SAAIC,EAAOC,EAASD,EAAYE,GA+EhC,OACIF,KA7EIC,SAAKE,KAALC,QACAC,WAAKC,SAALH,GACA,IAAAI,EAAKC,KACLC,KAAAN,QAAKO,EACLD,KAAAH,WAAKK,KAAAA,aACLF,KAAAD,iBAA0BC,KAAQG,EAAA,sBAClCH,KAAAC,kBAA0BD,KAAQG,EAAA,uBAFlCH,KAAKE,kBAAqBF,KAAKG,EAAG,uBAIlCH,KAAAI,YAAAJ,KAAAG,EAAA,gBACAH,KAAAK,YAAsBC,KAAKC,EAAAA,0BAG1BP,KAFDQ,WAAA,IAEgBF,EAAAC,WACZT,KAAAA,WAAKM,GAAAA,MAAYK,SAAjBC,GACHZ,EAJDM,YAAAO,OAImB,IAAUC,EAAAA,KAAWF,MAAAA,IAAAG,SAAAC,OACpChB,GAAAA,QAAKU,WAAkCI,EAAAA,YAAUG,UAAKC,GAAA,WAAtD,SAAAJ,GACHd,EAAEmB,WAAYvB,KANf,SAAAqB,GAAAH,EAAAG,OAMGE,MAAOjB,KAAKN,SAGfwB,OAAOC,MAAQnB,KAAKmB,MAAQ,IAAIC,GAAeZ,WAAYR,KAAKQ,aAK5DE,OAAAA,WAAUQ,KAAOG,WAD+C,IAAA5B,EAAA6B,gBAEhEC,MAAUL,OAAKb,KAFiDkB,GAApEvB,KAAAK,cAOIF,EAAAqB,QAAIC,GAAAA,QAAAA,SAAsBC,GAC1B,IAAAD,EAAKA,EAAeE,EAAAA,QAApBC,QAAkC,eACvB,GAAPH,EAAOE,SACkCE,IAArC1B,EAAAA,uBAAuBwB,QAC1BxB,EAAA,QAAAQ,OAAAR,EAAA,aAAA0B,KAAA,KAAA,YAAAC,QAEDC,EAAAA,uBAAAF,KAAA,MAAAJ,EAAAI,KAAA,SACHE,EAAAC,oBAEDhB,GAAA,eAAA,WACAlB,IAAAA,EAAKU,GAKD,GAJAV,EAAAU,WAAQE,KAAMuB,SAAKvB,GACnBwB,IAAAA,EAAAA,EAAOC,IAAQD,mBAAfxB,EAAAuB,IAAA,iBAAAvB,GACHwB,IAHDC,GAAAD,EAAA,OAKI,KAAAC,EACH,OAAAA,KAKLtB,OAAA,WAKH,OAJGb,KAAAE,kBAAKH,KAAiB8B,WAAc7B,KAAKN,QAAQ0C,OAAjD,KAAApC,KAAAN,QAAA2C,OAAA,KACArC,KAAAD,iBAAKE,KAAkB4B,OAAM7B,KAAON,QAAKA,UACzCM,KAAAC,kBAAgBY,KAAhB,MAAAb,KAAAN,QAAA4C,UACAtC,KAAAuC,WAAA1B,SA1DwBb,MA+DxBwC,UAAA,WAaH,MAAA","file":"../../scripts/layout/masthead.js","sourcesContent":["define([\n 'utils/utils',\n 'layout/menu',\n 'layout/scratchbook',\n 'mvc/user/user-quotameter',\n], function( Utils, Menu, Scratchbook, QuotaMeter ) {\n\n/** Masthead **/\nvar View = Backbone.View.extend({\n initialize : function( options ) {\n var self = this;\n this.options = options;\n this.setElement( this._template() );\n this.$navbarBrandLink = this.$( '.navbar-brand-link' );\n this.$navbarBrandImage = this.$( '.navbar-brand-image' );\n this.$navbarBrandTitle = this.$( '.navbar-brand-title' );\n this.$navbarTabs = this.$( '.navbar-tabs' );\n this.$quoteMeter = this.$( '.quota-meter-container' );\n\n // build tabs\n this.collection = new Menu.Collection();\n this.collection.on( 'add', function( model ) {\n self.$navbarTabs.append( new Menu.Tab( { model : model } ).render().$el );\n }).on( 'reset', function() {\n self.$navbarTabs.empty();\n }).on( 'dispatch', function( callback ) {\n self.collection.each( function ( m ) { callback( m ) });\n }).fetch( this.options );\n\n // scratchbook\n Galaxy.frame = this.frame = new Scratchbook( { collection: this.collection } );\n\n // set up the quota meter (And fetch the current user data from trans)\n // add quota meter to masthead\n Galaxy.quotaMeter = this.quotaMeter = new QuotaMeter.UserQuotaMeter({\n model : Galaxy.user,\n el : this.$quoteMeter\n });\n\n // loop through beforeunload functions if the user attempts to unload the page\n $( window ).on( 'click', function( e ) {\n var $download_link = $( e.target ).closest( 'a[download]' );\n if ( $download_link.length == 1 ) {\n if( $( 'iframe[id=download]' ).length === 0 ) {\n $( 'body' ).append( $( '' ).attr( 'id', 'download' ).hide() );\n }\n $( 'iframe[id=download]' ).attr( 'src', $download_link.attr( 'href' ) );\n e.preventDefault();\n }\n }).on( 'beforeunload', function() {\n var text = '';\n self.collection.each( function( model ) {\n var q = model.get( 'onbeforeunload' ) && model.get( 'onbeforeunload' )();\n q && ( text += q + ' ' );\n });\n if ( text !== '' ) {\n return text;\n }\n });\n },\n\n render: function() {\n this.$navbarBrandTitle.html( 'Galaxy ' + ( this.options.brand && '/ ' + this.options.brand || '' ) );\n this.$navbarBrandLink.attr( 'href', this.options.logo_url );\n this.$navbarBrandImage.attr( 'src', this.options.logo_src );\n this.quotaMeter.render();\n return this;\n },\n\n /** body template */\n _template: function() {\n return '
' +\n '
' +\n '' +\n '
' +\n '' +\n '![]()
' +\n '' +\n '
' +\n '' +\n '';\n }\n});\n\nreturn {\n View: View\n};\n\n});\n"]}
\ No newline at end of file
diff --git a/static/maps/layout/menu.js.map b/static/maps/layout/menu.js.map
index edb2c76e731..2e6fe77ec22 100644
--- a/static/maps/layout/menu.js.map
+++ b/static/maps/layout/menu.js.map
@@ -1 +1 @@
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Masthead Collection **/\ndefine(['layout/generic-nav-view', 'mvc/webhooks', 'utils/localization', 'utils/utils'], function( GenericNav, Webhooks, _l, Utils ) {\nvar Collection = Backbone.Collection.extend({\n model: Backbone.Model.extend({\n defaults: {\n visible : true,\n target : '_parent'\n }\n }),\n fetch: function( options ){\n var self = this;\n options = options || {};\n this.reset();\n\n //\n // Chat server tab\n //\n var extendedNavItem = new GenericNav.GenericNavView();\n this.add(extendedNavItem.render());\n\n //\n // Analyze data tab.\n //\n this.add({\n id : 'analysis',\n title : _l('Analyze Data'),\n url : '',\n tooltip : _l('Analysis home view')\n });\n\n //\n // Workflow tab.\n //\n this.add({\n id : 'workflow',\n title : _l('Workflow'),\n tooltip : _l('Chain tools into workflows'),\n disabled : !Galaxy.user.id,\n url : 'workflow'\n });\n\n //\n // 'Shared Items' or Libraries tab.\n //\n this.add({\n id : 'shared',\n title : _l('Shared Data'),\n url : 'library/index',\n tooltip : _l('Access published resources'),\n menu : [{\n title : _l('Data Libraries'),\n url : 'library/list'\n },{\n title : _l('Histories'),\n url : 'histories/list_published'\n },{\n title : _l('Workflows'),\n url : 'workflows/list_published'\n },{\n title : _l('Visualizations'),\n url : 'visualizations/list_published'\n },{\n title : _l('Pages'),\n url : 'pages/list_published'\n }]\n });\n\n //\n // Lab menu.\n //\n options.user_requests && this.add({\n id : 'lab',\n title : 'Lab',\n menu : [{\n title : 'Sequencing Requests',\n url : 'requests/index'\n },{\n title : 'Find Samples',\n url : 'requests/find_samples_index'\n },{\n title : 'Help',\n url : options.lims_doc_url\n }]\n });\n\n //\n // Visualization tab.\n //\n this.add({\n id : 'visualization',\n title : _l('Visualization'),\n url : 'visualizations/list',\n tooltip : _l('Visualize datasets'),\n disabled : !Galaxy.user.id,\n menu : [{\n title : _l('New Track Browser'),\n url : 'visualization/trackster',\n target : '_frame'\n },{\n title : _l('Saved Visualizations'),\n url : 'visualizations/list',\n target : '_frame'\n },{\n title : _l('Interactive Environments'),\n url : 'visualization/gie_list',\n target : 'galaxy_main'\n }\n ]\n });\n\n //\n // Webhooks\n //\n Webhooks.add({\n url: 'api/webhooks/masthead/all',\n callback: function(webhooks) {\n $(document).ready(function() {\n $.each(webhooks.models, function(index, model) {\n var webhook = model.toJSON();\n if (webhook.activate) {\n var obj = {\n id : webhook.name,\n icon : webhook.config.icon,\n url : webhook.config.url,\n tooltip : webhook.config.tooltip,\n onclick : webhook.config.function && new Function(webhook.config.function),\n };\n\n // Galaxy.page is undefined for data libraries, workflows pages\n if( Galaxy.page ) {\n Galaxy.page.masthead.collection.add(obj);\n }\n else if( Galaxy.masthead ) {\n Galaxy.masthead.collection.add(obj);\n }\n \n // Append masthead script and styles to Galaxy main\n Utils.appendScriptStyle( webhook );\n }\n });\n });\n }\n });\n\n //\n // Admin.\n //\n Galaxy.user.get( 'is_admin' ) && this.add({\n id : 'admin',\n title : _l('Admin'),\n url : 'admin',\n tooltip : _l('Administer this Galaxy'),\n cls : 'admin-only'\n });\n\n //\n // Help tab.\n //\n var helpTab = {\n id : 'help',\n title : _l('Help'),\n tooltip : _l('Support, contact, and community'),\n menu : [{\n title : _l('Support'),\n url : options.support_url,\n target : '_blank'\n },{\n title : _l('Search'),\n url : options.search_url,\n target : '_blank'\n },{\n title : _l('Mailing Lists'),\n url : options.mailing_lists,\n target : '_blank'\n },{\n title : _l('Videos'),\n url : options.screencasts_url,\n target : '_blank'\n },{\n title : _l('Wiki'),\n url : options.wiki_url,\n target : '_blank'\n },{\n title : _l('How to Cite Galaxy'),\n url : options.citation_url,\n target : '_blank'\n },{\n title : _l('Interactive Tours'),\n url : 'tours'\n }]\n };\n options.terms_url && helpTab.menu.push({\n title : _l('Terms and Conditions'),\n url : options.terms_url,\n target : '_blank'\n });\n options.biostar_url && helpTab.menu.unshift({\n title : _l('Ask a question'),\n url : 'biostar/biostar_question_redirect',\n target : '_blank'\n });\n options.biostar_url && helpTab.menu.unshift({\n title : _l('Galaxy Biostar'),\n url : options.biostar_url_redirect,\n target : '_blank'\n });\n this.add( helpTab );\n\n //\n // User tab.\n //\n var userTab = {};\n if ( !Galaxy.user.id ){\n if ( options.allow_user_creation ) {\n userTab = {\n id : 'user',\n title : _l('Login or Register'),\n cls : 'loggedout-only',\n tooltip : _l('Account registration or login'),\n menu : [{\n title : _l('Login'),\n url : 'user/login',\n target : 'galaxy_main',\n noscratchbook : true\n }, {\n title: _l('Register'),\n url: 'user/create',\n target: 'galaxy_main',\n noscratchbook: true\n }\n ]\n };\n } else {\n userTab = {\n id: 'user',\n title: _l('Login'),\n cls: 'loggedout-only',\n tooltip: _l('Login'),\n url: 'user/login',\n target: 'galaxy_main',\n noscratchbook: true\n };\n }\n } else {\n userTab = {\n id : 'user',\n title : _l('User'),\n cls : 'loggedin-only',\n tooltip : _l('Account and saved data'),\n menu : [{\n title : _l('Logged in as') + ' ' + Galaxy.user.get( 'email' )\n },{\n title : _l('Preferences'),\n url : 'user'\n },{\n title : _l('Custom Builds'),\n url : 'custom_builds'\n },{\n title : _l('Logout'),\n url : 'user/logout?session_csrf_token=' + Galaxy.session_csrf_token,\n target : '_top',\n divider : true\n },{\n title : _l('Saved Histories'),\n url : 'histories/list',\n target : '_top'\n },{\n title : _l('Saved Datasets'),\n url : 'datasets/list',\n target : '_top'\n },{\n title : _l('Saved Pages'),\n url : 'pages/list',\n target : '_top'\n }]\n };\n }\n this.add( userTab );\n var activeView = this.get( options.active_view );\n activeView && activeView.set( 'active', true );\n return new jQuery.Deferred().resolve().promise();\n }\n});\n\n/** Masthead tab **/\nvar Tab = Backbone.View.extend({\n initialize: function ( options ) {\n this.model = options.model;\n this.setElement( this._template() );\n this.$dropdown = this.$( '.dropdown' );\n this.$toggle = this.$( '.dropdown-toggle' );\n this.$menu = this.$( '.dropdown-menu' );\n this.$note = this.$( '.dropdown-note' );\n this.listenTo( this.model, 'change', this.render, this );\n },\n\n events: {\n 'click .dropdown-toggle' : '_toggleClick'\n },\n\n render: function() {\n var self = this;\n $( '.tooltip' ).remove();\n this.$el.attr( 'id', this.model.id )\n .css( { visibility : this.model.get( 'visible' ) && 'visible' || 'hidden' } );\n this.model.set( 'url', this._formatUrl( this.model.get( 'url' ) ) );\n this.$note.html( this.model.get( 'note' ) || '' )\n .removeClass().addClass( 'dropdown-note' )\n .addClass( this.model.get( 'note_cls' ) )\n .css( { 'display' : this.model.get( 'show_note' ) && 'block' || 'none' } );\n this.$toggle.html( this.model.get( 'title' ) || '' )\n .removeClass().addClass( 'dropdown-toggle' )\n .addClass( this.model.get( 'cls' ) )\n .addClass( this.model.get( 'icon' ) && 'dropdown-icon fa ' + this.model.get( 'icon' ) )\n .addClass( this.model.get( 'toggle' ) && 'toggle' )\n .attr( 'target', this.model.get( 'target' ) )\n .attr( 'href', this.model.get( 'url' ) )\n .attr( 'title', this.model.get( 'tooltip' ) )\n .tooltip( 'destroy' );\n this.model.get( 'tooltip' ) && this.$toggle.tooltip( { placement: 'bottom' } );\n this.$dropdown.removeClass().addClass( 'dropdown' )\n .addClass( this.model.get( 'disabled' ) && 'disabled' )\n .addClass( this.model.get( 'active' ) && 'active' );\n if ( this.model.get( 'menu' ) && this.model.get( 'show_menu' ) ) {\n this.$menu.show();\n $( '#dd-helper' ).show().off().on( 'click', function() {\n $( '#dd-helper' ).hide();\n self.model.set( 'show_menu', false );\n });\n } else {\n self.$menu.hide();\n $( '#dd-helper' ).hide();\n }\n this.$menu.empty().removeClass( 'dropdown-menu' );\n if ( this.model.get( 'menu' ) ) {\n _.each( this.model.get( 'menu' ), function( menuItem ) {\n self.$menu.append( self._buildMenuItem( menuItem ) );\n menuItem.divider && self.$menu.append( $( '' ).addClass( 'divider' ) );\n });\n self.$menu.addClass( 'dropdown-menu' );\n self.$toggle.append( $( '' ).addClass( 'caret' ) );\n }\n return this;\n },\n\n /** Add new menu item */\n _buildMenuItem: function ( options ) {\n var self = this;\n options = _.defaults( options || {}, {\n title : '',\n url : '',\n target : '_parent',\n noscratchbook : false\n });\n options.url = self._formatUrl( options.url );\n return $( '' ).append(\n $( '' ).attr( 'href', options.url )\n .attr( 'target', options.target )\n .html( options.title )\n .on( 'click', function( e ) {\n e.preventDefault();\n self.model.set( 'show_menu', false );\n if (options.onclick){\n options.onclick();\n } else {\n Galaxy.frame.add( options );\n }\n })\n );\n },\n\n /** Handle click event */\n _toggleClick: function( e ) {\n var self = this;\n var model = this.model;\n e.preventDefault();\n $( '.tooltip' ).hide();\n model.trigger( 'dispatch', function( m ) {\n model.id !== m.id && m.get( 'menu' ) && m.set( 'show_menu', false );\n });\n if ( !model.get( 'disabled' ) ) {\n if ( !model.get( 'menu' ) ) {\n model.get( 'onclick' ) ? model.get( 'onclick' )() : Galaxy.frame.add( model.attributes );\n } else {\n model.set( 'show_menu', true );\n }\n } else {\n function buildLink( label, url ) {\n return $( '' ).append( $( '' ).attr( 'href', Galaxy.root + url ).html( label ) ).html();\n }\n this.$toggle.popover && this.$toggle.popover( 'destroy' );\n this.$toggle.popover({\n html : true,\n placement : 'bottom',\n content : 'Please ' + buildLink( 'login', 'user/login?use_panels=True' ) + ' or ' +\n buildLink( 'register', 'user/create?use_panels=True' ) + ' to use this feature.'\n }).popover( 'show' );\n setTimeout( function() { self.$toggle.popover( 'destroy' ) }, 5000 );\n }\n },\n\n /** Url formatting */\n _formatUrl: function( url ) {\n return typeof url == 'string' && url.indexOf( '//' ) === -1 && url.charAt( 0 ) != '/' ? Galaxy.root + url : url;\n },\n\n /** body tempate */\n _template: function () {\n return '
- ' +\n '
- ' +\n '' +\n '
- ' +\n '
- ' +\n '' +\n '
- ' +\n '
- Click a dataset in the ',\n 'forward column ',\n 'to select it then click a dataset in the ',\n 'reverse column.',\n ' ',\n '
- Click one of the \"Pair these datasets\" buttons in the ',\n 'middle column ',\n 'to pair the datasets in a particular row.',\n ' ',\n '
- Click \"Auto-pair\" ',\n 'to have your datasets automatically paired based on name.',\n ' ',\n '
- Entering partial dataset names in either the ',\n 'forward filter or ',\n 'reverse filter.',\n ' ',\n '
- Choosing from a list of preset filters by clicking the ',\n '\"Choose filters\" link.',\n ' ',\n '
- Entering regular expressions to match dataset names. See: ',\n 'MDN\\'s JavaScript Regular Expression Tutorial. ',\n 'Note: forward slashes (\\\\) are not needed.',\n ' ',\n '
- Clearing the filters by clicking the ',\n '\"Clear filters\" link.',\n ' ',\n '
- Click a dataset in the ',\n 'forward column ',\n 'to select it then click a dataset in the ',\n 'reverse column.',\n ' ',\n '
- Click one of the \"Pair these datasets\" buttons in the ',\n 'middle column ',\n 'to pair the datasets in a particular row.',\n ' ',\n '
- Click \"Auto-pair\" ',\n 'to have your datasets automatically paired based on name.',\n ' ',\n '
- Entering partial dataset names in either the ',\n 'forward filter or ',\n 'reverse filter.',\n ' ',\n '
- Choosing from a list of preset filters by clicking the ',\n '\"Choose filters\" link.',\n ' ',\n '
- Entering regular expressions to match dataset names. See: ',\n 'MDN\\'s JavaScript Regular Expression Tutorial. ',\n 'Note: forward slashes (\\\\) are not needed.',\n ' ',\n '
- Clearing the filters by clicking the ',\n '\"Clear filters\" link.',\n ' ',\n '
- ', action.html, ' ' ].join( '' );\n return $( html ).click( function( ev ){\n ev.preventDefault();\n return action.func( ev );\n });\n });\n $newMenu.find( 'ul' ).append( $actions );\n $menu.replaceWith( $newMenu );\n return $newMenu;\n },\n\n /** return a list of plain objects used to render multiselect actions menu. Each object should have:\n * html: an html string used as the anchor contents\n * func: a function called when the anchor is clicked (passed the click event)\n */\n multiselectActions : function(){\n return [];\n },\n\n // ------------------------------------------------------------------------ sub-$element shortcuts\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer : function( $where ){\n // override or set via attributes.$scrollContainer\n return ( $where || this.$el ).parent().parent();\n },\n /** convenience selector for the section that displays the list controls */\n $controls : function( $where ){\n return ( $where || this.$el ).find( '> .controls' );\n },\n /** list-items: where the subviews are contained in the view's dom */\n $list : function( $where ){\n return ( $where || this.$el ).find( '> .list-items' );\n },\n /** container where list messages are attached */\n $messages : function( $where ){\n //TODO: controls isn't really correct here (only for ModelListPanel)\n return ( $where || this.$el ).find( '> .controls .messages' );\n },\n /** the message displayed when no views can be shown (no views, none matching search) */\n $emptyMessage : function( $where ){\n return ( $where || this.$el ).find( '> .empty-message' );\n },\n\n // ------------------------------------------------------------------------ hda sub-views\n /** render the subviews for the list's collection */\n renderItems : function( $whereTo ){\n $whereTo = $whereTo || this.$el;\n var panel = this;\n panel.log( this + '.renderItems', $whereTo );\n\n var $list = panel.$list( $whereTo );\n panel.freeViews();\n // console.log( 'views freed' );\n //TODO:? cache and re-use views?\n var shownModels = panel._filterCollection();\n // console.log( 'models filtered:', shownModels );\n\n panel.views = shownModels.map( function( itemModel ){\n var view = panel._createItemView( itemModel );\n return view;\n });\n\n $list.empty();\n // console.log( 'list emptied' );\n if( panel.views.length ){\n panel._attachItems( $whereTo );\n // console.log( 'items attached' );\n }\n panel._renderEmptyMessage( $whereTo ).toggle( !panel.views.length );\n panel.trigger( 'views:ready', panel.views );\n\n // console.log( '------------------------------------------- rendering items' );\n return panel.views;\n },\n\n /** Filter the collection to only those models that should be currently viewed */\n _filterCollection : function(){\n // override this\n var panel = this;\n return panel.collection.filter( _.bind( panel._filterItem, panel ) );\n },\n\n /** Should the model be viewable in the current state?\n * Checks against this.filters and this.searchFor\n */\n _filterItem : function( model ){\n // override this\n var panel = this;\n return ( _.every( panel.filters.map( function( fn ){ return fn.call( model ); }) ) )\n && ( !panel.searchFor || model.matchesAll( panel.searchFor ) );\n },\n\n /** Create a view for a model and set up it's listeners */\n _createItemView : function( model ){\n var ViewClass = this._getItemViewClass( model );\n var options = _.extend( this._getItemViewOptions( model ), {\n model : model\n });\n var view = new ViewClass( options );\n this._setUpItemViewListeners( view );\n return view;\n },\n\n /** Free a view for a model. Note: does not remove it from the DOM */\n _destroyItemView : function( view ){\n this.stopListening( view );\n this.views = _.without( this.views, view );\n },\n\n _destroyItemViews : function( view ){\n var self = this;\n self.views.forEach( function( v ){\n self.stopListening( v );\n });\n self.views = [];\n return self;\n },\n\n /** free any sub-views the list has */\n freeViews : function(){\n return this._destroyItemViews();\n },\n\n /** Get the bbone view class based on the model */\n _getItemViewClass : function( model ){\n // override this\n return this.viewClass;\n },\n\n /** Get the options passed to the new view based on the model */\n _getItemViewOptions : function( model ){\n // override this\n return {\n //logger : this.logger,\n fxSpeed : this.fxSpeed,\n expanded : false,\n selectable : this.selecting,\n selected : _.contains( this.selected, model.id ),\n draggable : this.dragItems\n };\n },\n\n /** Set up listeners for new models */\n _setUpItemViewListeners : function( view ){\n var panel = this;\n // send all events to the panel, re-namspaceing them with the view prefix\n this.listenTo( view, 'all', function(){\n var args = Array.prototype.slice.call( arguments, 0 );\n args[0] = 'view:' + args[0];\n panel.trigger.apply( panel, args );\n });\n\n // drag multiple - hijack ev.setData to add all selected items\n this.listenTo( view, 'draggable:dragstart', function( ev, v ){\n //TODO: set multiple drag data here\n var json = {},\n selected = this.getSelectedModels();\n if( selected.length ){\n json = selected.toJSON();\n } else {\n json = [ v.model.toJSON() ];\n }\n ev.dataTransfer.setData( 'text', JSON.stringify( json ) );\n //ev.dataTransfer.setDragImage( v.el, 60, 60 );\n }, this );\n\n return panel;\n },\n\n /** Attach views in this.views to the model based on $whereTo */\n _attachItems : function( $whereTo ){\n var self = this;\n // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );\n //ASSUMES: $list has been emptied\n this.$list( $whereTo ).append( this.views.map( function( view ){\n return self._renderItemView$el( view );\n }));\n return this;\n },\n\n /** get a given subview's $el (or whatever may wrap it) and return it */\n _renderItemView$el : function( view ){\n // useful to wrap and override\n return view.render(0).$el;\n },\n\n /** render the empty/none-found message */\n _renderEmptyMessage : function( $whereTo ){\n this.debug( '_renderEmptyMessage', $whereTo, this.searchFor );\n var text = this.searchFor? this.noneFoundMsg : this.emptyMsg;\n return this.$emptyMessage( $whereTo ).text( text );\n },\n\n /** expand all item views */\n expandAll : function(){\n _.each( this.views, function( view ){\n view.expand();\n });\n },\n\n /** collapse all item views */\n collapseAll : function(){\n _.each( this.views, function( view ){\n view.collapse();\n });\n },\n\n // ------------------------------------------------------------------------ collection/views syncing\n /** Add a view (if the model should be viewable) to the panel */\n addItemView : function( model, collection, options ){\n // console.log( this + '.addItemView:', model );\n var panel = this;\n // get the index of the model in the list of filtered models shown by this list\n // in order to insert the view in the proper place\n //TODO:? potentially expensive\n var modelIndex = panel._filterCollection().indexOf( model );\n if( modelIndex === -1 ){ return undefined; }\n var view = panel._createItemView( model );\n // console.log( 'adding and rendering:', modelIndex, view.toString() );\n\n $( view ).queue( 'fx', [\n function( next ){\n // hide the empty message first if only view\n if( panel.$emptyMessage().is( ':visible' ) ){\n panel.$emptyMessage().fadeOut( panel.fxSpeed, next );\n } else {\n next();\n }\n },\n function( next ){\n panel._attachView( view, modelIndex );\n next();\n }\n ]);\n return view;\n },\n\n /** internal fn to add view (to both panel.views and panel.$list) */\n _attachView : function( view, modelIndex, useFx ){\n // console.log( this + '._attachView:', view, modelIndex, useFx );\n useFx = _.isUndefined( useFx )? true : useFx;\n modelIndex = modelIndex || 0;\n var panel = this;\n\n // use the modelIndex to splice into views and insert at the proper index in the DOM\n panel.views.splice( modelIndex, 0, view );\n panel._insertIntoListAt( modelIndex, panel._renderItemView$el( view ).hide() );\n\n panel.trigger( 'view:attached', view );\n if( useFx ){\n view.$el.slideDown( panel.fxSpeed, function(){\n panel.trigger( 'view:attached:rendered' );\n });\n } else {\n view.$el.show();\n panel.trigger( 'view:attached:rendered' );\n }\n return view;\n },\n\n /** insert a jq object as a child of list-items at the specified *DOM index* */\n _insertIntoListAt : function( index, $what ){\n // console.log( this + '._insertIntoListAt:', index, $what );\n var $list = this.$list();\n if( index === 0 ){\n $list.prepend( $what );\n } else {\n $list.children().eq( index - 1 ).after( $what );\n }\n return $what;\n },\n\n /** Remove a view from the panel (if found) */\n removeItemView : function( model, collection, options ){\n var panel = this;\n var view = _.find( panel.views, function( v ){ return v.model === model; });\n if( !view ){ return undefined; }\n panel.views = _.without( panel.views, view );\n panel.trigger( 'view:removed', view );\n\n // potentially show the empty message if no views left\n // use anonymous queue here - since remove can happen multiple times\n $({}).queue( 'fx', [\n function( next ){\n view.$el.fadeOut( panel.fxSpeed, next );\n },\n function( next ){\n view.remove();\n panel.trigger( 'view:removed:rendered' );\n if( !panel.views.length ){\n panel._renderEmptyMessage().fadeIn( panel.fxSpeed, next );\n } else {\n next();\n }\n }\n ]);\n return view;\n },\n\n /** get views based on model.id */\n viewFromModelId : function( id ){\n return _.find( this.views, function( v ){ return v.model.id === id; });\n },\n\n /** get views based on model */\n viewFromModel : function( model ){\n return model ? this.viewFromModelId( model.id ) : undefined;\n },\n\n /** get views based on model properties */\n viewsWhereModel : function( properties ){\n return this.views.filter( function( view ){\n return _.isMatch( view.model.attributes, properties );\n });\n },\n\n /** A range of views between (and including) viewA and viewB */\n viewRange : function( viewA, viewB ){\n if( viewA === viewB ){ return ( viewA )?( [ viewA ] ):( [] ); }\n\n var indexA = this.views.indexOf( viewA ),\n indexB = this.views.indexOf( viewB );\n\n // handle not found\n if( indexA === -1 || indexB === -1 ){\n if( indexA === indexB ){ return []; }\n return ( indexA === -1 )?( [ viewB ] ):( [ viewA ] );\n }\n // reverse if indeces are\n //note: end inclusive\n return ( indexA < indexB )?\n this.views.slice( indexA, indexB + 1 ) :\n this.views.slice( indexB, indexA + 1 );\n },\n\n // ------------------------------------------------------------------------ searching\n /** render a search input for filtering datasets shown\n * (see SearchableMixin in base-mvc for implementation of the actual searching)\n * return will start the search\n * esc will clear the search\n * clicking the clear button will clear the search\n * uses searchInput in ui.js\n */\n _renderSearch : function( $where ){\n $where.find( '.controls .search-input' ).searchInput({\n placeholder : this.searchPlaceholder,\n initialVal : this.searchFor,\n onfirstsearch : _.bind( this._firstSearch, this ),\n onsearch : _.bind( this.searchItems, this ),\n onclear : _.bind( this.clearSearch, this )\n });\n return $where;\n },\n\n /** What to do on the first search entered */\n _firstSearch : function( searchFor ){\n // override to load model details if necc.\n this.log( 'onFirstSearch', searchFor );\n return this.searchItems( searchFor );\n },\n\n /** filter view list to those that contain the searchFor terms */\n searchItems : function( searchFor, force ){\n this.log( 'searchItems', searchFor, this.searchFor, force );\n if( !force && this.searchFor === searchFor ){ return this; }\n this.searchFor = searchFor;\n this.renderItems();\n this.trigger( 'search:searching', searchFor, this );\n var $search = this.$( '> .controls .search-query' );\n if( $search.val() !== searchFor ){\n $search.val( searchFor );\n }\n return this;\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch : function( searchFor ){\n //this.log( 'onSearchClear', this );\n this.searchFor = '';\n this.trigger( 'search:clear', this );\n this.$( '> .controls .search-query' ).val( '' );\n this.renderItems();\n return this;\n },\n\n // ------------------------------------------------------------------------ selection\n /** @type Integer when the number of list item views is >= to this, don't animate selectors */\n THROTTLE_SELECTOR_FX_AT : 20,\n\n /** show selectors on all visible itemViews and associated controls */\n showSelectors : function( speed ){\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n this.selecting = true;\n this.$( '.list-actions' ).slideDown( speed );\n speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT? 0 : speed;\n _.each( this.views, function( view ){\n view.showSelector( speed );\n });\n //this.selected = [];\n //this.lastSelected = null;\n },\n\n /** hide selectors on all visible itemViews and associated controls */\n hideSelectors : function( speed ){\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n this.selecting = false;\n this.$( '.list-actions' ).slideUp( speed );\n speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT? 0 : speed;\n _.each( this.views, function( view ){\n view.hideSelector( speed );\n });\n this.selected = [];\n this.lastSelected = null;\n },\n\n /** show or hide selectors on all visible itemViews and associated controls */\n toggleSelectors : function(){\n if( !this.selecting ){\n this.showSelectors();\n } else {\n this.hideSelectors();\n }\n },\n\n /** select all visible items */\n selectAll : function( event ){\n _.each( this.views, function( view ){\n view.select( event );\n });\n },\n\n /** deselect all visible items */\n deselectAll : function( event ){\n this.lastSelected = null;\n _.each( this.views, function( view ){\n view.deselect( event );\n });\n },\n\n /** select a range of datasets between A and B */\n selectRange : function( viewA, viewB ){\n var range = this.viewRange( viewA, viewB );\n _.each( range, function( view ){\n view.select();\n });\n return range;\n },\n\n /** return an array of all currently selected itemViews */\n getSelectedViews : function(){\n return _.filter( this.views, function( v ){\n return v.selected;\n });\n },\n\n /** return a collection of the models of all currenly selected items */\n getSelectedModels : function(){\n // console.log( '(getSelectedModels)' );\n return new this.collection.constructor( _.map( this.getSelectedViews(), function( view ){\n return view.model;\n }));\n },\n\n // ------------------------------------------------------------------------ loading indicator\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator : function( msg, speed, callback ){\n this.debug( '_showLoadingIndicator', this.indicator, msg, speed, callback );\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n if( !this.indicator ){\n this.indicator = new LoadingIndicator( this.$el );\n this.debug( '\\t created', this.indicator );\n }\n if( !this.$el.is( ':visible' ) ){\n this.indicator.show( 0, callback );\n } else {\n this.$el.fadeOut( speed );\n this.indicator.show( msg, speed, callback );\n }\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator : function( speed, callback ){\n this.debug( '_hideLoadingIndicator', this.indicator, speed, callback );\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n if( this.indicator ){\n this.indicator.hide( speed, callback );\n }\n },\n\n // ------------------------------------------------------------------------ scrolling\n /** get the current scroll position of the panel in its parent */\n scrollPosition : function(){\n return this.$scrollContainer().scrollTop();\n },\n\n /** set the current scroll position of the panel in its parent */\n scrollTo : function( pos, speed ){\n speed = speed || 0;\n this.$scrollContainer().animate({ scrollTop: pos }, speed );\n return this;\n },\n\n /** Scrolls the panel to the top. */\n scrollToTop : function( speed ){\n return this.scrollTo( 0, speed );\n },\n\n /** scroll to the given view in list-items */\n scrollToItem : function( view, speed ){\n if( !view ){ return this; }\n return this;\n },\n\n /** Scrolls the panel to show the content with the given id. */\n scrollToId : function( id, speed ){\n return this.scrollToItem( this.viewFromModelId( id ), speed );\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events : {\n 'click .select-all' : 'selectAll',\n 'click .deselect-all' : 'deselectAll'\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString : function(){\n return 'ListPanel(' + this.collection + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nListPanel.prototype.templates = (function(){\n\n var elTemplate = BASE_MVC.wrapTemplate([\n // temp container\n '
- ', action.html, ' ' ].join( '' );\n return $( html ).click( function( ev ){\n ev.preventDefault();\n return action.func( ev );\n });\n });\n $newMenu.find( 'ul' ).append( $actions );\n $menu.replaceWith( $newMenu );\n return $newMenu;\n },\n\n /** return a list of plain objects used to render multiselect actions menu. Each object should have:\n * html: an html string used as the anchor contents\n * func: a function called when the anchor is clicked (passed the click event)\n */\n multiselectActions : function(){\n return [];\n },\n\n // ------------------------------------------------------------------------ sub-$element shortcuts\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer : function( $where ){\n // override or set via attributes.$scrollContainer\n return ( $where || this.$el ).parent().parent();\n },\n /** convenience selector for the section that displays the list controls */\n $controls : function( $where ){\n return ( $where || this.$el ).find( '> .controls' );\n },\n /** list-items: where the subviews are contained in the view's dom */\n $list : function( $where ){\n return ( $where || this.$el ).find( '> .list-items' );\n },\n /** container where list messages are attached */\n $messages : function( $where ){\n //TODO: controls isn't really correct here (only for ModelListPanel)\n return ( $where || this.$el ).find( '> .controls .messages' );\n },\n /** the message displayed when no views can be shown (no views, none matching search) */\n $emptyMessage : function( $where ){\n return ( $where || this.$el ).find( '> .empty-message' );\n },\n\n // ------------------------------------------------------------------------ hda sub-views\n /** render the subviews for the list's collection */\n renderItems : function( $whereTo ){\n $whereTo = $whereTo || this.$el;\n var panel = this;\n panel.log( this + '.renderItems', $whereTo );\n\n var $list = panel.$list( $whereTo );\n panel.freeViews();\n // console.log( 'views freed' );\n //TODO:? cache and re-use views?\n var shownModels = panel._filterCollection();\n // console.log( 'models filtered:', shownModels );\n\n panel.views = shownModels.map( function( itemModel ){\n var view = panel._createItemView( itemModel );\n return view;\n });\n\n $list.empty();\n // console.log( 'list emptied' );\n if( panel.views.length ){\n panel._attachItems( $whereTo );\n // console.log( 'items attached' );\n }\n panel._renderEmptyMessage( $whereTo ).toggle( !panel.views.length );\n panel.trigger( 'views:ready', panel.views );\n\n // console.log( '------------------------------------------- rendering items' );\n return panel.views;\n },\n\n /** Filter the collection to only those models that should be currently viewed */\n _filterCollection : function(){\n // override this\n var panel = this;\n return panel.collection.filter( _.bind( panel._filterItem, panel ) );\n },\n\n /** Should the model be viewable in the current state?\n * Checks against this.filters and this.searchFor\n */\n _filterItem : function( model ){\n // override this\n var panel = this;\n return ( _.every( panel.filters.map( function( fn ){ return fn.call( model ); }) ) )\n && ( !panel.searchFor || model.matchesAll( panel.searchFor ) );\n },\n\n /** Create a view for a model and set up it's listeners */\n _createItemView : function( model ){\n var ViewClass = this._getItemViewClass( model );\n var options = _.extend( this._getItemViewOptions( model ), {\n model : model\n });\n var view = new ViewClass( options );\n this._setUpItemViewListeners( view );\n return view;\n },\n\n /** Free a view for a model. Note: does not remove it from the DOM */\n _destroyItemView : function( view ){\n this.stopListening( view );\n this.views = _.without( this.views, view );\n },\n\n _destroyItemViews : function( view ){\n var self = this;\n self.views.forEach( function( v ){\n self.stopListening( v );\n });\n self.views = [];\n return self;\n },\n\n /** free any sub-views the list has */\n freeViews : function(){\n return this._destroyItemViews();\n },\n\n /** Get the bbone view class based on the model */\n _getItemViewClass : function( model ){\n // override this\n return this.viewClass;\n },\n\n /** Get the options passed to the new view based on the model */\n _getItemViewOptions : function( model ){\n // override this\n return {\n //logger : this.logger,\n fxSpeed : this.fxSpeed,\n expanded : false,\n selectable : this.selecting,\n selected : _.contains( this.selected, model.id ),\n draggable : this.dragItems\n };\n },\n\n /** Set up listeners for new models */\n _setUpItemViewListeners : function( view ){\n var panel = this;\n // send all events to the panel, re-namspaceing them with the view prefix\n this.listenTo( view, 'all', function(){\n var args = Array.prototype.slice.call( arguments, 0 );\n args[0] = 'view:' + args[0];\n panel.trigger.apply( panel, args );\n });\n\n // drag multiple - hijack ev.setData to add all selected items\n this.listenTo( view, 'draggable:dragstart', function( ev, v ){\n //TODO: set multiple drag data here\n var json = {},\n selected = this.getSelectedModels();\n if( selected.length ){\n json = selected.toJSON();\n } else {\n json = [ v.model.toJSON() ];\n }\n ev.dataTransfer.setData( 'text', JSON.stringify( json ) );\n //ev.dataTransfer.setDragImage( v.el, 60, 60 );\n }, this );\n\n return panel;\n },\n\n /** Attach views in this.views to the model based on $whereTo */\n _attachItems : function( $whereTo ){\n var self = this;\n // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );\n //ASSUMES: $list has been emptied\n this.$list( $whereTo ).append( this.views.map( function( view ){\n return self._renderItemView$el( view );\n }));\n return this;\n },\n\n /** get a given subview's $el (or whatever may wrap it) and return it */\n _renderItemView$el : function( view ){\n // useful to wrap and override\n return view.render(0).$el;\n },\n\n /** render the empty/none-found message */\n _renderEmptyMessage : function( $whereTo ){\n this.debug( '_renderEmptyMessage', $whereTo, this.searchFor );\n var text = this.searchFor? this.noneFoundMsg : this.emptyMsg;\n return this.$emptyMessage( $whereTo ).text( text );\n },\n\n /** expand all item views */\n expandAll : function(){\n _.each( this.views, function( view ){\n view.expand();\n });\n },\n\n /** collapse all item views */\n collapseAll : function(){\n _.each( this.views, function( view ){\n view.collapse();\n });\n },\n\n // ------------------------------------------------------------------------ collection/views syncing\n /** Add a view (if the model should be viewable) to the panel */\n addItemView : function( model, collection, options ){\n // console.log( this + '.addItemView:', model );\n var panel = this;\n // get the index of the model in the list of filtered models shown by this list\n // in order to insert the view in the proper place\n //TODO:? potentially expensive\n var modelIndex = panel._filterCollection().indexOf( model );\n if( modelIndex === -1 ){ return undefined; }\n var view = panel._createItemView( model );\n // console.log( 'adding and rendering:', modelIndex, view.toString() );\n\n $( view ).queue( 'fx', [\n function( next ){\n // hide the empty message first if only view\n if( panel.$emptyMessage().is( ':visible' ) ){\n panel.$emptyMessage().fadeOut( panel.fxSpeed, next );\n } else {\n next();\n }\n },\n function( next ){\n panel._attachView( view, modelIndex );\n next();\n }\n ]);\n return view;\n },\n\n /** internal fn to add view (to both panel.views and panel.$list) */\n _attachView : function( view, modelIndex, useFx ){\n // console.log( this + '._attachView:', view, modelIndex, useFx );\n useFx = _.isUndefined( useFx )? true : useFx;\n modelIndex = modelIndex || 0;\n var panel = this;\n\n // use the modelIndex to splice into views and insert at the proper index in the DOM\n panel.views.splice( modelIndex, 0, view );\n panel._insertIntoListAt( modelIndex, panel._renderItemView$el( view ).hide() );\n\n panel.trigger( 'view:attached', view );\n if( useFx ){\n view.$el.slideDown( panel.fxSpeed, function(){\n panel.trigger( 'view:attached:rendered' );\n });\n } else {\n view.$el.show();\n panel.trigger( 'view:attached:rendered' );\n }\n return view;\n },\n\n /** insert a jq object as a child of list-items at the specified *DOM index* */\n _insertIntoListAt : function( index, $what ){\n // console.log( this + '._insertIntoListAt:', index, $what );\n var $list = this.$list();\n if( index === 0 ){\n $list.prepend( $what );\n } else {\n $list.children().eq( index - 1 ).after( $what );\n }\n return $what;\n },\n\n /** Remove a view from the panel (if found) */\n removeItemView : function( model, collection, options ){\n var panel = this;\n var view = _.find( panel.views, function( v ){ return v.model === model; });\n if( !view ){ return undefined; }\n panel.views = _.without( panel.views, view );\n panel.trigger( 'view:removed', view );\n\n // potentially show the empty message if no views left\n // use anonymous queue here - since remove can happen multiple times\n $({}).queue( 'fx', [\n function( next ){\n view.$el.fadeOut( panel.fxSpeed, next );\n },\n function( next ){\n view.remove();\n panel.trigger( 'view:removed:rendered' );\n if( !panel.views.length ){\n panel._renderEmptyMessage().fadeIn( panel.fxSpeed, next );\n } else {\n next();\n }\n }\n ]);\n return view;\n },\n\n /** get views based on model.id */\n viewFromModelId : function( id ){\n return _.find( this.views, function( v ){ return v.model.id === id; });\n },\n\n /** get views based on model */\n viewFromModel : function( model ){\n return model ? this.viewFromModelId( model.id ) : undefined;\n },\n\n /** get views based on model properties */\n viewsWhereModel : function( properties ){\n return this.views.filter( function( view ){\n return _.isMatch( view.model.attributes, properties );\n });\n },\n\n /** A range of views between (and including) viewA and viewB */\n viewRange : function( viewA, viewB ){\n if( viewA === viewB ){ return ( viewA )?( [ viewA ] ):( [] ); }\n\n var indexA = this.views.indexOf( viewA ),\n indexB = this.views.indexOf( viewB );\n\n // handle not found\n if( indexA === -1 || indexB === -1 ){\n if( indexA === indexB ){ return []; }\n return ( indexA === -1 )?( [ viewB ] ):( [ viewA ] );\n }\n // reverse if indeces are\n //note: end inclusive\n return ( indexA < indexB )?\n this.views.slice( indexA, indexB + 1 ) :\n this.views.slice( indexB, indexA + 1 );\n },\n\n // ------------------------------------------------------------------------ searching\n /** render a search input for filtering datasets shown\n * (see SearchableMixin in base-mvc for implementation of the actual searching)\n * return will start the search\n * esc will clear the search\n * clicking the clear button will clear the search\n * uses searchInput in ui.js\n */\n _renderSearch : function( $where ){\n $where.find( '.controls .search-input' ).searchInput({\n placeholder : this.searchPlaceholder,\n initialVal : this.searchFor,\n onfirstsearch : _.bind( this._firstSearch, this ),\n onsearch : _.bind( this.searchItems, this ),\n onclear : _.bind( this.clearSearch, this )\n });\n return $where;\n },\n\n /** What to do on the first search entered */\n _firstSearch : function( searchFor ){\n // override to load model details if necc.\n this.log( 'onFirstSearch', searchFor );\n return this.searchItems( searchFor );\n },\n\n /** filter view list to those that contain the searchFor terms */\n searchItems : function( searchFor, force ){\n this.log( 'searchItems', searchFor, this.searchFor, force );\n if( !force && this.searchFor === searchFor ){ return this; }\n this.searchFor = searchFor;\n this.renderItems();\n this.trigger( 'search:searching', searchFor, this );\n var $search = this.$( '> .controls .search-query' );\n if( $search.val() !== searchFor ){\n $search.val( searchFor );\n }\n return this;\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch : function( searchFor ){\n //this.log( 'onSearchClear', this );\n this.searchFor = '';\n this.trigger( 'search:clear', this );\n this.$( '> .controls .search-query' ).val( '' );\n this.renderItems();\n return this;\n },\n\n // ------------------------------------------------------------------------ selection\n /** @type Integer when the number of list item views is >= to this, don't animate selectors */\n THROTTLE_SELECTOR_FX_AT : 20,\n\n /** show selectors on all visible itemViews and associated controls */\n showSelectors : function( speed ){\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n this.selecting = true;\n this.$( '.list-actions' ).slideDown( speed );\n speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT? 0 : speed;\n _.each( this.views, function( view ){\n view.showSelector( speed );\n });\n //this.selected = [];\n //this.lastSelected = null;\n },\n\n /** hide selectors on all visible itemViews and associated controls */\n hideSelectors : function( speed ){\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n this.selecting = false;\n this.$( '.list-actions' ).slideUp( speed );\n speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT? 0 : speed;\n _.each( this.views, function( view ){\n view.hideSelector( speed );\n });\n this.selected = [];\n this.lastSelected = null;\n },\n\n /** show or hide selectors on all visible itemViews and associated controls */\n toggleSelectors : function(){\n if( !this.selecting ){\n this.showSelectors();\n } else {\n this.hideSelectors();\n }\n },\n\n /** select all visible items */\n selectAll : function( event ){\n _.each( this.views, function( view ){\n view.select( event );\n });\n },\n\n /** deselect all visible items */\n deselectAll : function( event ){\n this.lastSelected = null;\n _.each( this.views, function( view ){\n view.deselect( event );\n });\n },\n\n /** select a range of datasets between A and B */\n selectRange : function( viewA, viewB ){\n var range = this.viewRange( viewA, viewB );\n _.each( range, function( view ){\n view.select();\n });\n return range;\n },\n\n /** return an array of all currently selected itemViews */\n getSelectedViews : function(){\n return _.filter( this.views, function( v ){\n return v.selected;\n });\n },\n\n /** return a collection of the models of all currenly selected items */\n getSelectedModels : function(){\n // console.log( '(getSelectedModels)' );\n return new this.collection.constructor( _.map( this.getSelectedViews(), function( view ){\n return view.model;\n }));\n },\n\n // ------------------------------------------------------------------------ loading indicator\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator : function( msg, speed, callback ){\n this.debug( '_showLoadingIndicator', this.indicator, msg, speed, callback );\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n if( !this.indicator ){\n this.indicator = new LoadingIndicator( this.$el );\n this.debug( '\\t created', this.indicator );\n }\n if( !this.$el.is( ':visible' ) ){\n this.indicator.show( 0, callback );\n } else {\n this.$el.fadeOut( speed );\n this.indicator.show( msg, speed, callback );\n }\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator : function( speed, callback ){\n this.debug( '_hideLoadingIndicator', this.indicator, speed, callback );\n speed = ( speed !== undefined )?( speed ):( this.fxSpeed );\n if( this.indicator ){\n this.indicator.hide( speed, callback );\n }\n },\n\n // ------------------------------------------------------------------------ scrolling\n /** get the current scroll position of the panel in its parent */\n scrollPosition : function(){\n return this.$scrollContainer().scrollTop();\n },\n\n /** set the current scroll position of the panel in its parent */\n scrollTo : function( pos, speed ){\n speed = speed || 0;\n this.$scrollContainer().animate({ scrollTop: pos }, speed );\n return this;\n },\n\n /** Scrolls the panel to the top. */\n scrollToTop : function( speed ){\n return this.scrollTo( 0, speed );\n },\n\n /** scroll to the given view in list-items */\n scrollToItem : function( view, speed ){\n if( !view ){ return this; }\n return this;\n },\n\n /** Scrolls the panel to show the content with the given id. */\n scrollToId : function( id, speed ){\n return this.scrollToItem( this.viewFromModelId( id ), speed );\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events : {\n 'click .select-all' : 'selectAll',\n 'click .deselect-all' : 'deselectAll'\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString : function(){\n return 'ListPanel(' + this.collection + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nListPanel.prototype.templates = (function(){\n\n var elTemplate = BASE_MVC.wrapTemplate([\n // temp container\n '
- Create a parameter tree by using the icons next to the tool\\'s parameter names to add or remove parameters.' +\n '
- Adjust the tree by using parameter inputs to select min, max, and number of samples' +\n '
- Run the tool with different settings by clicking on tree nodes' +\n '
- Create a parameter tree by using the icons next to the tool\\'s parameter names to add or remove parameters.' +\n '
- Adjust the tree by using parameter inputs to select min, max, and number of samples' +\n '
- Run the tool with different settings by clicking on tree nodes' +\n '
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- "+WYMeditor.CLASS_TITLE+" ",classesItems:[],statusHtml:"
' +\n '' +\n '';\n }\n});\n\nreturn {\n Collection : Collection,\n Tab : Tab\n};\n\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map index a14cb8a5e76..2eb3adcc0fd 100644 --- a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map +++ b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map @@ -1 +1 @@ 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\"utils/levenshtein\",\n \"utils/natural-sort\",\n \"mvc/collection/base-creator\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/hoverhighlight\"\n], function( levenshteinDistance, naturalSort, baseCreator, baseMVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'collections';\n/* ============================================================================\nTODO:\n\n\nPROGRAMMATICALLY:\ncurrPanel.once( 'rendered', function(){\n currPanel.showSelectors();\n currPanel.selectAll();\n _.last( currPanel.actionsPopup.options ).func();\n});\n\n============================================================================ */\n/** A view for paired datasets in the collections creator.\n */\nvar PairView = Backbone.View.extend( baseMVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n tagName : 'li',\n className : 'dataset paired',\n\n initialize : function( attributes ){\n this.pair = attributes.pair || {};\n },\n\n template : _.template([\n '<%- pair.forward.name %>',\n '',\n '<%- pair.name %>',\n '',\n '<%- pair.reverse.name %>'\n ].join('')),\n\n render : function(){\n this.$el\n .attr( 'draggable', true )\n .data( 'pair', this.pair )\n .html( this.template({ pair: this.pair }) )\n .addClass( 'flex-column-container' );\n return this;\n },\n\n events : {\n 'dragstart' : '_dragstart',\n 'dragend' : '_dragend',\n 'dragover' : '_sendToParent',\n 'drop' : '_sendToParent'\n },\n\n /** dragging pairs for re-ordering */\n _dragstart : function( ev ){\n ev.currentTarget.style.opacity = '0.4';\n if( ev.originalEvent ){ ev = ev.originalEvent; }\n\n ev.dataTransfer.effectAllowed = 'move';\n ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) );\n\n this.$el.parent().trigger( 'pair.dragstart', [ this ] );\n },\n\n /** dragging pairs for re-ordering */\n _dragend : function( ev ){\n ev.currentTarget.style.opacity = '1.0';\n this.$el.parent().trigger( 'pair.dragend', [ this ] );\n },\n\n /** manually bubble up an event to the parent/container */\n 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){\n _regexps = [\n new RegExp( this.filters[0] ),\n new RegExp( this.filters[1] )\n ];\n }\n return _regexps;\n }\n // mangle params as needed\n options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch( params ){\n var regexps = getRegExps.call( this );\n return _.extend( params, {\n matchTo : params.matchTo.name.replace( regexps[0], '' ),\n possible : params.possible.name.replace( regexps[1], '' )\n });\n };\n\n return function _strategy( params ){\n this.debug( 'autopair _strategy ---------------------------' );\n params = params || {};\n var listA = params.listA,\n listB = params.listB,\n indexA = 0, indexB,\n bestMatch = {\n score : 0.0,\n index : null\n },\n paired = [];\n //console.debug( 'params:', JSON.stringify( params, null, ' ' ) );\n this.debug( 'starting list lens:', listA.length, listB.length );\n this.debug( 'bestMatch (starting):', JSON.stringify( bestMatch, null, ' ' ) );\n\n while( indexA < listA.length ){\n var matchTo = listA[ indexA ];\n bestMatch.score = 0.0;\n\n for( indexB=0; indexB' + JSON.stringify( xhr.responseJSON ) + '
';\n } else {\n content += ': ' + message;\n }\n }\n creator._showAlert( content, 'alert-danger' );\n },\n\n // ------------------------------------------------------------------------ rendering\n /** render the entire interface */\n render : function( speed, callback ){\n //this.debug( '-- _render' );\n //this.$el.empty().html( this.templates.main() );\n this.$el.empty().html( this.templates.main() );\n this._renderHeader( speed );\n this._renderMiddle( speed );\n this._renderFooter( speed );\n this._addPluginComponents();\n this.trigger( 'rendered', this );\n return this;\n },\n\n /** render the header section */\n _renderHeader : function( speed, callback ){\n //this.debug( '-- _renderHeader' );\n var $header = this.$( '.header' ).empty().html( this.templates.header() )\n .find( '.help-content' ).prepend( $( this.templates.helpContent() ) );\n\n this._renderFilters();\n return $header;\n },\n /** fill the filter inputs with the filter values */\n _renderFilters : function(){\n return this.$( '.forward-column .column-header input' ).val( this.filters[0] )\n .add( this.$( '.reverse-column .column-header input' ).val( this.filters[1] ) );\n },\n\n /** render the middle including unpaired and paired sections (which may be hidden) */\n _renderMiddle : function( speed, callback ){\n var $middle = this.$( '.middle' ).empty().html( this.templates.middle() );\n\n // (re-) hide the un/paired panels based on instance vars\n if( this.unpairedPanelHidden ){\n this.$( '.unpaired-columns' ).hide();\n } else if( this.pairedPanelHidden ){\n this.$( '.paired-columns' ).hide();\n }\n\n this._renderUnpaired();\n this._renderPaired();\n return $middle;\n },\n /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */\n _renderUnpaired : function( speed, callback ){\n //this.debug( '-- _renderUnpaired' );\n var creator = this,\n $fwd, $rev, $prd = [],\n split = this._splitByFilters();\n // update unpaired counts\n this.$( '.forward-column .title' )\n .text([ split[0].length, _l( 'unpaired forward' ) ].join( ' ' ));\n this.$( '.forward-column .unpaired-info' )\n .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[0].length ) );\n this.$( '.reverse-column .title' )\n .text([ split[1].length, _l( 'unpaired reverse' ) ].join( ' ' ));\n this.$( '.reverse-column .unpaired-info' )\n .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[1].length ) );\n\n this.$( '.unpaired-columns .column-datasets' ).empty();\n\n // show/hide the auto pair button if any unpaired are left\n this.$( '.autopair-link' ).toggle( this.unpaired.length !== 0 );\n if( this.unpaired.length === 0 ){\n this._renderUnpairedEmpty();\n return;\n }\n\n // create the dataset dom arrays\n $rev = split[1].map( function( dataset, i ){\n // if there'll be a fwd dataset across the way, add a button to pair the row\n if( ( split[0][ i ] !== undefined )\n && ( split[0][ i ] !== dataset ) ){\n $prd.push( creator._renderPairButton() );\n }\n return creator._renderUnpairedDataset( dataset );\n });\n $fwd = split[0].map( function( dataset ){\n return creator._renderUnpairedDataset( dataset );\n });\n\n if( !$fwd.length && !$rev.length ){\n this._renderUnpairedNotShown();\n return;\n }\n // add to appropo cols\n //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment\n // and swapping out that\n this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd )\n .add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) )\n .add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) );\n this._adjUnpairedOnScrollbar();\n },\n /** return a string to display the count of filtered out datasets */\n _renderUnpairedDisplayStr : function( numFiltered ){\n return [ '(', numFiltered, ' ', _l( 'filtered out' ), ')' ].join('');\n },\n /** return an unattached jQuery DOM element to represent an unpaired dataset */\n _renderUnpairedDataset : function( dataset ){\n //TODO: to underscore template\n return $( '')\n .attr( 'id', 'dataset-' + dataset.id )\n .addClass( 'dataset unpaired' )\n .attr( 'draggable', true )\n .addClass( dataset.selected? 'selected': '' )\n .append( $( '' ).addClass( 'dataset-name' ).text( dataset.name ) )\n //??\n .data( 'dataset', dataset );\n },\n /** render the button that may go between unpaired datasets, allowing the user to pair a row */\n _renderPairButton : function(){\n //TODO: *not* a dataset - don't pretend like it is\n return $( '').addClass( 'dataset unpaired' )\n .append( $( '' ).addClass( 'dataset-name' ).text( _l( 'Pair these datasets' ) ) );\n },\n /** a message to display when no unpaired left */\n _renderUnpairedEmpty : function(){\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $( '' )\n .text( '(' + _l( 'no remaining unpaired datasets' ) + ')' );\n this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg );\n return $msg;\n },\n /** a message to display when no unpaired can be shown with the current filters */\n _renderUnpairedNotShown : function(){\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $( '' )\n .text( '(' + _l( 'no datasets were found matching the current filters' ) + ')' );\n this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg );\n return $msg;\n },\n /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */\n _adjUnpairedOnScrollbar : function(){\n var $unpairedColumns = this.$( '.unpaired-columns' ).last(),\n $firstDataset = this.$( '.unpaired-columns .reverse-column .dataset' ).first();\n if( !$firstDataset.length ){ return; }\n var ucRight = $unpairedColumns.offset().left + $unpairedColumns.outerWidth(),\n dsRight = $firstDataset.offset().left + $firstDataset.outerWidth(),\n rightDiff = Math.floor( ucRight ) - Math.floor( dsRight );\n //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );\n this.$( '.unpaired-columns .forward-column' )\n .css( 'margin-left', ( rightDiff > 0 )? rightDiff: 0 );\n },\n\n /** render the paired section and update counts of paired datasets */\n _renderPaired : function( speed, callback ){\n //this.debug( '-- _renderPaired' );\n this.$( '.paired-column-title .title' ).text([ this.paired.length, _l( 'paired' ) ].join( ' ' ) );\n // show/hide the unpair all link\n this.$( '.unpair-all-link' ).toggle( this.paired.length !== 0 );\n if( this.paired.length === 0 ){\n this._renderPairedEmpty();\n return;\n //TODO: would be best to return here (the $columns)\n } else {\n // show/hide 'remove extensions link' when any paired and they seem to have extensions\n this.$( '.remove-extensions-link' ).show();\n }\n\n this.$( '.paired-columns .column-datasets' ).empty();\n var creator = this;\n this.paired.forEach( function( pair, i ){\n //TODO: cache these?\n var pairView = new PairView({ pair: pair });\n creator.$( '.paired-columns .column-datasets' )\n .append( pairView.render().$el )\n .append([\n ''\n ].join( '' ));\n });\n },\n /** a message to display when none paired */\n _renderPairedEmpty : function(){\n var $msg = $( '' )\n .text( '(' + _l( 'no paired datasets yet' ) + ')' );\n this.$( '.paired-columns .column-datasets' ).empty().prepend( $msg );\n return $msg;\n },\n\n footerSettings : {\n '.hide-originals': 'hideOriginals',\n '.remove-extensions': 'removeExtensions'\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents : function(){\n this._chooseFiltersPopover( '.choose-filters-link' );\n this.$( '.help-content i' ).hoverhighlight( '.collection-creator', 'rgba( 64, 255, 255, 1.0 )' );\n },\n\n /** build a filter selection popover allowing selection of common filter pairs */\n _chooseFiltersPopover : function( selector ){\n function filterChoice( val1, val2 ){\n return [\n ''\n ].join('');\n }\n var $popoverContent = $( _.template([\n '',\n ''\n ].join(''))({}));\n\n return this.$( selector ).popover({\n container : '.collection-creator',\n placement : 'bottom',\n html : true,\n //animation : false,\n content : $popoverContent\n });\n },\n\n /** add (or clear if clear is truthy) a validation warning to what */\n _validationWarning : function( what, clear ){\n var VALIDATION_CLASS = 'validation-warning';\n if( what === 'name' ){\n what = this.$( '.collection-name' ).add( this.$( '.collection-name-prompt' ) );\n this.$( '.collection-name' ).focus().select();\n }\n if( clear ){\n what = what || this.$( '.' + VALIDATION_CLASS );\n what.removeClass( VALIDATION_CLASS );\n } else {\n what.addClass( VALIDATION_CLASS );\n }\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors : function(){\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this.on( 'pair:new', function(){\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n\n // scroll to bottom where new pairs are added\n //TODO: this doesn't seem to work - innerHeight sticks at 133...\n // may have to do with improper flex columns\n //var $pairedView = this.$( '.paired-columns' );\n //$pairedView.scrollTop( $pairedView.innerHeight() );\n //this.debug( $pairedView.height() )\n this.$( '.paired-columns' ).scrollTop( 8000000 );\n });\n this.on( 'pair:unpair', function( pairs ){\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n this.splitView();\n });\n\n this.on( 'filter-change', function(){\n this.filters = [\n this.$( '.forward-unpaired-filter input' ).val(),\n this.$( '.reverse-unpaired-filter input' ).val()\n ];\n this.metric( 'filter-change', this.filters );\n this._renderFilters();\n this._renderUnpaired();\n });\n\n this.on( 'autopair', function(){\n this._renderUnpaired();\n this._renderPaired();\n\n var message, msgClass = null;\n if( this.paired.length ){\n msgClass = 'alert-success';\n message = this.paired.length + ' ' + _l( 'pairs created' );\n if( !this.unpaired.length ){\n message += ': ' + _l( 'all datasets have been successfully paired' );\n this.hideUnpaired();\n this.$( '.collection-name' ).focus();\n }\n } else {\n message = _l([\n 'Could not automatically create any pairs from the given dataset names.',\n 'You may want to choose or enter different filters and try auto-pairing again.',\n 'Close this message using the X on the right to view more help.'\n ].join( ' ' ));\n }\n this._showAlert( message, msgClass );\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n events : {\n // header\n 'click .more-help' : '_clickMoreHelp',\n 'click .less-help' : '_clickLessHelp',\n 'click .main-help' : '_toggleHelp',\n 'click .header .alert button' : '_hideAlert',\n 'click .forward-column .column-title' : '_clickShowOnlyUnpaired',\n 'click .reverse-column .column-title' : '_clickShowOnlyUnpaired',\n 'click .unpair-all-link' : '_clickUnpairAll',\n //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?\n 'change .forward-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); },\n 'focus .forward-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); },\n 'click .autopair-link' : '_clickAutopair',\n 'click .choose-filters .filter-choice' : '_clickFilterChoice',\n 'click .clear-filters-link' : '_clearFilters',\n 'change .reverse-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); },\n 'focus .reverse-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); },\n // unpaired\n 'click .forward-column .dataset.unpaired' : '_clickUnpairedDataset',\n 'click .reverse-column .dataset.unpaired' : '_clickUnpairedDataset',\n 'click .paired-column .dataset.unpaired' : '_clickPairRow',\n 'click .unpaired-columns' : 'clearSelectedUnpaired',\n 'mousedown .unpaired-columns .dataset' : '_mousedownUnpaired',\n // divider\n 'click .paired-column-title' : '_clickShowOnlyPaired',\n 'mousedown .flexible-partition-drag' : '_startPartitionDrag',\n // paired\n 'click .paired-columns .dataset.paired' : 'selectPair',\n 'click .paired-columns' : 'clearSelectedPaired',\n 'click .paired-columns .pair-name' : '_clickPairName',\n 'click .unpair-btn' : '_clickUnpair',\n // paired - drop target\n //'dragenter .paired-columns' : '_dragenterPairedColumns',\n //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',\n 'dragover .paired-columns .column-datasets' : '_dragoverPairedColumns',\n 'drop .paired-columns .column-datasets' : '_dropPairedColumns',\n\n 'pair.dragstart .paired-columns .column-datasets' : '_pairDragstart',\n 'pair.dragend .paired-columns .column-datasets' : '_pairDragend',\n\n // footer\n 'change .remove-extensions' : function( ev ){ this.toggleExtensions(); },\n 'change .collection-name' : '_changeName',\n 'keydown .collection-name' : '_nameCheckForEnter',\n 'change .hide-originals' : '_changeHideOriginals',\n 'click .cancel-create' : '_cancelCreate',\n 'click .create-collection' : '_clickCreate'//,\n },\n\n /** toggle between showing only unpaired and split view */\n _clickShowOnlyUnpaired : function( ev ){\n //this.debug( 'click unpaired', ev.currentTarget );\n if( this.$( '.paired-columns' ).is( ':visible' ) ){\n this.hidePaired();\n } else {\n this.splitView();\n }\n },\n /** toggle between showing only paired and split view */\n _clickShowOnlyPaired : function( ev ){\n //this.debug( 'click paired' );\n if( this.$( '.unpaired-columns' ).is( ':visible' ) ){\n this.hideUnpaired();\n } else {\n this.splitView();\n }\n },\n\n /** hide unpaired, show paired */\n hideUnpaired : function( speed, callback ){\n this.unpairedPanelHidden = true;\n this.pairedPanelHidden = false;\n this._renderMiddle( speed, callback );\n },\n /** hide paired, show unpaired */\n hidePaired : function( speed, callback ){\n this.unpairedPanelHidden = false;\n this.pairedPanelHidden = true;\n this._renderMiddle( speed, callback );\n },\n /** show both paired and unpaired (splitting evenly) */\n splitView : function( speed, callback ){\n this.unpairedPanelHidden = this.pairedPanelHidden = false;\n this._renderMiddle( speed, callback );\n return this;\n },\n\n /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */\n _clickUnpairAll : function( ev ){\n this.metric( 'unpairAll' );\n this.unpairAll();\n },\n\n /** attempt to autopair */\n _clickAutopair : function( ev ){\n var paired = this.autoPair();\n this.metric( 'autopair', paired.length, this.unpaired.length );\n this.trigger( 'autopair' );\n },\n\n /** set the filters based on the data attributes of the button click target */\n _clickFilterChoice : function( ev ){\n var $selected = $( ev.currentTarget );\n this.$( '.forward-unpaired-filter input' ).val( $selected.data( 'forward' ) );\n this.$( '.reverse-unpaired-filter input' ).val( $selected.data( 'reverse' ) );\n this._hideChooseFilters();\n this.trigger( 'filter-change' );\n },\n\n /** hide the choose filters popover */\n _hideChooseFilters : function(){\n //TODO: update bootstrap and remove the following hack\n // see also: https://github.com/twbs/bootstrap/issues/10260\n this.$( '.choose-filters-link' ).popover( 'hide' );\n this.$( '.popover' ).css( 'display', 'none' );\n },\n\n /** clear both filters */\n _clearFilters : function( ev ){\n this.$( '.forward-unpaired-filter input' ).val( '' );\n this.$( '.reverse-unpaired-filter input' ).val( '' );\n this.trigger( 'filter-change' );\n },\n\n // ........................................................................ unpaired\n /** select an unpaired dataset */\n _clickUnpairedDataset : function( ev ){\n ev.stopPropagation();\n return this.toggleSelectUnpaired( $( ev.currentTarget ) );\n },\n\n /** Toggle the selection of an unpaired dataset representation.\n * @param [jQuery] $dataset the unpaired dataset dom rep to select\n * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle\n */\n toggleSelectUnpaired : function( $dataset, options ){\n options = options || {};\n var dataset = $dataset.data( 'dataset' ),\n select = options.force !== undefined? options.force: !$dataset.hasClass( 'selected' );\n //this.debug( id, options.force, $dataset, dataset );\n if( !$dataset.length || dataset === undefined ){ return $dataset; }\n\n if( select ){\n $dataset.addClass( 'selected' );\n if( !options.waitToPair ){\n this.pairAllSelected();\n }\n\n } else {\n $dataset.removeClass( 'selected' );\n //delete dataset.selected;\n }\n return $dataset;\n },\n\n /** pair all the currently selected unpaired datasets */\n pairAllSelected : function( options ){\n options = options || {};\n var creator = this,\n fwds = [],\n revs = [],\n pairs = [];\n creator.$( '.unpaired-columns .forward-column .dataset.selected' ).each( function(){\n fwds.push( $( this ).data( 'dataset' ) );\n });\n creator.$( '.unpaired-columns .reverse-column .dataset.selected' ).each( function(){\n revs.push( $( this ).data( 'dataset' ) );\n });\n fwds.length = revs.length = Math.min( fwds.length, revs.length );\n //this.debug( fwds );\n //this.debug( revs );\n fwds.forEach( function( fwd, i ){\n try {\n pairs.push( creator._pair( fwd, revs[i], { silent: true }) );\n\n } catch( err ){\n //TODO: preserve selected state of those that couldn't be paired\n //TODO: warn that some could not be paired\n creator.error( err );\n }\n });\n if( pairs.length && !options.silent ){\n this.trigger( 'pair:new', pairs );\n }\n return pairs;\n },\n\n /** clear the selection on all unpaired datasets */\n clearSelectedUnpaired : function(){\n this.$( '.unpaired-columns .dataset.selected' ).removeClass( 'selected' );\n },\n\n /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */\n _mousedownUnpaired : function( ev ){\n if( ev.shiftKey ){\n var creator = this,\n $startTarget = $( ev.target ).addClass( 'selected' ),\n moveListener = function( ev ){\n creator.$( ev.target ).filter( '.dataset' ).addClass( 'selected' );\n };\n $startTarget.parent().on( 'mousemove', moveListener );\n\n // on any mouseup, stop listening to the move and try to pair any selected\n $( document ).one( 'mouseup', function( ev ){\n $startTarget.parent().off( 'mousemove', moveListener );\n creator.pairAllSelected();\n });\n }\n },\n\n /** attempt to pair two datasets directly across from one another */\n _clickPairRow : function( ev ){\n //if( !ev.currentTarget ){ return true; }\n var rowIndex = $( ev.currentTarget ).index(),\n fwd = $( '.unpaired-columns .forward-column .dataset' ).eq( rowIndex ).data( 'dataset' ),\n rev = $( '.unpaired-columns .reverse-column .dataset' ).eq( rowIndex ).data( 'dataset' );\n //this.debug( 'row:', rowIndex, fwd, rev );\n this._pair( fwd, rev );\n },\n\n // ........................................................................ divider/partition\n /** start dragging the visible divider/partition between unpaired and paired panes */\n _startPartitionDrag : function( ev ){\n var creator = this,\n startingY = ev.pageY;\n //this.debug( 'partition drag START:', ev );\n $( 'body' ).css( 'cursor', 'ns-resize' );\n creator.$( '.flexible-partition-drag' ).css( 'color', 'black' );\n\n function endDrag( ev ){\n //creator.debug( 'partition drag STOP:', ev );\n // doing this by an added class didn't really work well - kept flashing still\n creator.$( '.flexible-partition-drag' ).css( 'color', '' );\n $( 'body' ).css( 'cursor', '' ).unbind( 'mousemove', trackMouse );\n }\n function trackMouse( ev ){\n var offset = ev.pageY - startingY;\n //creator.debug( 'partition:', startingY, offset );\n if( !creator.adjPartition( offset ) ){\n //creator.debug( 'mouseup triggered' );\n $( 'body' ).trigger( 'mouseup' );\n }\n creator._adjUnpairedOnScrollbar();\n startingY += offset;\n }\n $( 'body' ).mousemove( trackMouse );\n $( 'body' ).one( 'mouseup', endDrag );\n },\n\n /** adjust the parition up/down +/-adj pixels */\n adjPartition : function( adj ){\n var $unpaired = this.$( '.unpaired-columns' ),\n $paired = this.$( '.paired-columns' ),\n unpairedHi = parseInt( $unpaired.css( 'height' ), 10 ),\n pairedHi = parseInt( $paired.css( 'height' ), 10 );\n //this.debug( adj, 'hi\\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );\n\n unpairedHi = Math.max( 10, unpairedHi + adj );\n pairedHi = pairedHi - adj;\n\n var movingUpwards = adj < 0;\n // when the divider gets close to the top - lock into hiding the unpaired section\n if( movingUpwards ){\n if( this.unpairedPanelHidden ){\n return false;\n } else if( unpairedHi <= 10 ){\n this.hideUnpaired();\n return false;\n }\n } else {\n if( this.unpairedPanelHidden ){\n $unpaired.show();\n this.unpairedPanelHidden = false;\n }\n }\n\n // when the divider gets close to the bottom - lock into hiding the paired section\n if( !movingUpwards ){\n if( this.pairedPanelHidden ){\n return false;\n } else if( pairedHi <= 15 ){\n this.hidePaired();\n return false;\n }\n\n } else {\n if( this.pairedPanelHidden ){\n $paired.show();\n this.pairedPanelHidden = false;\n }\n }\n\n $unpaired.css({\n height : unpairedHi + 'px',\n flex : '0 0 auto'\n });\n return true;\n },\n\n // ........................................................................ paired\n /** select a pair when clicked */\n selectPair : function( ev ){\n ev.stopPropagation();\n $( ev.currentTarget ).toggleClass( 'selected' );\n },\n\n /** deselect all pairs */\n clearSelectedPaired : function( ev ){\n this.$( '.paired-columns .dataset.selected' ).removeClass( 'selected' );\n },\n\n /** rename a pair when the pair name is clicked */\n _clickPairName : function( ev ){\n ev.stopPropagation();\n var $name = $( ev.currentTarget ),\n $pair = $name.parent().parent(),\n index = $pair.index( '.dataset.paired' ),\n pair = this.paired[ index ],\n response = prompt( 'Enter a new name for the pair:', pair.name );\n if( response ){\n pair.name = response;\n // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these\n // when adding/removing extensions\n //hackish\n pair.customizedName = true;\n $name.text( pair.name );\n }\n },\n\n /** unpair this pair */\n _clickUnpair : function( ev ){\n //if( !ev.currentTarget ){ return true; }\n var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) );\n //this.debug( 'pair:', pairIndex );\n this._unpair( this.paired[ pairIndex ] );\n },\n\n // ........................................................................ paired - drag and drop re-ordering\n //_dragenterPairedColumns : function( ev ){\n // this.debug( '_dragenterPairedColumns:', ev );\n //},\n //_dragleavePairedColumns : function( ev ){\n // //this.debug( '_dragleavePairedColumns:', ev );\n //},\n /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */\n _dragoverPairedColumns : function( ev ){\n //this.debug( '_dragoverPairedColumns:', ev );\n ev.preventDefault();\n\n var $list = this.$( '.paired-columns .column-datasets' );\n this._checkForAutoscroll( $list, ev.originalEvent.clientY );\n //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );\n var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY );\n\n $( '.element-drop-placeholder' ).remove();\n var $placeholder = $( '' );\n if( !$nearest.length ){\n $list.append( $placeholder );\n } else {\n $nearest.before( $placeholder );\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll : function( $element, y ){\n var AUTOSCROLL_SPEED = 2;\n var offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = ( offset.top + $element.outerHeight() ) - y;\n //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );\n if( upperDist >= 0 && upperDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop - AUTOSCROLL_SPEED );\n } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop + AUTOSCROLL_SPEED );\n }\n },\n\n /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestPairedDatasetLi : function( y ){\n var WIGGLE = 4,\n lis = this.$( '.paired-columns .column-datasets li' ).toArray();\n for( var i=0; i',\n _l( 'Choose from the following filters to change which unpaired reads are shown in the display' ),\n ':',\n _.values( this.commonFilters ).map( function( filterSet ){\n return filterChoice( filterSet[0], filterSet[1] );\n }).join( '' ),\n '',\n '', _l( 'More help' ), '',\n '',\n '',\n '', _l( 'Less' ), '',\n '',\n '',\n '',\n '',\n '',\n\n '',\n ''\n ].join('')),\n\n /** the middle: unpaired, divider, and paired */\n middle : _.template([\n // contains two flex rows (rows that fill available space) and a divider btwn\n '',\n '',\n '',\n '',\n '',\n '', _l( 'Unpaired forward' ), '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n _l( 'Choose filters' ),\n '',\n '',\n _l( 'Clear filters' ),\n '',\n '
',\n '',\n _l( 'Auto-pair' ),\n '',\n '',\n '',\n '',\n '',\n '',\n '', _l( 'Unpaired reverse' ), '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n _l( 'Unpair all' ),\n '',\n '',\n ''\n ].join('')),\n\n /** creation and cancel controls */\n footer : _.template([\n '',\n '',\n\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '', _l( 'Name' ), ':',\n '',\n '',\n\n '',\n ''\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '', _l([\n 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ',\n 'These collections can be passed to tools and workflows in order to have analyses done on each member of ',\n 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ',\n 'and re-order the final collection.'\n ].join( '' )), '
',\n '', _l([\n 'Unpaired datasets are shown in the unpaired section ',\n '(hover over the underlined words to highlight below). ',\n 'Paired datasets are shown in the paired section.',\n '
- To pair datasets, you can:',\n '
', _l([\n '
- You can filter what is shown in the unpaired sections by:',\n '
', _l([\n 'To unpair individual dataset pairs, click the ',\n 'unpair buttons ( ). ',\n 'Click the \"Unpair all\" link to unpair all pairs.'\n ].join( '' )), '
',\n '', _l([\n 'You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ',\n '\"Remove file extensions from pair names?\" control.'\n ].join( '' )), '
',\n '', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\". ',\n '(Note: you do not have to pair all unpaired datasets to finish.)'\n ].join( '' )), '
'\n ].join(''))\n })\n});\n\n//=============================================================================\n/** a modal version of the paired collection creator */\nvar pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){\n\n var deferred = jQuery.Deferred(),\n creator;\n\n options = _.defaults( options || {}, {\n datasets : datasets,\n oncancel : function(){\n Galaxy.modal.hide();\n deferred.reject( 'cancelled' );\n },\n oncreate : function( creator, response ){\n Galaxy.modal.hide();\n deferred.resolve( response );\n }\n });\n\n if( !window.Galaxy || !Galaxy.modal ){\n throw new Error( 'Galaxy or Galaxy.modal not found' );\n }\n\n creator = new PairedCollectionCreator( options );\n Galaxy.modal.show({\n title : 'Create a collection of paired datasets',\n body : creator.$el,\n width : '80%',\n height : '800px',\n closing_events: true\n });\n creator.render();\n window.creator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n\n//=============================================================================\nfunction createListOfPairsCollection( collection, defaultHideSourceItems ){\n var elements = collection.toJSON();\n//TODO: validate elements\n return pairedCollectionCreatorModal( elements, {\n historyId : collection.historyId,\n defaultHideSourceItems: defaultHideSourceItems\n });\n}\n\n\n//=============================================================================\n return {\n PairedCollectionCreator : PairedCollectionCreator,\n pairedCollectionCreatorModal : pairedCollectionCreatorModal,\n createListOfPairsCollection : createListOfPairsCollection\n };\n});\n"]} \ No newline at end of file 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\"utils/levenshtein\",\n \"utils/natural-sort\",\n \"mvc/collection/base-creator\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/hoverhighlight\"\n], function( levenshteinDistance, naturalSort, baseCreator, baseMVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'collections';\n/* ============================================================================\nTODO:\n\n\nPROGRAMMATICALLY:\ncurrPanel.once( 'rendered', function(){\n currPanel.showSelectors();\n currPanel.selectAll();\n _.last( currPanel.actionsPopup.options ).func();\n});\n\n============================================================================ */\n/** A view for paired datasets in the collections creator.\n */\nvar PairView = Backbone.View.extend( baseMVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n tagName : 'li',\n className : 'dataset paired',\n\n initialize : function( attributes ){\n this.pair = attributes.pair || {};\n },\n\n template : _.template([\n '<%- pair.forward.name %>',\n '',\n '<%- pair.name %>',\n '',\n '<%- pair.reverse.name %>'\n ].join('')),\n\n render : function(){\n this.$el\n .attr( 'draggable', true )\n .data( 'pair', this.pair )\n .html( this.template({ pair: this.pair }) )\n .addClass( 'flex-column-container' );\n return this;\n },\n\n events : {\n 'dragstart' : '_dragstart',\n 'dragend' : '_dragend',\n 'dragover' : '_sendToParent',\n 'drop' : '_sendToParent'\n },\n\n /** dragging pairs for re-ordering */\n _dragstart : function( ev ){\n ev.currentTarget.style.opacity = '0.4';\n if( ev.originalEvent ){ ev = ev.originalEvent; }\n\n ev.dataTransfer.effectAllowed = 'move';\n ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) );\n\n this.$el.parent().trigger( 'pair.dragstart', [ this ] );\n },\n\n /** dragging pairs for re-ordering */\n _dragend : function( ev ){\n ev.currentTarget.style.opacity = '1.0';\n this.$el.parent().trigger( 'pair.dragend', [ this ] );\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent : function( ev ){\n this.$el.parent().trigger( ev );\n },\n\n /** string rep */\n toString : function(){\n return 'PairView(' + this.pair.name + ')';\n }\n});\n\n\n// ============================================================================\n/** returns an autopair function that uses the provided options.match function */\nfunction autoPairFnBuilder( options ){\n options = options || {};\n options.createPair = options.createPair || function _defaultCreatePair( params ){\n params = params || {};\n var a = params.listA.splice( params.indexA, 1 )[0],\n b = params.listB.splice( params.indexB, 1 )[0],\n aInBIndex = params.listB.indexOf( a ),\n bInAIndex = params.listA.indexOf( b );\n if( aInBIndex !== -1 ){ params.listB.splice( aInBIndex, 1 ); }\n if( bInAIndex !== -1 ){ params.listA.splice( bInAIndex, 1 ); }\n return this._pair( a, b, { silent: true });\n };\n // compile these here outside of the loop\n var _regexps = [];\n function getRegExps(){\n if( !_regexps.length ){\n _regexps = [\n new RegExp( this.filters[0] ),\n new RegExp( this.filters[1] )\n ];\n }\n return _regexps;\n }\n // mangle params as needed\n options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch( params ){\n var regexps = getRegExps.call( this );\n return _.extend( params, {\n matchTo : params.matchTo.name.replace( regexps[0], '' ),\n possible : params.possible.name.replace( regexps[1], '' )\n });\n };\n\n return function _strategy( params ){\n this.debug( 'autopair _strategy ---------------------------' );\n params = params || {};\n var listA = params.listA,\n listB = params.listB,\n indexA = 0, indexB,\n bestMatch = {\n score : 0.0,\n index : null\n },\n paired = [];\n //console.debug( 'params:', JSON.stringify( params, null, ' ' ) );\n this.debug( 'starting list lens:', listA.length, listB.length );\n this.debug( 'bestMatch (starting):', JSON.stringify( bestMatch, null, ' ' ) );\n\n while( indexA < listA.length ){\n var matchTo = listA[ indexA ];\n bestMatch.score = 0.0;\n\n for( indexB=0; indexB' + JSON.stringify( xhr.responseJSON ) + '
';\n } else {\n content += ': ' + message;\n }\n }\n creator._showAlert( content, 'alert-danger' );\n },\n\n // ------------------------------------------------------------------------ rendering\n /** render the entire interface */\n render : function( speed, callback ){\n //this.debug( '-- _render' );\n //this.$el.empty().html( this.templates.main() );\n this.$el.empty().html( this.templates.main() );\n this._renderHeader( speed );\n this._renderMiddle( speed );\n this._renderFooter( speed );\n this._addPluginComponents();\n this.trigger( 'rendered', this );\n return this;\n },\n\n /** render the header section */\n _renderHeader : function( speed, callback ){\n //this.debug( '-- _renderHeader' );\n var $header = this.$( '.header' ).empty().html( this.templates.header() )\n .find( '.help-content' ).prepend( $( this.templates.helpContent() ) );\n\n this._renderFilters();\n return $header;\n },\n /** fill the filter inputs with the filter values */\n _renderFilters : function(){\n return this.$( '.forward-column .column-header input' ).val( this.filters[0] )\n .add( this.$( '.reverse-column .column-header input' ).val( this.filters[1] ) );\n },\n\n /** render the middle including unpaired and paired sections (which may be hidden) */\n _renderMiddle : function( speed, callback ){\n var $middle = this.$( '.middle' ).empty().html( this.templates.middle() );\n\n // (re-) hide the un/paired panels based on instance vars\n if( this.unpairedPanelHidden ){\n this.$( '.unpaired-columns' ).hide();\n } else if( this.pairedPanelHidden ){\n this.$( '.paired-columns' ).hide();\n }\n\n this._renderUnpaired();\n this._renderPaired();\n return $middle;\n },\n /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */\n _renderUnpaired : function( speed, callback ){\n //this.debug( '-- _renderUnpaired' );\n var creator = this,\n $fwd, $rev, $prd = [],\n split = this._splitByFilters();\n // update unpaired counts\n this.$( '.forward-column .title' )\n .text([ split[0].length, _l( 'unpaired forward' ) ].join( ' ' ));\n this.$( '.forward-column .unpaired-info' )\n .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[0].length ) );\n this.$( '.reverse-column .title' )\n .text([ split[1].length, _l( 'unpaired reverse' ) ].join( ' ' ));\n this.$( '.reverse-column .unpaired-info' )\n .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[1].length ) );\n\n this.$( '.unpaired-columns .column-datasets' ).empty();\n\n // show/hide the auto pair button if any unpaired are left\n this.$( '.autopair-link' ).toggle( this.unpaired.length !== 0 );\n if( this.unpaired.length === 0 ){\n this._renderUnpairedEmpty();\n return;\n }\n\n // create the dataset dom arrays\n $rev = split[1].map( function( dataset, i ){\n // if there'll be a fwd dataset across the way, add a button to pair the row\n if( ( split[0][ i ] !== undefined )\n && ( split[0][ i ] !== dataset ) ){\n $prd.push( creator._renderPairButton() );\n }\n return creator._renderUnpairedDataset( dataset );\n });\n $fwd = split[0].map( function( dataset ){\n return creator._renderUnpairedDataset( dataset );\n });\n\n if( !$fwd.length && !$rev.length ){\n this._renderUnpairedNotShown();\n return;\n }\n // add to appropo cols\n //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment\n // and swapping out that\n this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd )\n .add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) )\n .add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) );\n this._adjUnpairedOnScrollbar();\n },\n /** return a string to display the count of filtered out datasets */\n _renderUnpairedDisplayStr : function( numFiltered ){\n return [ '(', numFiltered, ' ', _l( 'filtered out' ), ')' ].join('');\n },\n /** return an unattached jQuery DOM element to represent an unpaired dataset */\n _renderUnpairedDataset : function( dataset ){\n //TODO: to underscore template\n return $( '')\n .attr( 'id', 'dataset-' + dataset.id )\n .addClass( 'dataset unpaired' )\n .attr( 'draggable', true )\n .addClass( dataset.selected? 'selected': '' )\n .append( $( '' ).addClass( 'dataset-name' ).text( dataset.name ) )\n //??\n .data( 'dataset', dataset );\n },\n /** render the button that may go between unpaired datasets, allowing the user to pair a row */\n _renderPairButton : function(){\n //TODO: *not* a dataset - don't pretend like it is\n return $( '').addClass( 'dataset unpaired' )\n .append( $( '' ).addClass( 'dataset-name' ).text( _l( 'Pair these datasets' ) ) );\n },\n /** a message to display when no unpaired left */\n _renderUnpairedEmpty : function(){\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $( '' )\n .text( '(' + _l( 'no remaining unpaired datasets' ) + ')' );\n this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg );\n return $msg;\n },\n /** a message to display when no unpaired can be shown with the current filters */\n _renderUnpairedNotShown : function(){\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $( '' )\n .text( '(' + _l( 'no datasets were found matching the current filters' ) + ')' );\n this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg );\n return $msg;\n },\n /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */\n _adjUnpairedOnScrollbar : function(){\n var $unpairedColumns = this.$( '.unpaired-columns' ).last(),\n $firstDataset = this.$( '.unpaired-columns .reverse-column .dataset' ).first();\n if( !$firstDataset.length ){ return; }\n var ucRight = $unpairedColumns.offset().left + $unpairedColumns.outerWidth(),\n dsRight = $firstDataset.offset().left + $firstDataset.outerWidth(),\n rightDiff = Math.floor( ucRight ) - Math.floor( dsRight );\n //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );\n this.$( '.unpaired-columns .forward-column' )\n .css( 'margin-left', ( rightDiff > 0 )? rightDiff: 0 );\n },\n\n /** render the paired section and update counts of paired datasets */\n _renderPaired : function( speed, callback ){\n //this.debug( '-- _renderPaired' );\n this.$( '.paired-column-title .title' ).text([ this.paired.length, _l( 'paired' ) ].join( ' ' ) );\n // show/hide the unpair all link\n this.$( '.unpair-all-link' ).toggle( this.paired.length !== 0 );\n if( this.paired.length === 0 ){\n this._renderPairedEmpty();\n return;\n //TODO: would be best to return here (the $columns)\n } else {\n // show/hide 'remove extensions link' when any paired and they seem to have extensions\n this.$( '.remove-extensions-link' ).show();\n }\n\n this.$( '.paired-columns .column-datasets' ).empty();\n var creator = this;\n this.paired.forEach( function( pair, i ){\n //TODO: cache these?\n var pairView = new PairView({ pair: pair });\n creator.$( '.paired-columns .column-datasets' )\n .append( pairView.render().$el )\n .append([\n ''\n ].join( '' ));\n });\n },\n /** a message to display when none paired */\n _renderPairedEmpty : function(){\n var $msg = $( '' )\n .text( '(' + _l( 'no paired datasets yet' ) + ')' );\n this.$( '.paired-columns .column-datasets' ).empty().prepend( $msg );\n return $msg;\n },\n\n footerSettings : {\n '.hide-originals': 'hideOriginals',\n '.remove-extensions': 'removeExtensions'\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents : function(){\n this._chooseFiltersPopover( '.choose-filters-link' );\n this.$( '.help-content i' ).hoverhighlight( '.collection-creator', 'rgba( 64, 255, 255, 1.0 )' );\n },\n\n /** build a filter selection popover allowing selection of common filter pairs */\n _chooseFiltersPopover : function( selector ){\n function filterChoice( val1, val2 ){\n return [\n ''\n ].join('');\n }\n var $popoverContent = $( _.template([\n '',\n ''\n ].join(''))({}));\n\n return this.$( selector ).popover({\n container : '.collection-creator',\n placement : 'bottom',\n html : true,\n //animation : false,\n content : $popoverContent\n });\n },\n\n /** add (or clear if clear is truthy) a validation warning to what */\n _validationWarning : function( what, clear ){\n var VALIDATION_CLASS = 'validation-warning';\n if( what === 'name' ){\n what = this.$( '.collection-name' ).add( this.$( '.collection-name-prompt' ) );\n this.$( '.collection-name' ).focus().select();\n }\n if( clear ){\n what = what || this.$( '.' + VALIDATION_CLASS );\n what.removeClass( VALIDATION_CLASS );\n } else {\n what.addClass( VALIDATION_CLASS );\n }\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors : function(){\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this.on( 'pair:new', function(){\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n\n // scroll to bottom where new pairs are added\n //TODO: this doesn't seem to work - innerHeight sticks at 133...\n // may have to do with improper flex columns\n //var $pairedView = this.$( '.paired-columns' );\n //$pairedView.scrollTop( $pairedView.innerHeight() );\n //this.debug( $pairedView.height() )\n this.$( '.paired-columns' ).scrollTop( 8000000 );\n });\n this.on( 'pair:unpair', function( pairs ){\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n this.splitView();\n });\n\n this.on( 'filter-change', function(){\n this.filters = [\n this.$( '.forward-unpaired-filter input' ).val(),\n this.$( '.reverse-unpaired-filter input' ).val()\n ];\n this.metric( 'filter-change', this.filters );\n this._renderFilters();\n this._renderUnpaired();\n });\n\n this.on( 'autopair', function(){\n this._renderUnpaired();\n this._renderPaired();\n\n var message, msgClass = null;\n if( this.paired.length ){\n msgClass = 'alert-success';\n message = this.paired.length + ' ' + _l( 'pairs created' );\n if( !this.unpaired.length ){\n message += ': ' + _l( 'all datasets have been successfully paired' );\n this.hideUnpaired();\n this.$( '.collection-name' ).focus();\n }\n } else {\n message = _l([\n 'Could not automatically create any pairs from the given dataset names.',\n 'You may want to choose or enter different filters and try auto-pairing again.',\n 'Close this message using the X on the right to view more help.'\n ].join( ' ' ));\n }\n this._showAlert( message, msgClass );\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n events : {\n // header\n 'click .more-help' : '_clickMoreHelp',\n 'click .less-help' : '_clickLessHelp',\n 'click .main-help' : '_toggleHelp',\n 'click .header .alert button' : '_hideAlert',\n 'click .forward-column .column-title' : '_clickShowOnlyUnpaired',\n 'click .reverse-column .column-title' : '_clickShowOnlyUnpaired',\n 'click .unpair-all-link' : '_clickUnpairAll',\n //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?\n 'change .forward-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); },\n 'focus .forward-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); },\n 'click .autopair-link' : '_clickAutopair',\n 'click .choose-filters .filter-choice' : '_clickFilterChoice',\n 'click .clear-filters-link' : '_clearFilters',\n 'change .reverse-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); },\n 'focus .reverse-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); },\n // unpaired\n 'click .forward-column .dataset.unpaired' : '_clickUnpairedDataset',\n 'click .reverse-column .dataset.unpaired' : '_clickUnpairedDataset',\n 'click .paired-column .dataset.unpaired' : '_clickPairRow',\n 'click .unpaired-columns' : 'clearSelectedUnpaired',\n 'mousedown .unpaired-columns .dataset' : '_mousedownUnpaired',\n // divider\n 'click .paired-column-title' : '_clickShowOnlyPaired',\n 'mousedown .flexible-partition-drag' : '_startPartitionDrag',\n // paired\n 'click .paired-columns .dataset.paired' : 'selectPair',\n 'click .paired-columns' : 'clearSelectedPaired',\n 'click .paired-columns .pair-name' : '_clickPairName',\n 'click .unpair-btn' : '_clickUnpair',\n // paired - drop target\n //'dragenter .paired-columns' : '_dragenterPairedColumns',\n //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',\n 'dragover .paired-columns .column-datasets' : '_dragoverPairedColumns',\n 'drop .paired-columns .column-datasets' : '_dropPairedColumns',\n\n 'pair.dragstart .paired-columns .column-datasets' : '_pairDragstart',\n 'pair.dragend .paired-columns .column-datasets' : '_pairDragend',\n\n // footer\n 'change .remove-extensions' : function( ev ){ this.toggleExtensions(); },\n 'change .collection-name' : '_changeName',\n 'keydown .collection-name' : '_nameCheckForEnter',\n 'change .hide-originals' : '_changeHideOriginals',\n 'click .cancel-create' : '_cancelCreate',\n 'click .create-collection' : '_clickCreate'//,\n },\n\n /** toggle between showing only unpaired and split view */\n _clickShowOnlyUnpaired : function( ev ){\n //this.debug( 'click unpaired', ev.currentTarget );\n if( this.$( '.paired-columns' ).is( ':visible' ) ){\n this.hidePaired();\n } else {\n this.splitView();\n }\n },\n /** toggle between showing only paired and split view */\n _clickShowOnlyPaired : function( ev ){\n //this.debug( 'click paired' );\n if( this.$( '.unpaired-columns' ).is( ':visible' ) ){\n this.hideUnpaired();\n } else {\n this.splitView();\n }\n },\n\n /** hide unpaired, show paired */\n hideUnpaired : function( speed, callback ){\n this.unpairedPanelHidden = true;\n this.pairedPanelHidden = false;\n this._renderMiddle( speed, callback );\n },\n /** hide paired, show unpaired */\n hidePaired : function( speed, callback ){\n this.unpairedPanelHidden = false;\n this.pairedPanelHidden = true;\n this._renderMiddle( speed, callback );\n },\n /** show both paired and unpaired (splitting evenly) */\n splitView : function( speed, callback ){\n this.unpairedPanelHidden = this.pairedPanelHidden = false;\n this._renderMiddle( speed, callback );\n return this;\n },\n\n /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */\n _clickUnpairAll : function( ev ){\n this.metric( 'unpairAll' );\n this.unpairAll();\n },\n\n /** attempt to autopair */\n _clickAutopair : function( ev ){\n var paired = this.autoPair();\n this.metric( 'autopair', paired.length, this.unpaired.length );\n this.trigger( 'autopair' );\n },\n\n /** set the filters based on the data attributes of the button click target */\n _clickFilterChoice : function( ev ){\n var $selected = $( ev.currentTarget );\n this.$( '.forward-unpaired-filter input' ).val( $selected.data( 'forward' ) );\n this.$( '.reverse-unpaired-filter input' ).val( $selected.data( 'reverse' ) );\n this._hideChooseFilters();\n this.trigger( 'filter-change' );\n },\n\n /** hide the choose filters popover */\n _hideChooseFilters : function(){\n //TODO: update bootstrap and remove the following hack\n // see also: https://github.com/twbs/bootstrap/issues/10260\n this.$( '.choose-filters-link' ).popover( 'hide' );\n this.$( '.popover' ).css( 'display', 'none' );\n },\n\n /** clear both filters */\n _clearFilters : function( ev ){\n this.$( '.forward-unpaired-filter input' ).val( '' );\n this.$( '.reverse-unpaired-filter input' ).val( '' );\n this.trigger( 'filter-change' );\n },\n\n // ........................................................................ unpaired\n /** select an unpaired dataset */\n _clickUnpairedDataset : function( ev ){\n ev.stopPropagation();\n return this.toggleSelectUnpaired( $( ev.currentTarget ) );\n },\n\n /** Toggle the selection of an unpaired dataset representation.\n * @param [jQuery] $dataset the unpaired dataset dom rep to select\n * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle\n */\n toggleSelectUnpaired : function( $dataset, options ){\n options = options || {};\n var dataset = $dataset.data( 'dataset' ),\n select = options.force !== undefined? options.force: !$dataset.hasClass( 'selected' );\n //this.debug( id, options.force, $dataset, dataset );\n if( !$dataset.length || dataset === undefined ){ return $dataset; }\n\n if( select ){\n $dataset.addClass( 'selected' );\n if( !options.waitToPair ){\n this.pairAllSelected();\n }\n\n } else {\n $dataset.removeClass( 'selected' );\n //delete dataset.selected;\n }\n return $dataset;\n },\n\n /** pair all the currently selected unpaired datasets */\n pairAllSelected : function( options ){\n options = options || {};\n var creator = this,\n fwds = [],\n revs = [],\n pairs = [];\n creator.$( '.unpaired-columns .forward-column .dataset.selected' ).each( function(){\n fwds.push( $( this ).data( 'dataset' ) );\n });\n creator.$( '.unpaired-columns .reverse-column .dataset.selected' ).each( function(){\n revs.push( $( this ).data( 'dataset' ) );\n });\n fwds.length = revs.length = Math.min( fwds.length, revs.length );\n //this.debug( fwds );\n //this.debug( revs );\n fwds.forEach( function( fwd, i ){\n try {\n pairs.push( creator._pair( fwd, revs[i], { silent: true }) );\n\n } catch( err ){\n //TODO: preserve selected state of those that couldn't be paired\n //TODO: warn that some could not be paired\n creator.error( err );\n }\n });\n if( pairs.length && !options.silent ){\n this.trigger( 'pair:new', pairs );\n }\n return pairs;\n },\n\n /** clear the selection on all unpaired datasets */\n clearSelectedUnpaired : function(){\n this.$( '.unpaired-columns .dataset.selected' ).removeClass( 'selected' );\n },\n\n /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */\n _mousedownUnpaired : function( ev ){\n if( ev.shiftKey ){\n var creator = this,\n $startTarget = $( ev.target ).addClass( 'selected' ),\n moveListener = function( ev ){\n creator.$( ev.target ).filter( '.dataset' ).addClass( 'selected' );\n };\n $startTarget.parent().on( 'mousemove', moveListener );\n\n // on any mouseup, stop listening to the move and try to pair any selected\n $( document ).one( 'mouseup', function( ev ){\n $startTarget.parent().off( 'mousemove', moveListener );\n creator.pairAllSelected();\n });\n }\n },\n\n /** attempt to pair two datasets directly across from one another */\n _clickPairRow : function( ev ){\n //if( !ev.currentTarget ){ return true; }\n var rowIndex = $( ev.currentTarget ).index(),\n fwd = $( '.unpaired-columns .forward-column .dataset' ).eq( rowIndex ).data( 'dataset' ),\n rev = $( '.unpaired-columns .reverse-column .dataset' ).eq( rowIndex ).data( 'dataset' );\n //this.debug( 'row:', rowIndex, fwd, rev );\n this._pair( fwd, rev );\n },\n\n // ........................................................................ divider/partition\n /** start dragging the visible divider/partition between unpaired and paired panes */\n _startPartitionDrag : function( ev ){\n var creator = this,\n startingY = ev.pageY;\n //this.debug( 'partition drag START:', ev );\n $( 'body' ).css( 'cursor', 'ns-resize' );\n creator.$( '.flexible-partition-drag' ).css( 'color', 'black' );\n\n function endDrag( ev ){\n //creator.debug( 'partition drag STOP:', ev );\n // doing this by an added class didn't really work well - kept flashing still\n creator.$( '.flexible-partition-drag' ).css( 'color', '' );\n $( 'body' ).css( 'cursor', '' ).unbind( 'mousemove', trackMouse );\n }\n function trackMouse( ev ){\n var offset = ev.pageY - startingY;\n //creator.debug( 'partition:', startingY, offset );\n if( !creator.adjPartition( offset ) ){\n //creator.debug( 'mouseup triggered' );\n $( 'body' ).trigger( 'mouseup' );\n }\n creator._adjUnpairedOnScrollbar();\n startingY += offset;\n }\n $( 'body' ).mousemove( trackMouse );\n $( 'body' ).one( 'mouseup', endDrag );\n },\n\n /** adjust the parition up/down +/-adj pixels */\n adjPartition : function( adj ){\n var $unpaired = this.$( '.unpaired-columns' ),\n $paired = this.$( '.paired-columns' ),\n unpairedHi = parseInt( $unpaired.css( 'height' ), 10 ),\n pairedHi = parseInt( $paired.css( 'height' ), 10 );\n //this.debug( adj, 'hi\\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );\n\n unpairedHi = Math.max( 10, unpairedHi + adj );\n pairedHi = pairedHi - adj;\n\n var movingUpwards = adj < 0;\n // when the divider gets close to the top - lock into hiding the unpaired section\n if( movingUpwards ){\n if( this.unpairedPanelHidden ){\n return false;\n } else if( unpairedHi <= 10 ){\n this.hideUnpaired();\n return false;\n }\n } else {\n if( this.unpairedPanelHidden ){\n $unpaired.show();\n this.unpairedPanelHidden = false;\n }\n }\n\n // when the divider gets close to the bottom - lock into hiding the paired section\n if( !movingUpwards ){\n if( this.pairedPanelHidden ){\n return false;\n } else if( pairedHi <= 15 ){\n this.hidePaired();\n return false;\n }\n\n } else {\n if( this.pairedPanelHidden ){\n $paired.show();\n this.pairedPanelHidden = false;\n }\n }\n\n $unpaired.css({\n height : unpairedHi + 'px',\n flex : '0 0 auto'\n });\n return true;\n },\n\n // ........................................................................ paired\n /** select a pair when clicked */\n selectPair : function( ev ){\n ev.stopPropagation();\n $( ev.currentTarget ).toggleClass( 'selected' );\n },\n\n /** deselect all pairs */\n clearSelectedPaired : function( ev ){\n this.$( '.paired-columns .dataset.selected' ).removeClass( 'selected' );\n },\n\n /** rename a pair when the pair name is clicked */\n _clickPairName : function( ev ){\n ev.stopPropagation();\n var $name = $( ev.currentTarget ),\n $pair = $name.parent().parent(),\n index = $pair.index( '.dataset.paired' ),\n pair = this.paired[ index ],\n response = prompt( 'Enter a new name for the pair:', pair.name );\n if( response ){\n pair.name = response;\n // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these\n // when adding/removing extensions\n //hackish\n pair.customizedName = true;\n $name.text( pair.name );\n }\n },\n\n /** unpair this pair */\n _clickUnpair : function( ev ){\n //if( !ev.currentTarget ){ return true; }\n var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) );\n //this.debug( 'pair:', pairIndex );\n this._unpair( this.paired[ pairIndex ] );\n },\n\n // ........................................................................ paired - drag and drop re-ordering\n //_dragenterPairedColumns : function( ev ){\n // this.debug( '_dragenterPairedColumns:', ev );\n //},\n //_dragleavePairedColumns : function( ev ){\n // //this.debug( '_dragleavePairedColumns:', ev );\n //},\n /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */\n _dragoverPairedColumns : function( ev ){\n //this.debug( '_dragoverPairedColumns:', ev );\n ev.preventDefault();\n\n var $list = this.$( '.paired-columns .column-datasets' );\n this._checkForAutoscroll( $list, ev.originalEvent.clientY );\n //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );\n var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY );\n\n $( '.element-drop-placeholder' ).remove();\n var $placeholder = $( '' );\n if( !$nearest.length ){\n $list.append( $placeholder );\n } else {\n $nearest.before( $placeholder );\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll : function( $element, y ){\n var AUTOSCROLL_SPEED = 2;\n var offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = ( offset.top + $element.outerHeight() ) - y;\n //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );\n if( upperDist >= 0 && upperDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop - AUTOSCROLL_SPEED );\n } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop + AUTOSCROLL_SPEED );\n }\n },\n\n /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestPairedDatasetLi : function( y ){\n var WIGGLE = 4,\n lis = this.$( '.paired-columns .column-datasets li' ).toArray();\n for( var i=0; i',\n _l( 'Choose from the following filters to change which unpaired reads are shown in the display' ),\n ':',\n _.values( this.commonFilters ).map( function( filterSet ){\n return filterChoice( filterSet[0], filterSet[1] );\n }).join( '' ),\n '',\n '', _l( 'More help' ), '',\n '',\n '',\n '', _l( 'Less' ), '',\n '',\n '',\n '',\n '',\n '',\n\n '',\n ''\n ].join('')),\n\n /** the middle: unpaired, divider, and paired */\n middle : _.template([\n // contains two flex rows (rows that fill available space) and a divider btwn\n '',\n '',\n '',\n '',\n '',\n '', _l( 'Unpaired forward' ), '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n _l( 'Choose filters' ),\n '',\n '',\n _l( 'Clear filters' ),\n '',\n '
',\n '',\n _l( 'Auto-pair' ),\n '',\n '',\n '',\n '',\n '',\n '',\n '', _l( 'Unpaired reverse' ), '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n _l( 'Unpair all' ),\n '',\n '',\n ''\n ].join('')),\n\n /** creation and cancel controls */\n footer : _.template([\n '',\n '',\n\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '', _l( 'Name' ), ':',\n '',\n '',\n\n '',\n ''\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '', _l([\n 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ',\n 'These collections can be passed to tools and workflows in order to have analyses done on each member of ',\n 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ',\n 'and re-order the final collection.'\n ].join( '' )), '
',\n '', _l([\n 'Unpaired datasets are shown in the unpaired section ',\n '(hover over the underlined words to highlight below). ',\n 'Paired datasets are shown in the paired section.',\n '
- To pair datasets, you can:',\n '
', _l([\n '
- You can filter what is shown in the unpaired sections by:',\n '
', _l([\n 'To unpair individual dataset pairs, click the ',\n 'unpair buttons ( ). ',\n 'Click the \"Unpair all\" link to unpair all pairs.'\n ].join( '' )), '
',\n '', _l([\n 'You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ',\n '\"Remove file extensions from pair names?\" control.'\n ].join( '' )), '
',\n '', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\". ',\n '(Note: you do not have to pair all unpaired datasets to finish.)'\n ].join( '' )), '
'\n ].join(''))\n })\n});\n\n//=============================================================================\n/** a modal version of the paired collection creator */\nvar pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){\n\n var deferred = jQuery.Deferred(),\n creator;\n\n options = _.defaults( options || {}, {\n datasets : datasets,\n oncancel : function(){\n Galaxy.modal.hide();\n deferred.reject( 'cancelled' );\n },\n oncreate : function( creator, response ){\n Galaxy.modal.hide();\n deferred.resolve( response );\n }\n });\n\n if( !window.Galaxy || !Galaxy.modal ){\n throw new Error( 'Galaxy or Galaxy.modal not found' );\n }\n\n creator = new PairedCollectionCreator( options );\n Galaxy.modal.show({\n title : 'Create a collection of paired datasets',\n body : creator.$el,\n width : '80%',\n height : '800px',\n closing_events: true\n });\n creator.render();\n window.creator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n\n//=============================================================================\nfunction createListOfPairsCollection( collection, defaultHideSourceItems ){\n var elements = collection.toJSON();\n//TODO: validate elements\n return pairedCollectionCreatorModal( elements, {\n historyId : collection.historyId,\n defaultHideSourceItems: defaultHideSourceItems\n });\n}\n\n\n//=============================================================================\n return {\n PairedCollectionCreator : PairedCollectionCreator,\n pairedCollectionCreatorModal : pairedCollectionCreatorModal,\n createListOfPairsCollection : createListOfPairsCollection\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/dataset-choice.js.map b/static/maps/mvc/dataset/dataset-choice.js.map index eb9e187b6a1..18f166f5d8f 100644 --- a/static/maps/mvc/dataset/dataset-choice.js.map +++ b/static/maps/mvc/dataset/dataset-choice.js.map @@ -1 +1 @@ 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'mvc/dataset/dataset-model',\n 'mvc/dataset/dataset-list',\n 'mvc/ui/ui-modal',\n 'mvc/base-mvc',\n 'utils/localization'\n], function( DATASET, DATASET_LIST, MODAL, BASE_MVC, _l ){\n'use strict';\n\nvar logNamespace = 'dataset';\n/* ============================================================================\nTODO:\n does this really work with mixed contents?\n Single dataset choice: allow none?\n tooltips rendered *behind* modal\n collection selector\n better handling when no results returned from filterDatasetJSON\n pass optional subtitle from choice display to modal\n onfirstclick\n drop target\n return modal with promise?\n\n auto showing the modal may not be best\n\n============================================================================ */\n/** Filters an array of dataset plain JSON objs.\n */\nfunction _filterDatasetJSON( datasetJSON, where, datasetsOnly ){\n//TODO: replace with _.matches (underscore 1.6.0)\n function matches( obj, toMatch ){\n for( var key in toMatch ){\n if( toMatch.hasOwnProperty( key ) ){\n if( obj[ key ] !== toMatch[ key ] ){\n return false;\n }\n }\n }\n return true;\n }\n\n return datasetJSON.filter( function( json ){\n console.debug( json )\n return ( !json.deleted && json.visible )\n && ( !datasetsOnly || json.collection_type === undefined )\n && ( matches( json, where ) );\n });\n}\n\n// ============================================================================\n/** Given an array of plain JSON objs rep. datasets, show a modal allowing a choice\n * of one or more of those datasets.\n *\n * Pass:\n * an array of plain JSON objects representing allowed dataset choices\n * a map of options (see below)\n *\n * Options:\n * datasetsOnly: T: display only datasets, F: datasets + dataset collections\n * where: a map of attributes available choices *must have* (defaults to { state: 'ok' })\n * multiselect: T: user can select more than one, F: only one\n * selected: array of dataset ids to make them selected by default\n *\n * @example:\n * var datasetJSON = // from ajax or bootstrap\n * // returns a jQuery promise (that 'fail's only if no datasets are found matching 'where' below)\n * var choice = new DatasetChoiceModal( datasetJSON, {\n * datasetsOnly : false,\n * where : { state: 'ok', file_ext: 'bed', ... },\n * multiselect : true,\n * selected : [ 'df7a1f0c02a5b08e', 'abcdef0123456789' ]\n *\n * }).done( function( json ){\n * if( json ){\n * console.debug( json );\n * // returned choice will always be an array (single or multi)\n * // [{, , ... }]\n * // ... do stuff\n * } else {\n * // json will === null if the user cancelled selection\n * console.debug( 'cancelled' );\n * }\n * });\n */\nvar DatasetChoiceModal = function( datasetJSON, options ){\n\n // option defaults\n options = _.defaults( options || {}, {\n // show datasets or datasets and collections\n datasetsOnly : true,\n // map of attributes to filter datasetJSON by\n where : { state: 'ok' },\n // select more than one dataset?\n multiselect : false,\n // any dataset ids that will display as already selected\n selected : []\n });\n // default title should depend on multiselect\n options.title = options.title ||\n ( options.multiselect? _l( 'Choose datasets:' ): _l( 'Choose a dataset:' ) );\n\n var modal, list, buttons,\n promise = jQuery.Deferred(),\n filterFn = options.filter || _filterDatasetJSON;\n\n // filter the given datasets and if none left return a rejected promise for use with fail()\n datasetJSON = filterFn( datasetJSON, options.where, options.datasetsOnly );\n if( !datasetJSON.length ){\n return promise.reject( 'No matches found' );\n }\n\n // resolve the returned promise with the json of the selected datasets\n function resolveWithSelected(){\n promise.resolve( list.getSelectedModels().map( function( model ){\n return model.toJSON();\n }));\n }\n // if multiselect - add a button for the user to complete the changes\n if( options.multiselect ){\n buttons = {};\n buttons[ _l( 'Ok' ) ] = resolveWithSelected;\n }\n\n // create a full-height modal that's cancellable, remove unneeded elements and styles\n modal = new MODAL.View({\n height : 'auto',\n buttons : buttons,\n closing_events : true,\n closing_callback : function(){ promise.resolve( null ); },\n body : [\n ''\n ].join('')\n });\n modal.$( '.modal-header' ).remove();\n modal.$( '.modal-footer' ).css( 'margin-top', '0px' );\n\n // attach a dataset list (of the filtered datasets) to that modal that's selectable\n list = new DATASET_LIST.DatasetList({\n title : options.title,\n subtitle : options.subtitle || _l([\n//TODO: as option\n 'Click the checkboxes on the right to select datasets. ',\n 'Click the datasets names to see their details. '\n ].join('')),\n el : modal.$body.find( '.list-panel' ),\n selecting : true,\n selected : options.selected,\n collection : new DATASET.DatasetAssociationCollection( datasetJSON )\n });\n\n // when the list is rendered, show the modal (also add a specifying class for css)\n list.once( 'rendered:initial', function(){\n modal.show();\n modal.$el.addClass( 'dataset-choice-modal' );\n });\n if( !options.multiselect ){\n // if single select, remove the all/none list actions from the panel\n list.on( 'rendered', function(){\n list.$( '.list-actions' ).hide();\n });\n // if single select, immediately resolve on a single selection\n list.on( 'view:selected', function( view ){\n promise.resolve([ view.model.toJSON() ]);\n });\n }\n list.render( 0 );\n\n // return the promise, and on any resolution close the modal\n return promise.always( function(){\n modal.hide();\n });\n};\n\n\n// ============================================================================\n/** Activator for single dataset selection modal and display of the selected dataset.\n * The activator/display will show as a single div and, when a dataset is selected,\n * show the name and details of the selected dataset.\n *\n * When clicked the div will generate a DatasetChoiceModal of the available choices.\n *\n * Options:\n * datasetJSON: array of plain json objects representing allowed choices\n * datasetsOnly: T: only show datasets in the allowed choices, F: datasets + collections\n * where: map of attributes to filter datasetJSON by (e.g. { file_ext: 'bed' })\n * label: the label/prompt displayed\n * selected: array of dataset ids that will show as already selected in the control\n *\n * @example:\n * var choice1 = new DATASET_CHOICE.DatasetChoice({\n * datasetJSON : datasetJSON,\n * label : 'Input dataset',\n * selected : [ 'df7a1f0c02a5b08e' ]\n * });\n * $( 'body' ).append( choice1.render().$el )\n *\n * Listen to the DatasetChoice to react to changes in the user's choice/selection:\n * @example:\n * choice1.on( 'selected', function( chooser, selectionJSONArray ){\n * // ... do stuff with new selections\n * });\n */\nvar DatasetChoice = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n className : 'dataset-choice',\n\n /** set up defaults, options, and listeners */\n initialize : function( attributes ){\n this.debug( this + '(DatasetChoice).initialize:', attributes );\n\n this.label = attributes.label !== undefined? _l( attributes.label ) : '';\n this.where = attributes.where;\n this.datasetsOnly = attributes.datasetsOnly !== undefined? attributes.datasetsOnly: true;\n\n this.datasetJSON = attributes.datasetJSON || [];\n this.selected = attributes.selected || [];\n\n this._setUpListeners();\n },\n\n /** add any (bbone) listeners */\n _setUpListeners : function(){\n //this.on( 'all', function(){\n // this.log( this + '', arguments );\n //});\n },\n\n /** render the view */\n render : function(){\n var json = this.toJSON();\n this.$el.html( this._template( json ) );\n this.$( '.selected' ).replaceWith( this._renderSelected( json ) );\n return this;\n },\n\n /** return plain html for the overall control */\n _template : function( json ){\n return _.template([\n ''\n ].join(''))( json );\n },\n\n /** return jQ DOM for the selected dataset (only one) */\n _renderSelected : function( json ){\n if( json.selected.length ){\n//TODO: break out?\n return $( _.template([\n ' ',\n '<%- selected.hid %>: <%- selected.name %>',\n '',\n '<%- selected.misc_blurb %>',\n '', _l( 'format' ) + ': ', '<%- selected.file_ext %>',\n '<%- selected.misc_info %>',\n '',\n ''\n ].join( '' ), { variable : 'selected' })( json.selected[0] ));\n }\n return $([\n '(',\n _l( 'click to select a dataset' ),\n ')'\n ].join( '' ));\n },\n\n//TODO:?? why not just pass in view?\n /** return a plain JSON object with both the view and dataset attributes */\n toJSON : function(){\n var chooser = this;\n return {\n label : chooser.label,\n datasets : chooser.datasetJSON,\n selected : _.compact( _.map( chooser.selected, function( id ){\n return _.findWhere( chooser.datasetJSON, { id: id });\n }))\n };\n },\n\n /** event map: when to open the modal */\n events : {\n // the whole thing functions as a button\n 'click' : 'chooseWithModal'\n },\n\n//TODO:?? modal to prop of this?\n//TODO:?? should be able to handle 'none selectable' on initialize\n /** open the modal and handle the promise representing the user's choice\n * @fires 'selected' when the user selects dataset(s) - passed full json of the selected datasets\n * @fires 'cancelled' when the user clicks away/closes the modal (no selection made) - passed this\n * @fires 'error' if the modal has no selectable datasets based on this.where - passed this and other args\n */\n chooseWithModal : function(){\n var chooser = this;\n\n return this._createModal()\n .done( function( json ){\n if( json ){\n chooser.selected = _.pluck( json, 'id' );\n chooser.trigger( 'selected', chooser, json );\n chooser.render();\n\n } else {\n chooser.trigger( 'cancelled', chooser );\n }\n })\n\n .fail( function(){\n chooser.trigger( 'error', chooser, arguments );\n });\n },\n\n /** create and return the modal to use for choosing */\n _createModal : function(){\n return new DatasetChoiceModal( this.datasetJSON, this._getModalOptions() );\n },\n\n /** return a plain JSON containing the options to pass to the modal */\n _getModalOptions : function(){\n return {\n title : this.label,\n multiselect : false,\n selected : this.selected,\n where : this.where,\n datasetsOnly : this.datasetsOnly\n };\n },\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString : function(){\n return 'DatasetChoice(' + this.selected + ')';\n }\n});\n\n\n// ============================================================================\n/** Activator for multiple dataset selection modal and display of the selected datasets.\n * The activator/display will show as a table of all choices.\n *\n * See DatasetChoice (above) for example usage.\n *\n * Additional options:\n * showHeaders: T: show headers for selected dataset attributes in the display table\n * cells: map of attribute keys -> Human readable/localized column headers\n * (e.g. { file_ext: _l( 'Format' ) }) - defaults are listed below\n */\nvar MultiDatasetChoice = DatasetChoice.extend({\n\n className : DatasetChoice.prototype.className + ' multi',\n\n /** default (dataset attribute key -> table header text) map of what cells to display in the table */\n cells : {\n hid : _l( 'History #' ),\n name : _l( 'Name' ),\n misc_blurb : _l( 'Summary' ),\n file_ext : _l( 'Format' ),\n genome_build : _l( 'Genome' ),\n tags : _l( 'Tags' ),\n annotation : _l( 'Annotation' )\n },\n\n /** in this override, add the showHeaders and cells options */\n initialize : function( attributes ){\n this.showHeaders = attributes.showHeaders !== undefined? attributes.showHeaders : true;\n this.cells = attributes.cells || this.cells;\n DatasetChoice.prototype.initialize.call( this, attributes );\n },\n\n /** in this override, display the selected datasets as a table with optional headers */\n _renderSelected : function( json ){\n if( json.selected.length ){\n return $( _.template([\n '',\n '<% if( json.showHeaders ){ %>',\n '
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'mvc/dataset/dataset-model',\n 'mvc/dataset/dataset-list',\n 'mvc/ui/ui-modal',\n 'mvc/base-mvc',\n 'utils/localization'\n], function( DATASET, DATASET_LIST, MODAL, BASE_MVC, _l ){\n'use strict';\n\nvar logNamespace = 'dataset';\n/* ============================================================================\nTODO:\n does this really work with mixed contents?\n Single dataset choice: allow none?\n tooltips rendered *behind* modal\n collection selector\n better handling when no results returned from filterDatasetJSON\n pass optional subtitle from choice display to modal\n onfirstclick\n drop target\n return modal with promise?\n\n auto showing the modal may not be best\n\n============================================================================ */\n/** Filters an array of dataset plain JSON objs.\n */\nfunction _filterDatasetJSON( datasetJSON, where, datasetsOnly ){\n//TODO: replace with _.matches (underscore 1.6.0)\n function matches( obj, toMatch ){\n for( var key in toMatch ){\n if( toMatch.hasOwnProperty( key ) ){\n if( obj[ key ] !== toMatch[ key ] ){\n return false;\n }\n }\n }\n return true;\n }\n\n return datasetJSON.filter( function( json ){\n console.debug( json )\n return ( !json.deleted && json.visible )\n && ( !datasetsOnly || json.collection_type === undefined )\n && ( matches( json, where ) );\n });\n}\n\n// ============================================================================\n/** Given an array of plain JSON objs rep. datasets, show a modal allowing a choice\n * of one or more of those datasets.\n *\n * Pass:\n * an array of plain JSON objects representing allowed dataset choices\n * a map of options (see below)\n *\n * Options:\n * datasetsOnly: T: display only datasets, F: datasets + dataset collections\n * where: a map of attributes available choices *must have* (defaults to { state: 'ok' })\n * multiselect: T: user can select more than one, F: only one\n * selected: array of dataset ids to make them selected by default\n *\n * @example:\n * var datasetJSON = // from ajax or bootstrap\n * // returns a jQuery promise (that 'fail's only if no datasets are found matching 'where' below)\n * var choice = new DatasetChoiceModal( datasetJSON, {\n * datasetsOnly : false,\n * where : { state: 'ok', file_ext: 'bed', ... },\n * multiselect : true,\n * selected : [ 'df7a1f0c02a5b08e', 'abcdef0123456789' ]\n *\n * }).done( function( json ){\n * if( json ){\n * console.debug( json );\n * // returned choice will always be an array (single or multi)\n * // [{',\n '<% _.map( json.cells, function( val, key ){ %>',\n ' ',\n '<% } %>',\n '',\n '<% _.map( json.selected, function( selected ){ %>',\n '<%- val %> ',\n '<% }); %>',\n '',\n '<% _.map( json.cells, function( val, key ){ %>',\n ' ',\n '<% }); %>',\n '',\n '\"><%- selected[ key ] %> ',\n '<% }) %>',\n ', , ... }]\n * // ... do stuff\n * } else {\n * // json will === null if the user cancelled selection\n * console.debug( 'cancelled' );\n * }\n * });\n */\nvar DatasetChoiceModal = function( datasetJSON, options ){\n\n // option defaults\n options = _.defaults( options || {}, {\n // show datasets or datasets and collections\n datasetsOnly : true,\n // map of attributes to filter datasetJSON by\n where : { state: 'ok' },\n // select more than one dataset?\n multiselect : false,\n // any dataset ids that will display as already selected\n selected : []\n });\n // default title should depend on multiselect\n options.title = options.title ||\n ( options.multiselect? _l( 'Choose datasets:' ): _l( 'Choose a dataset:' ) );\n\n var modal, list, buttons,\n promise = jQuery.Deferred(),\n filterFn = options.filter || _filterDatasetJSON;\n\n // filter the given datasets and if none left return a rejected promise for use with fail()\n datasetJSON = filterFn( datasetJSON, options.where, options.datasetsOnly );\n if( !datasetJSON.length ){\n return promise.reject( 'No matches found' );\n }\n\n // resolve the returned promise with the json of the selected datasets\n function resolveWithSelected(){\n promise.resolve( list.getSelectedModels().map( function( model ){\n return model.toJSON();\n }));\n }\n // if multiselect - add a button for the user to complete the changes\n if( options.multiselect ){\n buttons = {};\n buttons[ _l( 'Ok' ) ] = resolveWithSelected;\n }\n\n // create a full-height modal that's cancellable, remove unneeded elements and styles\n modal = new MODAL.View({\n height : 'auto',\n buttons : buttons,\n closing_events : true,\n closing_callback : function(){ promise.resolve( null ); },\n body : [\n ''\n ].join('')\n });\n modal.$( '.modal-header' ).remove();\n modal.$( '.modal-footer' ).css( 'margin-top', '0px' );\n\n // attach a dataset list (of the filtered datasets) to that modal that's selectable\n list = new DATASET_LIST.DatasetList({\n title : options.title,\n subtitle : options.subtitle || _l([\n//TODO: as option\n 'Click the checkboxes on the right to select datasets. ',\n 'Click the datasets names to see their details. '\n ].join('')),\n el : modal.$body.find( '.list-panel' ),\n selecting : true,\n selected : options.selected,\n collection : new DATASET.DatasetAssociationCollection( datasetJSON )\n });\n\n // when the list is rendered, show the modal (also add a specifying class for css)\n list.once( 'rendered:initial', function(){\n modal.show();\n modal.$el.addClass( 'dataset-choice-modal' );\n });\n if( !options.multiselect ){\n // if single select, remove the all/none list actions from the panel\n list.on( 'rendered', function(){\n list.$( '.list-actions' ).hide();\n });\n // if single select, immediately resolve on a single selection\n list.on( 'view:selected', function( view ){\n promise.resolve([ view.model.toJSON() ]);\n });\n }\n list.render( 0 );\n\n // return the promise, and on any resolution close the modal\n return promise.always( function(){\n modal.hide();\n });\n};\n\n\n// ============================================================================\n/** Activator for single dataset selection modal and display of the selected dataset.\n * The activator/display will show as a single div and, when a dataset is selected,\n * show the name and details of the selected dataset.\n *\n * When clicked the div will generate a DatasetChoiceModal of the available choices.\n *\n * Options:\n * datasetJSON: array of plain json objects representing allowed choices\n * datasetsOnly: T: only show datasets in the allowed choices, F: datasets + collections\n * where: map of attributes to filter datasetJSON by (e.g. { file_ext: 'bed' })\n * label: the label/prompt displayed\n * selected: array of dataset ids that will show as already selected in the control\n *\n * @example:\n * var choice1 = new DATASET_CHOICE.DatasetChoice({\n * datasetJSON : datasetJSON,\n * label : 'Input dataset',\n * selected : [ 'df7a1f0c02a5b08e' ]\n * });\n * $( 'body' ).append( choice1.render().$el )\n *\n * Listen to the DatasetChoice to react to changes in the user's choice/selection:\n * @example:\n * choice1.on( 'selected', function( chooser, selectionJSONArray ){\n * // ... do stuff with new selections\n * });\n */\nvar DatasetChoice = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n className : 'dataset-choice',\n\n /** set up defaults, options, and listeners */\n initialize : function( attributes ){\n this.debug( this + '(DatasetChoice).initialize:', attributes );\n\n this.label = attributes.label !== undefined? 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].join( '-' );\n },\n\n /** Set up: instance vars, options, and event handlers */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( this + '.initialize:', attributes );\n _super.prototype.initialize.call( this, attributes );\n\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || '_blank';\n },\n\n /** event listeners */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n var self = this;\n\n // re-rendering on any model changes\n return self.listenTo( self.model, {\n 'change': function( model ){\n // if the model moved into the ready state and is expanded without details, fetch those details now\n if( self.model.changedAttributes().state &&\n self.model.inReadyState() &&\n self.expanded &&\n !self.model.hasDetails() ){\n // normally, will render automatically (due to fetch -> change),\n // but! setting_metadata sometimes doesn't cause any other changes besides state\n // so, not rendering causes it to seem frozen in setting_metadata state\n self.model.fetch({ silent : true })\n .done( function(){ self.render(); });\n } else {\n if( _.has( model.changed, 'tags' ) && _.keys( model.changed ).length === 1 ){\n // If only the tags have changed, rerender specifically\n // the titlebar region. Otherwise default to the full\n // render.\n self.$( '.nametags' ).html( self._renderNametags() );\n } else {\n self.render();\n }\n }\n }\n });\n },\n\n // ......................................................................... expandable\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... removal\n /** Remove this view's html from the DOM and remove all event listeners.\n * @param {Number or String} speed jq effect speed\n * @param {Function} callback an optional function called when removal is done (scoped to this view)\n */\n remove : function( speed, callback ){\n var view = this;\n speed = speed || this.fxSpeed;\n this.$el.fadeOut( speed, function(){\n Backbone.View.prototype.remove.call( view );\n if( callback ){ callback.call( view ); }\n });\n },\n\n // ......................................................................... rendering\n /* TODO:\n dataset states are the issue primarily making dataset rendering complex\n each state should have it's own way of displaying/set of details\n often with different actions that can be applied\n throw in deleted/purged/visible and things get complicated easily\n I've considered (a couple of times) - creating a view for each state\n - but recreating the view during an update...seems wrong\n */\n /** In this override, add the dataset state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n if( this.model.has( 'state' ) ){\n this.$el.addClass( 'state-' + this.model.get( 'state' ) );\n }\n return this.$el;\n },\n\n // ................................................................................ titlebar\n /** In this override, add the dataset display button. */\n _renderPrimaryActions : function(){\n // render just the display for read-only\n return [ this._renderDisplayButton() ];\n },\n\n /** Render icon-button to display dataset data */\n _renderDisplayButton : function(){\n // don't show display if not viewable or not accessible\n var state = this.model.get( 'state' );\n if( ( state === STATES.NOT_VIEWABLE ) ||\n ( state === STATES.DISCARDED ) ||\n ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var displayBtnData = {\n target : this.linkTarget,\n classes : 'display-btn'\n };\n\n // show a disabled display if the data's been purged\n if( this.model.get( 'purged' ) ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'Cannot display datasets removed from disk' );\n\n // disable if still uploading\n } else if( state === STATES.UPLOAD ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' );\n\n // disable if still new\n } else if( state === STATES.NEW ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'This dataset is not yet viewable' );\n\n } else {\n displayBtnData.title = _l( 'View data' );\n\n // default link for dataset\n displayBtnData.href = this.model.urls.display;\n\n // add frame manager option onclick event\n var self = this;\n displayBtnData.onclick = function( ev ){\n if (Galaxy.frame && Galaxy.frame.active) {\n // Add dataset to frames.\n Galaxy.frame.addDataset(self.model.get('id'));\n ev.preventDefault();\n }\n };\n }\n displayBtnData.faIcon = 'fa-eye';\n return faIconButton( displayBtnData );\n },\n\n // ......................................................................... rendering details\n /** Render the enclosing div of the hda body and, if expanded, the html in the body\n * @returns {jQuery} rendered DOM\n */\n _renderDetails : function(){\n //TODO: generalize to be allow different details for each state\n\n // no access - render nothing but a message\n if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){\n return $( this.templates.noAccess( this.model.toJSON(), this ) );\n }\n\n var $details = _super.prototype._renderDetails.call( this );\n $details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() );\n $details.find( '.summary' ).html( this._renderSummary() )\n .prepend( this._renderDetailMessages() );\n $details.find( '.display-applications' ).html( this._renderDisplayApplications() );\n\n this._setUpBehaviors( $details );\n return $details;\n },\n\n /** Defer to the appropo summary rendering fn based on state */\n _renderSummary : function(){\n var json = this.model.toJSON(),\n summaryRenderFn = this.templates.summaries[ json.state ];\n summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;\n return summaryRenderFn( json, this );\n },\n\n /** Render messages to be displayed only when the details are shown */\n _renderDetailMessages : function(){\n var view = this,\n $warnings = $( '' ),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each( view.templates.detailMessages, function( templateFn ){\n $warnings.append( $( templateFn( json, view ) ) );\n });\n return $warnings;\n },\n\n /** Render the external display application links */\n _renderDisplayApplications : function(){\n if( this.model.isDeletedOrPurged() ){ return ''; }\n // render both old and new display apps using the same template\n return [\n this.templates.displayApplications( this.model.get( 'display_apps' ), this ),\n this.templates.displayApplications( this.model.get( 'display_types' ), this )\n ].join( '' );\n },\n\n // ......................................................................... secondary/details actions\n /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n _renderSecondaryActions : function(){\n this.debug( '_renderSecondaryActions' );\n switch( this.model.get( 'state' ) ){\n case STATES.NOT_VIEWABLE:\n return [];\n case STATES.OK:\n case STATES.FAILED_METADATA:\n case STATES.ERROR:\n return [ this._renderDownloadButton(), this._renderShowParamsButton() ];\n }\n return [ this._renderShowParamsButton() ];\n },\n\n /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n * @returns {jQuery} rendered DOM\n */\n _renderShowParamsButton : function(){\n // gen. safe to show in all cases\n return faIconButton({\n title : _l( 'View details' ),\n classes : 'params-btn',\n href : this.model.urls.show_params,\n target : this.linkTarget,\n faIcon : 'fa-info-circle',\n onclick : function( ev ) {\n if ( Galaxy.frame && Galaxy.frame.active ) {\n Galaxy.frame.add( { title: 'Dataset details', url: this.href } );\n ev.preventDefault();\n ev.stopPropagation();\n }\n }\n });\n },\n\n\n /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n * @returns {jQuery} rendered DOM\n */\n _renderDownloadButton : function(){\n // don't show anything if the data's been purged\n if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; }\n\n // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n // or a single download icon-button (if there are no meta files)\n if( !_.isEmpty( this.model.get( 'meta_files' ) ) ){\n return this._renderMetaFileDownloadButton();\n }\n\n return $([\n '',\n '',\n ''\n ].join( '' ));\n },\n\n /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n _renderMetaFileDownloadButton : function(){\n var urls = this.model.urls;\n return $([\n ''\n ].join( '\\n' ));\n },\n\n _renderNametags : function(){\n var tpl = _.template([\n '<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>',\n '<% if (tag.indexOf(\"name:\") == 0){ %>',\n '<%- tag.slice(5) %>',\n '<% } %>',\n '<% }); %>'].join(''));\n return tpl({tags: this.model.get('tags')});\n },\n\n // ......................................................................... misc\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },\n 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },\n 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }\n }),\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'DatasetListItemView(' + modelString + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemView.prototype.templates = (function(){\n//TODO: move to require text! plugin\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n failed_metadata : BASE_MVC.wrapTemplate([\n // failed metadata is rendered as a warning on an otherwise ok dataset view\n '<% if( model.state === \"failed_metadata\" ){ %>',\n '',\n '<% } %>'\n ]),\n error : BASE_MVC.wrapTemplate([\n // error during index fetch - show error on dataset\n '<% if( model.error ){ %>',\n '',\n '<% } %>'\n ]),\n purged : BASE_MVC.wrapTemplate([\n '<% if( model.purged ){ %>',\n '',\n '<% _.map( json.cells, function( val, key ){ %>',\n ' ',\n '<% } %>',\n '',\n '<% _.map( json.selected, function( selected ){ %>',\n '<%- val %> ',\n '<% }); %>',\n '',\n '<% _.map( json.cells, function( val, key ){ %>',\n ' ',\n '<% }); %>',\n '',\n '\"><%- selected[ key ] %> ',\n '<% }) %>',\n '',\n _l( 'This dataset has been deleted and removed from disk' ),\n '',\n '<% } %>'\n ]),\n deleted : BASE_MVC.wrapTemplate([\n // deleted not purged\n '<% if( model.deleted && !model.purged ){ %>',\n '',\n _l( 'This dataset has been deleted' ),\n '',\n '<% } %>'\n ])\n\n //NOTE: hidden warning is only needed for HDAs\n });\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n '',\n '',\n\n ''\n ], 'dataset' );\n\n var noAccessTemplate = BASE_MVC.wrapTemplate([\n '',\n '',\n '',\n '',\n\n // do not display tags, annotation, display apps, or peek when deleted\n '<% if( !dataset.deleted && !dataset.purged ){ %>',\n '',\n '',\n\n '',\n\n '<% if( dataset.peek ){ %>',\n '<%= dataset.peek %>
',\n '<% } %>',\n '<% } %>',\n '',\n ''\n ], 'dataset' );\n\n//TODO: still toooooooooooooo complex - rework\n var summaryTemplates = {};\n summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([\n '<% if( dataset.misc_blurb ){ %>',\n '',\n _l( 'You do not have permission to view this dataset' ),\n '',\n '',\n '<%- dataset.misc_blurb %>',\n '',\n '<% } %>',\n\n '<% if( dataset.file_ext ){ %>',\n '',\n '',\n '<%- dataset.file_ext %>',\n '',\n '<% } %>',\n\n '<% if( dataset.metadata_dbkey ){ %>',\n '',\n '',\n '',\n '<%- dataset.metadata_dbkey %>',\n '',\n '',\n '<% } %>',\n\n '<% if( dataset.misc_info ){ %>',\n '',\n '<%- dataset.misc_info %>',\n '',\n '<% } %>'\n ], 'dataset' );\n summaryTemplates[ STATES.NEW ] = BASE_MVC.wrapTemplate([\n '', _l( 'This is a new dataset and not all of its data are available yet' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.NOT_VIEWABLE ] = BASE_MVC.wrapTemplate([\n '', _l( 'You do not have permission to view this dataset' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.DISCARDED ] = BASE_MVC.wrapTemplate([\n '', _l( 'The job creating this dataset was cancelled before completion' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([\n '', _l( 'This job is waiting to run' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([\n '', _l( 'This job is currently running' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([\n '', _l( 'This dataset is currently uploading' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([\n '', _l( 'Metadata is being auto-detected' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([\n '', _l( 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.ERROR ] = BASE_MVC.wrapTemplate([\n '<% if( !dataset.purged ){ %>',\n '<%- dataset.misc_blurb %>',\n '<% } %>',\n '', _l( 'An error occurred with this dataset' ), ':',\n '<%- dataset.misc_info %>'\n ], 'dataset' );\n summaryTemplates[ STATES.EMPTY ] = BASE_MVC.wrapTemplate([\n '', _l( 'No data' ), ': <%- dataset.misc_blurb %>'\n ], 'dataset' );\n summaryTemplates.unknown = BASE_MVC.wrapTemplate([\n 'Error: unknown dataset state: \"<%- dataset.state %>\"'\n ], 'dataset' );\n\n // messages to be displayed only within the details section ('below the fold')\n var detailMessageTemplates = {\n resubmitted : BASE_MVC.wrapTemplate([\n // deleted not purged\n '<% if( model.resubmitted ){ %>',\n '',\n _l( 'The job creating this dataset has been resubmitted' ),\n '',\n '<% } %>'\n ])\n };\n\n // this is applied to both old and new style display apps\n var displayApplicationsTemplate = BASE_MVC.wrapTemplate([\n '<% _.each( apps, function( app ){ %>',\n '',\n '<%- app.label %> ',\n '',\n '<% _.each( app.links, function( link ){ %>',\n '\" href=\"<%- link.href %>\">',\n '<% print( _l( link.text ) ); %>',\n ' ',\n '<% }); %>',\n '',\n '',\n '<% }); %>'\n ], 'apps' );\n\n return _.extend( {}, _super.prototype.templates, {\n warnings : warnings,\n details : detailsTemplate,\n noAccess : noAccessTemplate,\n summaries : summaryTemplates,\n detailMessages : detailMessageTemplates,\n displayApplications : displayApplicationsTemplate\n });\n}());\n\n\n// ============================================================================\n return {\n DatasetListItemView : DatasetListItemView\n };\n});\n"]} \ No newline at end of file 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].join( '-' );\n },\n\n /** Set up: instance vars, options, and event handlers */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( this + '.initialize:', attributes );\n _super.prototype.initialize.call( this, attributes );\n\n /** where should pages from links be displayed? 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}\n // render both old and new display apps using the same template\n return [\n this.templates.displayApplications( this.model.get( 'display_apps' ), this ),\n this.templates.displayApplications( this.model.get( 'display_types' ), this )\n ].join( '' );\n },\n\n // ......................................................................... secondary/details actions\n /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n _renderSecondaryActions : function(){\n this.debug( '_renderSecondaryActions' );\n switch( this.model.get( 'state' ) ){\n case STATES.NOT_VIEWABLE:\n return [];\n case STATES.OK:\n case STATES.FAILED_METADATA:\n case STATES.ERROR:\n return [ this._renderDownloadButton(), this._renderShowParamsButton() ];\n }\n return [ this._renderShowParamsButton() ];\n },\n\n /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n * @returns {jQuery} rendered DOM\n */\n _renderShowParamsButton : function(){\n // gen. safe to show in all cases\n return faIconButton({\n title : _l( 'View details' ),\n classes : 'params-btn',\n href : this.model.urls.show_params,\n target : this.linkTarget,\n faIcon : 'fa-info-circle',\n onclick : function( ev ) {\n if ( Galaxy.frame && Galaxy.frame.active ) {\n Galaxy.frame.add( { title: 'Dataset details', url: this.href } );\n ev.preventDefault();\n ev.stopPropagation();\n }\n }\n });\n },\n\n\n /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n * @returns {jQuery} rendered DOM\n */\n _renderDownloadButton : function(){\n // don't show anything if the data's been purged\n if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; }\n\n // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n // or a single download icon-button (if there are no meta files)\n if( !_.isEmpty( this.model.get( 'meta_files' ) ) ){\n return this._renderMetaFileDownloadButton();\n }\n\n return $([\n '',\n '',\n ''\n ].join( '' ));\n },\n\n /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n _renderMetaFileDownloadButton : function(){\n var urls = this.model.urls;\n return $([\n ''\n ].join( '\\n' ));\n },\n\n _renderNametags : function(){\n var tpl = _.template([\n '<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>',\n '<% if (tag.indexOf(\"name:\") == 0){ %>',\n '<%- tag.slice(5) %>',\n '<% } %>',\n '<% }); %>'].join(''));\n return tpl({tags: this.model.get('tags')});\n },\n\n // ......................................................................... misc\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },\n 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },\n 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }\n }),\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'DatasetListItemView(' + modelString + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemView.prototype.templates = (function(){\n//TODO: move to require text! plugin\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n failed_metadata : BASE_MVC.wrapTemplate([\n // failed metadata is rendered as a warning on an otherwise ok dataset view\n '<% if( model.state === \"failed_metadata\" ){ %>',\n '',\n '<% } %>'\n ]),\n error : BASE_MVC.wrapTemplate([\n // error during index fetch - show error on dataset\n '<% if( model.error ){ %>',\n '',\n '<% } %>'\n ]),\n purged : BASE_MVC.wrapTemplate([\n '<% if( model.purged ){ %>',\n '',\n _l( 'This dataset has been deleted and removed from disk' ),\n '',\n '<% } %>'\n ]),\n deleted : BASE_MVC.wrapTemplate([\n // deleted not purged\n '<% if( model.deleted && !model.purged ){ %>',\n '',\n _l( 'This dataset has been deleted' ),\n '',\n '<% } %>'\n ])\n\n //NOTE: hidden warning is only needed for HDAs\n });\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n '',\n '',\n\n ''\n ], 'dataset' );\n\n var noAccessTemplate = BASE_MVC.wrapTemplate([\n '',\n '',\n '',\n '',\n\n // do not display tags, annotation, display apps, or peek when deleted\n '<% if( !dataset.deleted && !dataset.purged ){ %>',\n '',\n '',\n\n '',\n\n '<% if( dataset.peek ){ %>',\n '<%= dataset.peek %>
',\n '<% } %>',\n '<% } %>',\n '',\n ''\n ], 'dataset' );\n\n//TODO: still toooooooooooooo complex - rework\n var summaryTemplates = {};\n summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([\n '<% if( dataset.misc_blurb ){ %>',\n '',\n _l( 'You do not have permission to view this dataset' ),\n '',\n '',\n '<%- dataset.misc_blurb %>',\n '',\n '<% } %>',\n\n '<% if( dataset.file_ext ){ %>',\n '',\n '',\n '<%- dataset.file_ext %>',\n '',\n '<% } %>',\n\n '<% if( dataset.metadata_dbkey ){ %>',\n '',\n '',\n '',\n '<%- dataset.metadata_dbkey %>',\n '',\n '',\n '<% } %>',\n\n '<% if( dataset.misc_info ){ %>',\n '',\n '<%- dataset.misc_info %>',\n '',\n '<% } %>'\n ], 'dataset' );\n summaryTemplates[ STATES.NEW ] = BASE_MVC.wrapTemplate([\n '', _l( 'This is a new dataset and not all of its data are available yet' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.NOT_VIEWABLE ] = BASE_MVC.wrapTemplate([\n '', _l( 'You do not have permission to view this dataset' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.DISCARDED ] = BASE_MVC.wrapTemplate([\n '', _l( 'The job creating this dataset was cancelled before completion' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([\n '', _l( 'This job is waiting to run' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([\n '', _l( 'This job is currently running' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([\n '', _l( 'This dataset is currently uploading' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([\n '', _l( 'Metadata is being auto-detected' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([\n '', _l( 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume' ), ''\n ], 'dataset' );\n summaryTemplates[ STATES.ERROR ] = BASE_MVC.wrapTemplate([\n '<% if( !dataset.purged ){ %>',\n '<%- dataset.misc_blurb %>',\n '<% } %>',\n '', _l( 'An error occurred with this dataset' ), ':',\n '<%- dataset.misc_info %>'\n ], 'dataset' );\n summaryTemplates[ STATES.EMPTY ] = BASE_MVC.wrapTemplate([\n '', _l( 'No data' ), ': <%- dataset.misc_blurb %>'\n ], 'dataset' );\n summaryTemplates.unknown = BASE_MVC.wrapTemplate([\n 'Error: unknown dataset state: \"<%- dataset.state %>\"'\n ], 'dataset' );\n\n // messages to be displayed only within the details section ('below the fold')\n var detailMessageTemplates = {\n resubmitted : BASE_MVC.wrapTemplate([\n // deleted not purged\n '<% if( model.resubmitted ){ %>',\n '',\n _l( 'The job creating this dataset has been resubmitted' ),\n '',\n '<% } %>'\n ])\n };\n\n // this is applied to both old and new style display apps\n var displayApplicationsTemplate = BASE_MVC.wrapTemplate([\n '<% _.each( apps, function( app ){ %>',\n '',\n '<%- app.label %> ',\n '',\n '<% _.each( app.links, function( link ){ %>',\n '\" href=\"<%- link.href %>\">',\n '<% print( _l( link.text ) ); %>',\n ' ',\n '<% }); %>',\n '',\n '',\n '<% }); %>'\n ], 'apps' );\n\n return _.extend( {}, _super.prototype.templates, {\n warnings : warnings,\n details : detailsTemplate,\n noAccess : noAccessTemplate,\n summaries : summaryTemplates,\n detailMessages : detailMessageTemplates,\n displayApplications : displayApplicationsTemplate\n });\n}());\n\n\n// ============================================================================\n return {\n DatasetListItemView : DatasetListItemView\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/dataset-model.js.map b/static/maps/mvc/dataset/dataset-model.js.map index 4cb98a34f5e..9110a1ef685 100644 --- a/static/maps/mvc/dataset/dataset-model.js.map +++ b/static/maps/mvc/dataset/dataset-model.js.map @@ -1 +1 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\"mvc/dataset/states\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, BASE_MVC, _l ){\n'use strict';\n\nvar logNamespace = 'dataset';\n//==============================================================================\nvar searchableMixin = BASE_MVC.SearchableModelMixin;\n/** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).\n * No knowledge of what type (HDA/LDDA/DCDA) should be needed here.\n * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.\n */\nvar DatasetAssociation = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( BASE_MVC.mixin( searchableMixin, /** @lends DatasetAssociation.prototype */{\n _logNamespace : logNamespace,\n\n /** default attributes for a model */\n defaults : {\n state : STATES.NEW,\n deleted : false,\n purged : false,\n name : '(unnamed dataset)',\n accessible : true,\n // sniffed datatype (sam, tabular, bed, etc.)\n data_type : '',\n file_ext : '',\n file_size : 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[ 'bam_index', ... ])\n meta_files : [],\n\n misc_blurb : '',\n misc_info : '',\n\n tags : []\n // do NOT default on annotation, as this default is valid and will be passed on 'save'\n // which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)\n //annotation : ''\n },\n\n /** instance vars and listeners */\n initialize : function( attributes, options ){\n this.debug( this + '(Dataset).initialize', attributes, options );\n\n //!! this state is not in trans.app.model.Dataset.states - set it here -\n if( !this.get( 'accessible' ) ){\n this.set( 'state', STATES.NOT_VIEWABLE );\n }\n\n /** Datasets rely/use some web controllers - have the model generate those URLs on startup */\n this.urls = this._generateUrls();\n\n this._setUpListeners();\n },\n\n /** returns misc. web urls for rendering things like re-run, display, etc. */\n _generateUrls : function(){\n var id = this.get( 'id' );\n if( !id ){ return {}; }\n var urls = {\n 'purge' : 'datasets/' + id + '/purge_async',\n 'display' : 'datasets/' + id + '/display/?preview=True',\n 'edit' : 'datasets/' + id + '/edit',\n 'download' : 'datasets/' + id + '/display' + this._downloadQueryParameters(),\n 'report_error' : 'dataset/errors?id=' + id,\n 'rerun' : 'tool_runner/rerun?id=' + id,\n 'show_params' : 'datasets/' + id + '/show_params',\n 'visualization' : 'visualization',\n 'meta_download' : 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name='\n };\n _.each( urls, function( value, key ){\n urls[ key ] = Galaxy.root + value;\n });\n this.urls = urls;\n return urls;\n },\n\n _downloadQueryParameters : function() {\n return '?to_ext=' + this.get( 'file_ext' );\n },\n\n /** set up any event listeners\n * event: state:ready fired when this DA moves into/is already in a ready state\n */\n _setUpListeners : function(){\n // if the state has changed and the new state is a ready state, fire an event\n this.on( 'change:state', function( currModel, newState ){\n this.log( 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_.contains( STATES.READY_STATES, this.get( 'state' ) );\n return ( this.isDeletedOrPurged() || ready );\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails : function(){\n // if it's inaccessible assume it has everything it needs\n if( !this.get( 'accessible' ) ){ return true; }\n return this.has( 'annotation' );\n },\n\n /** Convenience function to match dataset.has_data. */\n hasData : function(){\n return ( this.get( 'file_size' ) > 0 );\n },\n\n // ........................................................................ ajax\n fetch : function( options ){\n var dataset = this;\n return Backbone.Model.prototype.fetch.call( this, options )\n .always( function(){\n dataset._generateUrls();\n });\n },\n\n /** override to use actual Dates objects for create/update times */\n parse : function( response, options ){\n var parsed = Backbone.Model.prototype.parse.call( this, response, options );\n if( parsed.create_time ){\n parsed.create_time = new Date( parsed.create_time );\n }\n if( parsed.update_time ){\n parsed.update_time = new Date( parsed.update_time );\n }\n return parsed;\n },\n\n /** override to wait by default */\n save : function( attrs, options ){\n options = options || {};\n options.wait = _.isUndefined( options.wait ) ? true : options.wait;\n return Backbone.Model.prototype.save.call( this, attrs, options );\n },\n\n //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n 'delete' : function( options ){\n if( this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: true }, options );\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete : function( options ){\n if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }\n return this.save( { deleted: false }, options );\n },\n\n /** remove the file behind this dataset from the filesystem (if permitted) */\n purge : function _purge( options ){\n //TODO: use, override model.destroy, HDA.delete({ purge: true })\n if( this.get( 'purged' ) ){ return jQuery.when(); }\n options = options || {};\n options.url = this.urls.purge;\n\n //TODO: ideally this would be a DELETE call to the api\n // using purge async for now\n var hda = this,\n xhr = jQuery.ajax( options );\n xhr.done( function( message, status, responseObj ){\n hda.set({ deleted: true, purged: true });\n });\n xhr.fail( function( xhr, status, message ){\n // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'\n // unbury and re-add to xhr\n var error = _l( \"Unable to purge dataset\" );\n var messageBuriedInUnfortunatelyFormattedError = ( 'Removal of datasets by users '\n + 'is not allowed in this Galaxy instance' );\n if( xhr.responseJSON && xhr.responseJSON.error ){\n error = xhr.responseJSON.error;\n } else if( xhr.responseText.indexOf( messageBuriedInUnfortunatelyFormattedError ) !== -1 ){\n error = messageBuriedInUnfortunatelyFormattedError;\n }\n xhr.responseText = error;\n hda.trigger( 'error', hda, xhr, options, _l( error ), { error: error } );\n });\n return xhr;\n },\n\n // ........................................................................ searching\n /** what attributes of an HDA will be used in a text search */\n searchAttributes : [\n 'name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags'\n ],\n\n /** our attr keys don't often match the labels we display to the user - so, when using\n * attribute specifiers ('name=\"bler\"') in a term, allow passing in aliases for the\n * following attr keys.\n */\n searchAliases : {\n title : 'name',\n format : 'file_ext',\n database : 'genome_build',\n blurb : 'misc_blurb',\n description : 'misc_blurb',\n info : 'misc_info',\n tag : 'tags'\n },\n\n // ........................................................................ misc\n /** String representation */\n toString : function(){\n var nameAndId = this.get( 'id' ) || '';\n if( this.get( 'name' ) ){\n nameAndId = '\"' + this.get( 'name' ) + '\",' + nameAndId;\n }\n return 'Dataset(' + nameAndId + ')';\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection for dataset associations.\n */\nvar DatasetAssociationCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend(\n/** @lends HistoryContents.prototype */{\n _logNamespace : logNamespace,\n\n model : DatasetAssociation,\n\n /** root api url */\n urlRoot : Galaxy.root + 'api/datasets',\n\n /** url fn */\n url : function(){\n return this.urlRoot;\n },\n\n // ........................................................................ common queries\n /** Get the ids of every item in this collection\n * @returns array of encoded ids\n */\n ids : function(){\n return this.map( function( item ){ return item.get('id'); });\n },\n\n /** 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\"mvc/dataset/states\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, BASE_MVC, _l ){\n'use strict';\n\nvar logNamespace = 'dataset';\n//==============================================================================\nvar searchableMixin = BASE_MVC.SearchableModelMixin;\n/** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).\n * No knowledge of what type (HDA/LDDA/DCDA) should be needed here.\n * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.\n */\nvar DatasetAssociation = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( BASE_MVC.mixin( searchableMixin, /** @lends DatasetAssociation.prototype */{\n _logNamespace : logNamespace,\n\n /** default attributes for a model */\n defaults : {\n state : STATES.NEW,\n deleted : false,\n purged : false,\n name : '(unnamed dataset)',\n accessible : true,\n // sniffed datatype (sam, tabular, bed, etc.)\n data_type : '',\n file_ext : '',\n file_size : 0,\n\n // array of associated file types (eg. [ 'bam_index', ... ])\n meta_files : [],\n\n misc_blurb : '',\n misc_info : '',\n\n tags : []\n // do NOT default on annotation, as this default is valid and will be passed on 'save'\n // which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)\n //annotation : ''\n },\n\n /** instance vars and listeners */\n initialize : function( attributes, options ){\n this.debug( this + '(Dataset).initialize', attributes, options );\n\n //!! this state is not in trans.app.model.Dataset.states - set it here -\n if( !this.get( 'accessible' ) ){\n this.set( 'state', STATES.NOT_VIEWABLE );\n }\n\n /** Datasets rely/use some web controllers - have the model generate those URLs on startup */\n this.urls = this._generateUrls();\n\n this._setUpListeners();\n },\n\n /** returns misc. web urls for rendering things like re-run, display, etc. */\n _generateUrls : function(){\n var id = this.get( 'id' );\n if( !id ){ return {}; }\n var urls = {\n 'purge' : 'datasets/' + id + '/purge_async',\n 'display' : 'datasets/' + id + '/display/?preview=True',\n 'edit' : 'datasets/' + id + '/edit',\n 'download' : 'datasets/' + id + '/display' + this._downloadQueryParameters(),\n 'report_error' : 'dataset/errors?id=' + id,\n 'rerun' : 'tool_runner/rerun?id=' + id,\n 'show_params' : 'datasets/' + id + '/show_params',\n 'visualization' : 'visualization',\n 'meta_download' : 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name='\n };\n _.each( urls, function( value, key ){\n urls[ key ] = Galaxy.root + value;\n });\n this.urls = urls;\n return urls;\n },\n\n _downloadQueryParameters : function() {\n return '?to_ext=' + this.get( 'file_ext' );\n },\n\n /** set up any event listeners\n * event: state:ready fired when this DA moves into/is already in a ready state\n */\n _setUpListeners : function(){\n // if the state has changed and the new state is a ready state, fire an event\n this.on( 'change:state', function( currModel, newState ){\n this.log( this + ' has changed state:', currModel, newState );\n if( this.inReadyState() ){\n this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) );\n }\n });\n // the download url (currently) relies on having a correct file extension\n this.on( 'change:id change:file_ext', function( currModel ){\n this._generateUrls();\n });\n },\n\n // ........................................................................ common queries\n /** override to add urls */\n toJSON : function(){\n var json = Backbone.Model.prototype.toJSON.call( this );\n //console.warn( 'returning json?' );\n //return json;\n return _.extend( json, {\n urls : this.urls\n });\n },\n\n /** Is this dataset deleted or purged? */\n isDeletedOrPurged : function(){\n return ( this.get( 'deleted' ) || this.get( 'purged' ) );\n },\n\n /** Is this dataset in a 'ready' state; where 'Ready' states are states where no\n * processing (for the ds) is left to do on the server.\n */\n inReadyState : function(){\n var ready = _.contains( STATES.READY_STATES, this.get( 'state' ) );\n return ( this.isDeletedOrPurged() || ready );\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails : function(){\n // if it's inaccessible assume it has everything it needs\n if( !this.get( 'accessible' ) ){ return true; }\n return this.has( 'annotation' );\n },\n\n /** Convenience function to match dataset.has_data. */\n hasData : function(){\n return ( this.get( 'file_size' ) > 0 );\n },\n\n // ........................................................................ ajax\n fetch : function( options ){\n var dataset = this;\n return Backbone.Model.prototype.fetch.call( this, options )\n .always( function(){\n dataset._generateUrls();\n });\n },\n\n /** override to use actual Dates objects for create/update times */\n parse : function( response, options ){\n var parsed = Backbone.Model.prototype.parse.call( this, response, options );\n if( parsed.create_time ){\n parsed.create_time = new Date( parsed.create_time );\n }\n if( parsed.update_time ){\n parsed.update_time = new Date( parsed.update_time );\n }\n return parsed;\n },\n\n /** override to wait by default */\n save : function( attrs, options ){\n options = options || {};\n options.wait = _.isUndefined( options.wait ) ? true : options.wait;\n return Backbone.Model.prototype.save.call( this, attrs, options );\n },\n\n //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n 'delete' : function( options ){\n if( this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: true }, options );\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete : function( options ){\n if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }\n return this.save( { deleted: false }, options );\n },\n\n /** remove the file behind this dataset from the filesystem (if permitted) */\n purge : function _purge( options ){\n //TODO: use, override model.destroy, HDA.delete({ purge: true })\n if( this.get( 'purged' ) ){ return jQuery.when(); }\n options = options || {};\n options.url = this.urls.purge;\n\n //TODO: ideally this would be a DELETE call to the api\n // using purge async for now\n var hda = this,\n xhr = jQuery.ajax( options );\n xhr.done( function( message, status, responseObj ){\n hda.set({ deleted: true, purged: true });\n });\n xhr.fail( function( xhr, status, message ){\n // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'\n // unbury and re-add to xhr\n var error = _l( \"Unable to purge dataset\" );\n var messageBuriedInUnfortunatelyFormattedError = ( 'Removal of datasets by users '\n + 'is not allowed in this Galaxy instance' );\n if( xhr.responseJSON && xhr.responseJSON.error ){\n error = xhr.responseJSON.error;\n } else if( xhr.responseText.indexOf( messageBuriedInUnfortunatelyFormattedError ) !== -1 ){\n error = messageBuriedInUnfortunatelyFormattedError;\n }\n xhr.responseText = error;\n hda.trigger( 'error', hda, xhr, options, _l( error ), { error: error } );\n });\n return xhr;\n },\n\n // ........................................................................ searching\n /** what attributes of an HDA will be used in a text search */\n searchAttributes : [\n 'name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags'\n ],\n\n /** our attr keys don't often match the labels we display to the user - so, when using\n * attribute specifiers ('name=\"bler\"') in a term, allow passing in aliases for the\n * following attr keys.\n */\n searchAliases : {\n title : 'name',\n format : 'file_ext',\n database : 'genome_build',\n blurb : 'misc_blurb',\n description : 'misc_blurb',\n info : 'misc_info',\n tag : 'tags'\n },\n\n // ........................................................................ misc\n /** String representation */\n toString : function(){\n var nameAndId = this.get( 'id' ) || '';\n if( this.get( 'name' ) ){\n nameAndId = '\"' + this.get( 'name' ) + '\",' + nameAndId;\n }\n return 'Dataset(' + nameAndId + ')';\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection for dataset associations.\n */\nvar DatasetAssociationCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend(\n/** @lends HistoryContents.prototype */{\n _logNamespace : logNamespace,\n\n model : DatasetAssociation,\n\n /** root api url */\n urlRoot : Galaxy.root + 'api/datasets',\n\n /** url fn */\n url : function(){\n return this.urlRoot;\n },\n\n // ........................................................................ common queries\n /** Get the ids of every item in this collection\n * @returns array of encoded ids\n */\n ids : function(){\n return this.map( function( item ){ return item.get('id'); });\n },\n\n /** Get contents that are not ready\n * @returns array of content models\n */\n notReady : function(){\n return this.filter( function( content ){\n return !content.inReadyState();\n });\n },\n\n /** return true if any datasets don't have details */\n haveDetails : function(){\n return this.all( function( dataset ){ return dataset.hasDetails(); });\n },\n\n // ........................................................................ ajax\n /** using a queue, perform ajaxFn on each of the models in this collection */\n ajaxQueue : function( ajaxFn, options ){\n var deferred = jQuery.Deferred(),\n startingLength = this.length,\n responses = [];\n\n if( !startingLength ){\n deferred.resolve([]);\n return deferred;\n }\n\n // use reverse order (stylistic choice)\n var ajaxFns = this.chain().reverse().map( function( dataset, i ){\n return function(){\n var xhr = ajaxFn.call( dataset, options );\n // if successful, notify using the deferred to allow tracking progress\n xhr.done( function( response 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This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n*/\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-section', 'mvc/form/form-data' ],\nfunction( Utils, Portlet, Ui, FormSection, FormData ) {\n return Backbone.View.extend({\n initialize: function( options ) {\n this.model = new Backbone.Model({\n initial_errors : false,\n cls : 'ui-portlet-limited',\n icon : null,\n always_refresh : true,\n status : 'warning',\n onchange : function(){}\n }).set( options );\n this.setElement( '' );\n this.render();\n },\n\n /** Update available options */\n update: function( new_model ){\n var self = this;\n this.data.matchModel( new_model, function( node, input_id ) {\n var input = self.input_list[ input_id ];\n if ( input && input.options ) {\n if ( !_.isEqual( input.options, node.options ) ) {\n input.options = node.options;\n var field = self.field_list[ input_id ];\n if ( field.update ) {\n var new_options = [];\n if ( ( [ 'data', 'data_collection', 'drill_down' ] ).indexOf( input.type ) != -1 ) {\n new_options = input.options;\n } else {\n for ( var i in node.options ) {\n var opt = node.options[ i ];\n if ( opt.length > 2 ) {\n new_options.push( { label: opt[ 0 ], value: opt[ 1 ] } );\n }\n }\n }\n field.update( new_options );\n field.trigger( 'change' );\n Galaxy.emit.debug( 'form-view::update()', 'Updating options for ' + input_id );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function( active ) {\n for ( var i in this.input_list ) {\n var field = this.field_list[ i ];\n var input = this.input_list[ i ];\n if ( input.is_dynamic && field.wait && field.unwait ) {\n field[ active ? 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input_id ];\n if ( !input || input.refresh_on_change || self.model.get( 'always_refresh' ) ) {\n var new_check = self.data.checksum();\n if ( new_check != current_check ) {\n current_check = new_check;\n self.model.get( 'onchange' )();\n }\n }\n });\n this.on('reset', function() {\n _.each( self.element_list, function( input_element ) { input_element.reset() } );\n });\n return this;\n },\n\n /** Renders/appends dom elements of the form */\n _renderForm: function() {\n $( '.tooltip' ).remove();\n var options = this.model.attributes;\n this.message = new Ui.UnescapedMessage();\n this.section = new FormSection.View( this, { inputs: options.inputs } );\n this.portlet = new Portlet.View({\n icon : options.icon,\n title : options.title,\n cls : options.cls,\n operations : options.operations,\n buttons : options.buttons,\n collapsible : options.collapsible,\n collapsed : options.collapsed,\n onchange_title : options.onchange_title\n });\n this.portlet.append( this.message.$el );\n 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It is referenced as 'app' in lower level modules.\n*/\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-section', 'mvc/form/form-data' ],\nfunction( Utils, Portlet, Ui, FormSection, FormData ) {\n return Backbone.View.extend({\n initialize: function( options ) {\n this.model = new Backbone.Model({\n initial_errors : false,\n cls : 'ui-portlet-limited',\n icon : null,\n always_refresh : true,\n status : 'warning',\n onchange : function(){}\n }).set( options );\n this.setElement( '' );\n this.render();\n },\n\n /** Update available options */\n update: function( new_model ){\n var self = this;\n this.data.matchModel( new_model, function( node, input_id ) {\n var input = self.input_list[ input_id ];\n if ( input && input.options ) {\n if ( !_.isEqual( input.options, node.options ) ) {\n input.options = node.options;\n var field = self.field_list[ input_id ];\n if ( field.update ) {\n var new_options = [];\n if ( ( [ 'data', 'data_collection', 'drill_down' ] ).indexOf( input.type ) != -1 ) {\n new_options = input.options;\n } else {\n for ( var i in node.options ) {\n var opt = node.options[ i ];\n if ( opt.length > 2 ) {\n new_options.push( { label: opt[ 0 ], value: opt[ 1 ] } );\n }\n }\n }\n field.update( new_options );\n field.trigger( 'change' );\n Galaxy.emit.debug( 'form-view::update()', 'Updating options for ' + input_id );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function( active ) {\n for ( var i in this.input_list ) {\n var field = this.field_list[ i ];\n var input = this.input_list[ i ];\n if ( input.is_dynamic && field.wait && field.unwait ) {\n field[ active ? 'wait' : 'unwait' ]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function ( input_id, message, silent ) {\n var input_element = this.element_list[ input_id ];\n if ( input_element ) {\n input_element.error( message || 'Please verify this parameter.' );\n this.portlet.expand();\n this.trigger( 'expand', input_id );\n if ( !silent ) {\n var $panel = this.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500 );\n }\n }\n },\n\n /** Highlights errors */\n errors: function( options ) {\n this.trigger( 'reset' );\n if ( options && options.errors ) {\n var error_messages = this.data.matchResponse( options.errors );\n for ( var input_id in this.element_list ) {\n var input = this.element_list[ input_id ];\n if ( error_messages[ input_id ] ) {\n this.highlight( input_id, error_messages[ input_id ], true );\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off('change');\n this.off('reset');\n // contains the dom field elements as created by the parameter factory i.e. form-parameters\n this.field_list = {};\n // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n this.input_list = {};\n // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n this.element_list = {};\n // converts the form into a json data structure\n this.data = new FormData.Manager( this );\n this._renderForm();\n this.data.create();\n this.model.get( 'initial_errors' ) && this.errors( this.model.attributes );\n // add listener which triggers on checksum change, and reset the form input wrappers\n var current_check = this.data.checksum();\n this.on( 'change', function( input_id ) {\n var input = self.input_list[ 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\"mvc/list/list-item\",\n \"ui/loading-indicator\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/search-input\"\n], function( LIST_ITEM, LoadingIndicator, BASE_MVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'list';\n/* ============================================================================\nTODO:\n\n============================================================================ */\n/** @class View for a list/collection of models and the sub-views of those models.\n * Sub-views must (at least have the interface if not) inherit from ListItemView.\n * (For a list panel that also includes some 'container' model (History->HistoryContents)\n * use ModelWithListPanel)\n *\n * Allows for:\n * searching collection/sub-views\n * selecting/multi-selecting sub-views\n *\n * Currently used:\n * for dataset/dataset-choice\n * as superclass of ModelListPanel\n */\nvar ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(/** @lends ListPanel.prototype */{\n _logNamespace : logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass : LIST_ITEM.ListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass : Backbone.Collection,\n\n tagName : 'div',\n className : 'list-panel',\n\n /** (in ms) that jquery effects will use */\n fxSpeed : 'fast',\n\n /** string to display when the collection has no contents */\n emptyMsg : _l( 'This list is empty' ),\n /** displayed when no items match the search terms */\n noneFoundMsg : _l( 'No matching items found' ),\n /** string used for search placeholder */\n searchPlaceholder : _l( 'search' ),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the list\n */\n initialize : function( attributes, options ){\n attributes = attributes || {};\n // set the logger if requested\n if( attributes.logger ){\n this.logger = attributes.logger;\n }\n this.log( this + '.initialize:', attributes );\n\n // ---- instance vars\n /** how quickly should jquery fx run? */\n this.fxSpeed = _.has( attributes, 'fxSpeed' )?( attributes.fxSpeed ):( this.fxSpeed );\n\n /** filters for displaying subviews */\n this.filters = [];\n /** current search terms */\n this.searchFor = attributes.searchFor || '';\n\n /** loading indicator */\n // this.indicator = new LoadingIndicator( this.$el );\n\n /** currently showing selectors on items? */\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : true;\n //this.selecting = false;\n\n /** cached selected item.model.ids to persist btwn renders */\n this.selected = attributes.selected || [];\n /** the last selected item.model.id */\n this.lastSelected = null;\n\n /** are sub-views draggable */\n this.dragItems = attributes.dragItems || false;\n\n /** list item view class (when passed models) */\n this.viewClass = attributes.viewClass || this.viewClass;\n\n /** list item views */\n this.views = [];\n /** list item models */\n this.collection = attributes.collection || this._createDefaultCollection();\n\n /** filter fns run over collection items to see if they should show in the list */\n this.filters = attributes.filters || [];\n\n /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n this.$scrollContainer = attributes.$scrollContainer || this.$scrollContainer;\n\n /** @type {String} generic title */\n this.title = attributes.title || '';\n /** @type {String} generic subtitle */\n this.subtitle = attributes.subtitle || '';\n\n this._setUpListeners();\n },\n\n // ------------------------------------------------------------------------ listeners\n /** create any event listeners for the list */\n _setUpListeners : function(){\n this.off();\n\n //TODO: move errorHandler down into list-view from history-view or\n // pass to global error handler (Galaxy)\n this.on({\n error: function( model, xhr, options, msg, details ){\n //this.errorHandler( model, xhr, options, msg, details );\n console.error( model, xhr, options, msg, details );\n },\n // show hide the loading indicator\n loading: function(){\n this._showLoadingIndicator( 'loading...', 40 );\n },\n 'loading-done': function(){\n this._hideLoadingIndicator( 40 );\n },\n });\n\n // throw the first render up as a diff namespace using once (for outside consumption)\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this._setUpCollectionListeners();\n this._setUpViewListeners();\n return this;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection : function(){\n // override\n return new this.collectionClass([]);\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n this.log( this + '._setUpCollectionListeners', this.collection );\n this.stopListening( this.collection );\n\n // bubble up error events\n this.listenTo( this.collection, {\n error : function( model, xhr, options, msg, details ){\n this.trigger( 'error', model, xhr, options, msg, details );\n },\n update : function( collection, options ){\n var changes = options.changes;\n // console.info( collection + ', update:', changes, '\\noptions:', options );\n // more than one: render everything\n if( options.renderAll || ( changes.added.length + changes.removed.length > 1 ) ){\n return this.renderItems();\n }\n // otherwise, let the single add/remove handlers do it\n if( changes.added.length === 1 ){\n return this.addItemView( _.first( changes.added ), collection, options );\n }\n if( changes.removed.length === 1 ){\n return this.removeItemView( _.first( changes.removed ), collection, options );\n }\n }\n });\n return this;\n },\n\n /** listening for sub-view events that bubble up with the 'view:' prefix */\n _setUpViewListeners : function(){\n this.log( this + '._setUpViewListeners' );\n\n // shift to select a range\n this.on({\n 'view:selected': function( view, ev ){\n if( ev && ev.shiftKey && this.lastSelected ){\n var lastSelectedView = this.viewFromModelId( this.lastSelected );\n if( lastSelectedView ){\n this.selectRange( view, lastSelectedView );\n }\n } else if( ev && ev.altKey && !this.selecting ){\n this.showSelectors();\n }\n this.selected.push( view.model.id );\n this.lastSelected = view.model.id;\n },\n\n 'view:de-selected': function( view, ev ){\n this.selected = _.without( this.selected, view.model.id );\n }\n });\n },\n\n // ------------------------------------------------------------------------ rendering\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render : function( speed ){\n this.log( this + '.render', speed );\n var $newRender = this._buildNewRender();\n this._setUpBehaviors( $newRender );\n this._queueNewRender( $newRender, speed );\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _buildNewRender : function(){\n this.debug( this + '(ListPanel)._buildNewRender' );\n var $newRender = $( this.templates.el( {}, this ) );\n this._renderControls( $newRender );\n this._renderTitle( $newRender );\n this._renderSubtitle( $newRender );\n this._renderSearch( $newRender );\n this.renderItems( $newRender );\n return $newRender;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _renderControls : function( $newRender ){\n this.debug( this + '(ListPanel)._renderControls' );\n var $controls = $( this.templates.controls( {}, this ) );\n $newRender.find( '.controls' ).replaceWith( $controls );\n 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this.multiselectActions();\n if( !actions.length ){\n return $menu.empty();\n }\n\n var $newMenu = $([\n ''\n ].join(''));\n var $actions = actions.map( function( action ){\n var html = [ '',\n '',\n '',\n '',\n ''\n ]);\n\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '',\n ''\n ]);\n\n return {\n el : elTemplate,\n controls : controlsTemplate\n };\n}());\n\n\n//=============================================================================\n/** View for a model that has a sub-collection (e.g. History, DatasetCollection)\n * Allows:\n * the model to be reset\n * auto assign panel.collection to panel.model[ panel.modelCollectionKey ]\n *\n */\nvar ModelListPanel = ListPanel.extend({\n\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey : 'contents',\n\n initialize : function( attributes ){\n ListPanel.prototype.initialize.call( this, attributes );\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : false;\n\n 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\"mvc/list/list-item\",\n \"ui/loading-indicator\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/search-input\"\n], function( LIST_ITEM, LoadingIndicator, BASE_MVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'list';\n/* ============================================================================\nTODO:\n\n============================================================================ */\n/** @class View for a list/collection of models and the sub-views of those models.\n * Sub-views must (at least have the interface if not) inherit from ListItemView.\n * (For a list panel that also includes some 'container' model (History->HistoryContents)\n * use ModelWithListPanel)\n *\n * Allows for:\n * searching collection/sub-views\n * selecting/multi-selecting sub-views\n *\n * Currently used:\n * for dataset/dataset-choice\n * as superclass of ModelListPanel\n */\nvar ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(/** @lends ListPanel.prototype */{\n _logNamespace : logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass : LIST_ITEM.ListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass : Backbone.Collection,\n\n tagName : 'div',\n className : 'list-panel',\n\n /** (in ms) that jquery effects will use */\n fxSpeed : 'fast',\n\n /** string to display when the collection has no contents */\n emptyMsg : _l( 'This list is empty' ),\n /** displayed when no items match the search terms */\n noneFoundMsg : _l( 'No matching items found' ),\n /** string used for search placeholder */\n searchPlaceholder : _l( 'search' ),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the list\n */\n initialize : function( attributes, options ){\n attributes = attributes || {};\n // set the logger if requested\n if( attributes.logger ){\n this.logger = attributes.logger;\n }\n this.log( this + '.initialize:', attributes );\n\n // ---- instance vars\n /** how quickly should jquery fx run? */\n this.fxSpeed = _.has( attributes, 'fxSpeed' )?( attributes.fxSpeed ):( this.fxSpeed );\n\n /** filters for displaying subviews */\n this.filters = [];\n /** current search terms */\n this.searchFor = attributes.searchFor || '';\n\n /** loading indicator */\n // this.indicator = new LoadingIndicator( this.$el );\n\n /** currently showing selectors on items? */\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : true;\n //this.selecting = false;\n\n /** cached selected item.model.ids to persist btwn renders */\n this.selected = attributes.selected || [];\n /** the last selected item.model.id */\n this.lastSelected = null;\n\n /** are sub-views draggable */\n this.dragItems = attributes.dragItems || false;\n\n /** list item view class (when passed models) */\n this.viewClass = attributes.viewClass || this.viewClass;\n\n /** list item views */\n this.views = [];\n /** list item models */\n this.collection = attributes.collection || this._createDefaultCollection();\n\n /** filter fns run over collection items to see if they should show in the list */\n this.filters = attributes.filters || [];\n\n /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n this.$scrollContainer = attributes.$scrollContainer || this.$scrollContainer;\n\n /** @type {String} generic title */\n this.title = attributes.title || '';\n /** @type {String} generic subtitle */\n this.subtitle = attributes.subtitle || '';\n\n this._setUpListeners();\n },\n\n // ------------------------------------------------------------------------ listeners\n /** create any event listeners for the list */\n _setUpListeners : function(){\n this.off();\n\n //TODO: move errorHandler down into list-view from history-view or\n // pass to global error handler (Galaxy)\n this.on({\n error: function( model, xhr, options, msg, details ){\n //this.errorHandler( model, xhr, options, msg, details );\n console.error( model, xhr, options, msg, details );\n },\n // show hide the loading indicator\n loading: function(){\n this._showLoadingIndicator( 'loading...', 40 );\n },\n 'loading-done': function(){\n this._hideLoadingIndicator( 40 );\n },\n });\n\n // throw the first render up as a diff namespace using once (for outside consumption)\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this._setUpCollectionListeners();\n this._setUpViewListeners();\n return this;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection : function(){\n // override\n return new this.collectionClass([]);\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n this.log( this + '._setUpCollectionListeners', this.collection );\n this.stopListening( this.collection );\n\n // bubble up error events\n this.listenTo( this.collection, {\n error : function( model, xhr, options, msg, details ){\n this.trigger( 'error', model, xhr, options, msg, details );\n },\n update : function( collection, options ){\n var changes = options.changes;\n // console.info( collection + ', update:', changes, '\\noptions:', options );\n // more than one: render everything\n if( options.renderAll || ( changes.added.length + changes.removed.length > 1 ) ){\n return this.renderItems();\n }\n // otherwise, let the single add/remove handlers do it\n if( changes.added.length === 1 ){\n return this.addItemView( _.first( changes.added ), collection, options );\n }\n if( changes.removed.length === 1 ){\n return this.removeItemView( _.first( changes.removed ), collection, options );\n }\n }\n });\n return this;\n },\n\n /** listening for sub-view events that bubble up with the 'view:' prefix */\n _setUpViewListeners : function(){\n this.log( this + '._setUpViewListeners' );\n\n // shift to select a range\n this.on({\n 'view:selected': function( view, ev ){\n if( ev && ev.shiftKey && this.lastSelected ){\n var lastSelectedView = this.viewFromModelId( this.lastSelected );\n if( lastSelectedView ){\n this.selectRange( view, lastSelectedView );\n }\n } else if( ev && ev.altKey && !this.selecting ){\n this.showSelectors();\n }\n this.selected.push( view.model.id );\n this.lastSelected = view.model.id;\n },\n\n 'view:de-selected': function( view, ev ){\n this.selected = _.without( this.selected, view.model.id );\n }\n });\n },\n\n // ------------------------------------------------------------------------ rendering\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render : function( speed ){\n this.log( this + '.render', speed );\n var $newRender = this._buildNewRender();\n this._setUpBehaviors( $newRender );\n this._queueNewRender( $newRender, speed );\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _buildNewRender : function(){\n this.debug( this + '(ListPanel)._buildNewRender' );\n var $newRender = $( this.templates.el( {}, this ) );\n this._renderControls( $newRender );\n this._renderTitle( $newRender );\n this._renderSubtitle( $newRender );\n this._renderSearch( $newRender );\n this.renderItems( $newRender );\n return $newRender;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _renderControls : function( $newRender ){\n this.debug( this + '(ListPanel)._renderControls' );\n var $controls = $( this.templates.controls( {}, this ) );\n $newRender.find( '.controls' ).replaceWith( $controls );\n return $controls;\n },\n\n /** return a jQuery object containing the title DOM */\n _renderTitle : function( $where ){\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** return a jQuery object containing the subtitle DOM (if any) */\n _renderSubtitle : function( $where ){\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** Fade out the old el, swap in the new contents, then fade in.\n * @param {Number or String} speed jq speed to use for rendering effects\n * @fires rendered when rendered\n */\n _queueNewRender : function( $newRender, speed ) {\n speed = ( speed === undefined )?( this.fxSpeed ):( speed );\n var panel = this;\n panel.log( '_queueNewRender:', $newRender, speed );\n\n $( panel ).queue( 'fx', [\n function( next ){\n panel.$el.fadeOut( speed, next );\n },\n function( next ){\n panel._swapNewRender( $newRender );\n next();\n },\n function( next ){\n panel.$el.fadeIn( speed, next );\n },\n function( next ){\n panel.trigger( 'rendered', panel );\n next();\n }\n ]);\n },\n\n /** empty out the current el, move the $newRender's children in */\n _swapNewRender : function( $newRender ){\n this.$el.empty().attr( 'class', this.className ).append( $newRender.children() );\n if( this.selecting ){ this.showSelectors( 0 ); }\n return this;\n },\n\n /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n * not attached to the page yet.\n */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n this.$controls( $where ).find('[title]').tooltip();\n // set up the pupup for actions available when multi selecting\n this._renderMultiselectActionMenu( $where );\n return this;\n },\n\n /** render a menu containing the actions available to sets of selected items */\n _renderMultiselectActionMenu : function( $where ){\n $where = $where || this.$el;\n var $menu = $where.find( '.list-action-menu' ),\n actions = this.multiselectActions();\n if( !actions.length ){\n return $menu.empty();\n }\n\n var $newMenu = $([\n ''\n ].join(''));\n var $actions = actions.map( function( action ){\n var html = [ '',\n //TODO: this is really the only difference - consider factoring titlebar out\n '',\n '<%- model.name %>',\n '<%- view.subtitle %>',\n '',\n '',\n\n '',\n '',\n '',\n\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n ''\n ]);\n\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '',\n ''\n ]);\n\n return {\n el : elTemplate,\n controls : controlsTemplate\n };\n}());\n\n\n//=============================================================================\n/** View for a model that has a sub-collection (e.g. History, DatasetCollection)\n * Allows:\n * the model to be reset\n * auto assign panel.collection to panel.model[ panel.modelCollectionKey ]\n *\n */\nvar ModelListPanel = ListPanel.extend({\n\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey : 'contents',\n\n initialize : function( attributes ){\n ListPanel.prototype.initialize.call( this, attributes );\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : false;\n\n this.setModel( this.model, attributes );\n },\n\n /** release/free/shutdown old models and set up panel for new models\n * @fires new-model with the panel as parameter\n */\n setModel : function( model, attributes ){\n attributes = attributes || {};\n this.debug( this + '.setModel:', model, attributes );\n\n this.freeModel();\n this.freeViews();\n\n if( model ){\n var oldModelId = this.model? this.model.get( 'id' ): null;\n\n // set up the new model with user, logger, storage, events\n this.model = model;\n if( this.logger ){\n this.model.logger = this.logger;\n }\n this._setUpModelListeners();\n\n //TODO: relation btwn model, collection becoming tangled here\n // free the collection, and assign the new collection to either\n // the model[ modelCollectionKey ], attributes.collection, or an empty vanilla collection\n this.stopListening( this.collection );\n this.collection = this.model[ this.modelCollectionKey ]\n || attributes.collection\n || this._createDefaultCollection();\n this._setUpCollectionListeners();\n\n if( oldModelId && model.get( 'id' ) !== oldModelId ){\n this.trigger( 'new-model', this );\n }\n }\n return this;\n },\n\n /** free the current model and all listeners for it, free any views for the model */\n freeModel : function(){\n // stop/release the previous model, and clear cache to sub-views\n if( this.model ){\n this.stopListening( this.model );\n //TODO: see base-mvc\n //this.model.free();\n //this.model = null;\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ listening\n /** listening for model events */\n _setUpModelListeners : function(){\n // override\n this.log( this + '._setUpModelListeners', this.model );\n // bounce model errors up to the panel\n this.listenTo( this.model, 'error', function(){\n var args = Array.prototype.slice.call( arguments, 0 );\n //args.unshift( 'model:error' );\n args.unshift( 'error' );\n this.trigger.apply( this, args );\n }, this );\n\n // debugging\n if( this.logger ){\n this.listenTo( this.model, 'all', function( event ){\n this.info( this + '(model)', event, arguments );\n });\n }\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el.\n */\n _renderControls : function( $newRender ){\n this.debug( this + '(ModelListPanel)._renderControls' );\n var json = this.model? this.model.toJSON() : {},\n $controls = $( this.templates.controls( json, this ) );\n $newRender.find( '.controls' ).replaceWith( $controls );\n return $controls;\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString : function(){\n return 'ModelListPanel(' + this.model + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nModelListPanel.prototype.templates = (function(){\n\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '',\n '',\n '<%- view.title %>',\n '<%- view.subtitle %>',\n // buttons, controls go here\n '',\n // deleted msg, etc.\n '',\n\n '',\n '',\n '',\n\n // show when selectors are shown\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n ''\n ]);\n\n return _.extend( _.clone( ListPanel.prototype.templates ), {\n controls : controlsTemplate\n });\n}());\n\n\n//=============================================================================\n return {\n ListPanel : ListPanel,\n ModelListPanel : ModelListPanel\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/tool/tool-form-base.js.map b/static/maps/mvc/tool/tool-form-base.js.map index cd008a54c65..7a7a3a727fc 100644 --- a/static/maps/mvc/tool/tool-form-base.js.map +++ b/static/maps/mvc/tool/tool-form-base.js.map @@ -1 +1 @@ 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self = this;\n callback = callback || this.model.get( 'buildmodel' );\n if ( callback ) {\n this.deferred.reset();\n this.deferred.execute( function( process ) {\n callback( process, self );\n process.then( function() { self._render() } );\n });\n } else {\n this._render();\n }\n },\n\n /** Wait for deferred build processes before removal */\n _destroy: function() {\n var self = this;\n this.$el.off().hide();\n this.deferred.execute( function() {\n FormBase.prototype.remove.call( self );\n Galaxy.emit.debug( 'tool-form-base::_destroy()', 'Destroy view.' );\n });\n },\n\n /** Build form */\n _render: function() {\n var self = this;\n var options = this.model.attributes;\n this.model.set({\n title : options.fixed_title || '' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n operations : !options.hide_operations && this._operations(),\n onchange : function() {\n self.deferred.reset();\n self.deferred.execute( function ( process ) {\n self.model.get( 'postchange' )( process, self );\n });\n }\n });\n this.render();\n if ( !this.model.get( 'collapsible' ) ) {\n this.$el.append( $( '' ).addClass( 'ui-margin-top-large' ).append( this._footer() ) );\n }\n this.show_message && this.message.update({\n status : 'success',\n message : 'Now you are using \\'' + options.name + '\\' version ' + options.version + ', id \\'' + options.id + '\\'.',\n persistent : false\n });\n this.show_message = true;\n },\n\n /** Create tool operation menu */\n _operations: function() {\n var self = this;\n var options = this.model.attributes;\n\n // button for version selection\n var versions_button = new Ui.ButtonMenu({\n icon : 'fa-cubes',\n title : ( !options.narrow && 'Versions' ) || null,\n tooltip : 'Select another tool version'\n });\n if ( !options.sustain_version && options.versions && options.versions.length > 1 ) {\n for ( var i in options.versions ) {\n var version = options.versions[ i ];\n if ( version != options.version ) {\n versions_button.addMenu({\n title : 'Switch to ' + version,\n version : version,\n icon : 'fa-cube',\n onclick : function() {\n // here we update the tool version (some tools encode the version also in the id)\n self.model.set( 'id', options.id.replace( options.version, this.version ) );\n self.model.set( 'version', this.version );\n self._update();\n }\n });\n }\n }\n } else {\n versions_button.$el.hide();\n }\n\n // button for options e.g. search, help\n var menu_button = new Ui.ButtonMenu({\n icon : 'fa-caret-down',\n title : ( !options.narrow && 'Options' ) || null,\n tooltip : 'View available options'\n });\n if ( options.biostar_url ) {\n menu_button.addMenu({\n icon : 'fa-question-circle',\n title : 'Question?',\n onclick : function() {\n window.open( options.biostar_url + '/p/new/post/' );\n }\n });\n menu_button.addMenu({\n icon : 'fa-search',\n title : 'Search',\n onclick : function() {\n window.open( options.biostar_url + '/local/search/page/?q=' + options.name );\n }\n });\n };\n menu_button.addMenu({\n icon : 'fa-share',\n title : 'Share',\n onclick : function() {\n prompt( 'Copy to clipboard: Ctrl+C, Enter', window.location.origin + Galaxy.root + 'root?tool_id=' + options.id );\n }\n });\n\n // add admin operations\n if ( Galaxy.user && Galaxy.user.get( 'is_admin' ) ) {\n menu_button.addMenu({\n icon : 'fa-download',\n title : 'Download',\n onclick : function() {\n window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\n }\n });\n menu_button.addMenu({\n icon : 'fa-refresh',\n title : 'Reload XML',\n onclick : function() {\n Utils.get({\n url : Galaxy.root + 'api/tools/' + options.id + '/reload',\n success : function( response ) {\n self.message.update( { persistent : false, message : 'Tool XML has been reloaded.', status : 'success' } );\n },\n error : function( response ) {\n self.message.update( { persistent : false, message : response.err_msg, status : 'danger' } );\n }\n });\n }\n });\n }\n\n // button for version selection\n if ( options.requirements && options.requirements.length > 0 ) {\n menu_button.addMenu({\n icon : 'fa-info-circle',\n title : 'Requirements',\n onclick : function() {\n if ( !this.requirements_visible || self.portlet.collapsed ) {\n this.requirements_visible = true;\n self.portlet.expand();\n self.message.update( { persistent : true, message : self._templateRequirements( options ), status : 'info' } );\n } else {\n this.requirements_visible = false;\n self.message.update( { message : '' } );\n }\n }\n });\n }\n\n // add toolshed url\n if ( options.sharable_url ) {\n menu_button.addMenu({\n icon : 'fa-external-link',\n title : 'See in Tool Shed',\n onclick : function() {\n window.open( options.sharable_url );\n }\n });\n }\n\n // add tool menu webhooks\n $.getJSON('/api/webhooks/tool-menu/all', function(webhooks) {\n _.each(webhooks, function(webhook) {\n if (webhook.activate && webhook.config.function) {\n menu_button.addMenu({\n icon : webhook.config.icon,\n title : webhook.config.title,\n onclick : function() {\n var func = new Function('options', webhook.config.function);\n func(options);\n }\n });\n }\n });\n });\n\n return {\n menu : menu_button,\n versions : versions_button\n }\n },\n\n /** Create footer */\n _footer: function() {\n var options = this.model.attributes;\n var $el = $( '' ).append( this._templateHelp( options ) );\n if ( options.citations ) {\n var $citations = $( '' );\n var citations = new CitationModel.ToolCitationCollection();\n citations.tool_id = options.id;\n var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations });\n citation_list_view.render();\n citations.fetch();\n $el.append( $citations );\n }\n return $el;\n },\n\n /** Templates */\n _templateHelp: function( options ) {\n var $tmpl = $( '' ).addClass( 'ui-form-help' ).append( options.help );\n $tmpl.find( 'a' ).attr( 'target', '_blank' );\n return $tmpl;\n },\n\n _templateRequirements: function( options ) {\n var nreq = 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This module contains all button views. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n var ButtonDefault = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : 'btn btn-default',\n wait : false,\n wait_text : 'Sending...',\n wait_cls : 'btn btn-info',\n disabled : false,\n percentage : -1\n }).set( options );\n this.setElement( $( '' ).attr( 'type', 'button' )\n .append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) )\n .append( this.$progress = $( '' ).append( this.$progress_bar = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'ui-button-default' )\n .addClass( options.disabled && 'disabled' )\n .attr( 'id', options.id )\n .attr( 'disabled', options.disabled )\n .off( 'click' ).on( 'click' , function() {\n $( '.tooltip' ).hide();\n options.onclick && !self.disabled && options.onclick();\n })\n .tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$progress.addClass( 'progress' ).css( 'display', options.percentage !== -1 ? 'block' : 'none' );\n this.$progress_bar.addClass( 'progress-bar' ).css( { width : options.percentage + '%' } );\n this.$icon.removeClass().addClass( 'icon fa' );\n this.$title.removeClass().addClass( 'title' );\n if ( options.wait ) {\n this.$el.addClass( options.wait_cls ).prop( 'disabled', true );\n this.$icon.addClass( 'fa-spinner fa-spin ui-margin-right' );\n this.$title.html( options.wait_text );\n } else {\n this.$el.addClass( options.cls );\n this.$icon.addClass( options.icon );\n this.$title.html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n },\n\n /** Show button */\n show: function() {\n this.$el.show();\n },\n\n /** Hide button */\n hide: function() {\n this.$el.hide();\n },\n\n /** Disable button */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Enable button */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Show spinner to indicate that the button is not ready to be clicked */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner to indicate that the button is ready to be clicked */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Change icon */\n setIcon: function( icon ) {\n this.model.set( 'icon', icon );\n }\n });\n\n /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n var ButtonLink = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : ''\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .attr( { id : options.id,\n href : options.href || 'javascript:void(0)',\n title : options.title,\n target : options.target || '_top',\n disabled : options.disabled } )\n .tooltip( { placement: 'bottom' } )\n .off( 'click' ).on( 'click' , function() {\n options.onclick && !options.disabled && options.onclick();\n });\n this.$icon.removeClass().addClass( options.icon );\n }\n });\n\n /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n var ButtonCheck = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : 'Select/Unselect all',\n icons : [ 'fa-square-o', 'fa-minus-square-o', 'fa-check-square-o' ],\n value : 0,\n onchange : function(){}\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.addClass( 'ui-button-check' )\n .off( 'click' ).on('click', function() {\n self.model.set( 'value', ( self.model.get( 'value' ) === 0 && 2 ) || 0 );\n options.onclick && options.onclick();\n });\n this.$title.html( options.title );\n this.$icon.removeClass()\n .addClass( 'icon fa ui-margin-right' )\n .addClass( options.icons[ options.value ] );\n },\n\n /* Sets a new value and/or returns the value.\n * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n * OR:\n * @param{Integer} new_val - Number of selected options.\n * @param{Integer} total - Total number of available options.\n */\n value: function ( new_val, total ) {\n if ( new_val !== undefined ) {\n if ( total && new_val !== 0 ) {\n new_val = ( new_val !== total ) && 1 || 2;\n }\n this.model.set( 'value', new_val );\n this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n return this.model.get( 'value' );\n }\n });\n\n /** This renders a differently styled, more compact button version. */\n var ButtonIcon = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : 'ui-button-icon',\n disabled : false\n }).set( options );\n this.setElement( $( '' ).append( this.$button = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render : function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .addClass( options.disabled && 'disabled' )\n .attr( 'disabled', options.disabled )\n .attr( 'id', options.id )\n .off( 'click' ).on( 'click', function() {\n $( '.tooltip' ).hide();\n !options.disabled && options.onclick && options.onclick();\n });\n this.$button.addClass( 'button' ).tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n });\n\n /** This class creates a button with dropdown menu. */\n var ButtonMenu = ButtonDefault.extend({\n $menu: null,\n initialize: function ( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : '',\n title : '',\n pull : 'right',\n icon : null,\n onclick : null,\n cls : 'ui-button-icon ui-button-menu',\n tooltip : '',\n target : '',\n href : '',\n onunload : null,\n visible : true,\n tag : ''\n }).set( options );\n this.collection = new Backbone.Collection();\n this.setElement( $( '' ).append( this.$root = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.listenTo( this.collection, 'change add remove reset', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'dropdown' )\n .addClass( options.cls )\n .attr( 'id', options.id )\n .css( { display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } );\n this.$root.addClass( 'root button dropdown-toggle' )\n .attr( 'data-toggle', 'dropdown' )\n .tooltip( { title: options.tooltip, placement: 'bottom' } )\n .off( 'click' ).on( 'click', function( e ) {\n $( '.tooltip' ).hide();\n e.preventDefault();\n options.onclick && options.onclick();\n } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.removeClass().addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n this.$menu && this.$menu.remove();\n if ( this.collection.length > 0 ) {\n this.$menu = $( '',\n //TODO: this is really the only difference - consider factoring titlebar out\n '',\n '<%- model.name %>',\n '<%- view.subtitle %>',\n '',\n '',\n\n '',\n '',\n '',\n\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n '' +\n '' +\n '
' +\n '' + options.title +\n '' +\n '';\n },\n\n /* Thumbnail template with image and description */\n _templateRegularItem: function( options ) {\n return '' +\n '' +\n '
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title : title.substr( 0, title_length ) + '...',\n title_icon : model.get( 'title_icon' ),\n image_src : model.get( 'image_src' )\n })).tooltip( { title: model.get( 'description' ), placement: 'bottom' } ) );\n }\n });\n if ( $el.children().length > 0 ) {\n this.tabs.add( { id: Utils.uid(), title: self.model.get( 'title_default' ), $el: $el } );\n }\n },\n\n _renderList: function() {\n var self = this;\n if ( this.collection.length > 0 ) {\n this.first = this.first || this.collection.first().id;\n var $el = $( '' ).addClass( 'ui-thumbnails-grid' );\n this.collection.each( function( model ) {\n $el.append( self._templateRegularItem( model.attributes ) );\n });\n this.tabs.add( { id: Utils.uid(), title: self.model.get( 'title_list' ), $el: $el } );\n }\n },\n\n /** Set/Get value */\n value: function( new_value ) {\n if ( new_value !== undefined ) {\n new_value = new_value == '__first' ? this.first : new_value;\n var before = this.$( '.ui-thumbnail-current' ).attr( 'value' );\n this.$( '.ui-thumbnail-current' ).removeClass( 'ui-thumbnail-current' );\n this.$( '[value=\"' + new_value + '\"]' ).addClass( 'ui-thumbnail-current' );\n var after = this.$( '.ui-thumbnail-current' ).attr( 'value' );\n var change_handler = this.model.get( 'onchange' );\n after != before && change_handler && change_handler( after );\n }\n return this.$( '.ui-thumbnail-current' ).attr( 'value' );\n },\n\n /** Add click handler */\n _onclick: function( e ) {\n this.value( $( e.target ).closest( '.ui-thumbnails-item' ).attr( 'value' ) );\n },\n\n /** Add double click handler */\n _ondblclick: function( e ) {\n this.model.get( 'ondblclick' ) && this.model.get( 'ondblclick' )( this.value() );\n },\n\n /* Thumbnail template with image */\n _templateThumbnailItem: function( options ) {\n return '' +\n '' +\n '' + options.title +\n '' +\n '';\n },\n\n /* Thumbnail template with image and description */\n _templateRegularItem: function( options ) {\n return '' +\n '' +\n '
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View for upload/progress bar button */\ndefine( [], function() {\n var View = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n icon : 'fa-upload',\n tooltip : 'Download from URL or upload files from disk',\n label : 'Load Data',\n percentage : 0,\n status : '',\n onunload : function(){},\n onclick : function(){}\n }).set( options );\n this.setElement( this._template() );\n this.$progress = this.$( '.progress-bar' );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n $( window ).on( 'beforeunload', function() {\n return self.model.get( 'onunload' )();\n });\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.off( 'click' ).on( 'click', function( e ) { options.onclick( e ) } )\n .tooltip( { title: this.model.get('tooltip'), placement: 'bottom' } );\n this.$progress.removeClass()\n .addClass( 'progress-bar' )\n .addClass( 'progress-bar-notransition' )\n .addClass( options.status != '' && 'progress-bar-' + options.status )\n .css( { width : options.percentage + '%' } );\n },\n\n /** Template */\n _template: function() {\n return '' +\n '' +\n '' +\n '';\n }\n });\n return { View : View };\n});\n"]} \ No newline at end of file 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View for upload/progress bar button */\ndefine( [], function() {\n var View = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n icon : 'fa-upload',\n tooltip : 'Download from URL or upload files from disk',\n label : 'Load Data',\n percentage : 0,\n status : '',\n onunload : function(){},\n onclick : function(){}\n }).set( options );\n this.setElement( this._template() );\n this.$progress = this.$( '.progress-bar' );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n $( window ).on( 'beforeunload', function() {\n return self.model.get( 'onunload' )();\n });\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.off( 'click' ).on( 'click', function( e ) { options.onclick( e ) } )\n .tooltip( { title: this.model.get('tooltip'), placement: 'bottom' } );\n this.$progress.removeClass()\n .addClass( 'progress-bar' )\n .addClass( 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[ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], function( Utils, Form, ToolFormBase ) {\n\n /** Default form wrapper for non-tool modules in the workflow editor. */\n var Default = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n var node = options.node;\n this.form = new Form( Utils.merge( options, {\n onchange: function() {\n Utils.request({\n type : 'POST',\n url : Galaxy.root + 'api/workflows/build_module',\n data : {\n id : node.id,\n type : node.type,\n content_id : node.content_id,\n inputs : self.form.data.create()\n },\n success : function( data ) {\n node.update_field_data( data );\n }\n } );\n }\n } ) );\n _addLabelAnnotation( this.form );\n this.form.render();\n }\n });\n\n /** Tool form wrapper for the workflow editor. */\n var Tool = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n var node = options.node;\n this.form = new ToolFormBase( Utils.merge( options, {\n text_enable : 'Set in Advance',\n text_disable : 'Set at Runtime',\n narrow : true,\n initial_errors : true,\n cls : 'ui-portlet-narrow',\n initialmodel : function( process, form ) {\n self._customize( form );\n process.resolve();\n },\n buildmodel : function( process, form ) {\n form.model.get( 'postchange' )( process, form );\n },\n postchange : function( process, form ) {\n var options = form.model.attributes;\n var current_state = {\n tool_id : options.id,\n tool_version : options.version,\n type : 'tool',\n inputs : $.extend( true, {}, form.data.create() )\n }\n Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Sending current state.', current_state );\n Utils.request({\n type : 'POST',\n url : Galaxy.root + 'api/workflows/build_module',\n data : current_state,\n success : function( data ) {\n form.model.set( data.config_form );\n self._customize( form );\n form.update( data.config_form );\n form.errors( data.config_form );\n // This hasn't modified the workflow, just returned\n // module information for the tool to update the workflow\n // state stored on the client with. User needs to save\n // for this to take effect.\n node.update_field_data( data );\n Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Received new model.', data );\n process.resolve();\n },\n error : function( response ) {\n Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Refresh request failed.', response );\n process.reject();\n }\n });\n }\n }));\n },\n\n _customize: function( form ) {\n var options = form.model.attributes;\n Utils.deepeach( options.inputs, function( input ) {\n if ( input.type ) {\n if ( [ 'data', 'data_collection' ].indexOf( input.type ) != -1 ) {\n input.type = 'hidden';\n input.info = 'Data input \\'' + input.name + '\\' (' + Utils.textify( input.extensions ) + ')';\n input.value = { '__class__': 'RuntimeValue' };\n } else if ( !input.fixed ) {\n input.collapsible_value = { '__class__': 'RuntimeValue' };\n input.is_workflow = ( input.options && input.options.length == 0 ) ||\n ( [ 'integer', 'float' ].indexOf( input.type ) != -1 );\n }\n }\n });\n Utils.deepeach( options.inputs, function( input ) {\n input.type == 'conditional' && ( input.test_param.collapsible_value = undefined );\n });\n _addSections( form );\n _addLabelAnnotation( form );\n }\n });\n\n /** Augments the module form definition by adding label and annotation fields */\n function _addLabelAnnotation ( form ) {\n var options = form.model.attributes;\n var workflow = options.workflow;\n var node = options.node;\n options.inputs.unshift({\n type : 'text',\n name : '__annotation',\n label : 'Annotation',\n fixed : true,\n value : node.annotation,\n area : true,\n help : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'\n });\n options.inputs.unshift({\n type : 'text',\n name : '__label',\n label : 'Label',\n value : node.label,\n help : 'Add a step label.',\n fixed : true,\n onchange: function( new_label ) {\n var duplicate = false;\n for ( var i in workflow.nodes ) {\n var n = workflow.nodes[ i ];\n if ( n.label && n.label == new_label && n.id != node.id ) {\n duplicate = true;\n break;\n }\n }\n var input_id = form.data.match( '__label' );\n var input_element = form.element_list[ input_id ];\n input_element.model.set( 'error_text', duplicate && 'Duplicate label. Please fix this before saving the workflow.' );\n form.trigger( 'change' );\n }\n });\n }\n\n /** Builds all sub sections */\n function _addSections( form ) {\n var options = form.model.attributes;\n var inputs = options.inputs;\n var datatypes = options.datatypes;\n var node = options.node;\n var workflow = options.workflow;\n var post_job_actions = node.post_job_actions;\n var output_id = node.output_terminals && Object.keys( node.output_terminals )[ 0 ];\n\n /** Visit input nodes and enrich by name/value pairs from server data */\n function visit( head, head_list ) {\n head_list = head_list || [];\n head_list.push( head );\n for ( var i in head.inputs ) {\n var input = head.inputs[ i ];\n var action = input.action;\n if ( action ) {\n input.name = 'pja__' + output_id + '__' + input.action;\n if ( input.pja_arg ) {\n input.name += '__' + input.pja_arg;\n }\n if ( input.payload ) {\n for ( var p_id in input.payload ) {\n input.payload[ input.name + '__' + p_id ] = input.payload[ p_id ];\n delete input.payload[ p_id ];\n }\n }\n var d = post_job_actions[ input.action + output_id ];\n if ( d ) {\n for ( var j in head_list ) {\n head_list[ j ].expanded = true;\n }\n if ( input.pja_arg ) {\n input.value = d.action_arguments && d.action_arguments[ input.pja_arg ] || input.value;\n } else {\n input.value = 'true';\n }\n }\n }\n input.inputs && visit( input, head_list.slice( 0 ) );\n }\n }\n\n /** Builds sub section with step actions/annotation */\n function _makeSection( output_id, datatypes ) {\n var extensions = [];\n var input_terminal_names = [];\n for (var key in datatypes ) {\n extensions.push( { 0 : datatypes[ key ], 1 : datatypes[ key ] } );\n }\n for ( key in node.input_terminals ){\n input_terminal_names.push( node.input_terminals[ key ].name );\n }\n extensions.sort( function( a, b ) {\n return a.label > b.label ? 1 : a.label < b.label ? -1 : 0;\n });\n extensions.unshift({\n 0 : 'Sequences',\n 1 : 'Sequences'\n });\n extensions.unshift({\n 0 : 'Roadmaps',\n 1 : 'Roadmaps'\n });\n extensions.unshift({\n 0 : 'Leave unchanged',\n 1 : '__empty__'\n });\n var output;\n var input_config = {\n title : 'Configure Output: \\'' + output_id + '\\'',\n type : 'section',\n flat : true,\n inputs : [{\n label : 'Label',\n type : 'text',\n value : ( output = node.getWorkflowOutput( output_id ) ) && output.label || '',\n help : 'This will provide a short name to describe the output - this must be unique across workflows.',\n onchange : function( new_value ) {\n workflow.attemptUpdateOutputLabel( node, output_id, new_value );\n }\n },{\n action : 'RenameDatasetAction',\n pja_arg : 'newname',\n label : 'Rename dataset',\n type : 'text',\n value : '',\n ignore : '',\n help : 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' + input_terminal_names.join(', ') + '.'\n },{\n action : 'ChangeDatatypeAction',\n pja_arg : 'newtype',\n label : 'Change datatype',\n type : 'select',\n ignore : '__empty__',\n value : '__empty__',\n options : extensions,\n help : 'This action will change the datatype of the output to the indicated value.'\n },{\n action : 'TagDatasetAction',\n pja_arg : 'tags',\n label : 'Add Tags',\n type : 'text',\n value : '',\n ignore : '',\n help : 'This action will set tags for the dataset.'\n },{\n action : 'RemoveTagDatasetAction',\n pja_arg : 'tags',\n label : 'Remove Tags',\n type : 'text',\n value : '',\n ignore : '',\n help : 'This action will remove tags for the dataset.'\n },{\n title : 'Assign columns',\n type : 'section',\n flat : true,\n inputs : [{\n action : 'ColumnSetAction',\n pja_arg : 'chromCol',\n label : 'Chrom column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'startCol',\n label : 'Start column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'endCol',\n label : 'End column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'strandCol',\n label : 'Strand column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'nameCol',\n label : 'Name column',\n type : 'integer',\n value : '',\n ignore : ''\n }],\n help : 'This action will set column assignments in the output dataset. Blank fields are ignored.'\n }]\n };\n visit( input_config );\n return input_config;\n }\n\n if ( output_id ) {\n inputs.push({\n name : 'pja__' + output_id + '__EmailAction',\n label : 'Email notification',\n type : 'boolean',\n value : String( Boolean( post_job_actions[ 'EmailAction' + output_id ] ) ),\n ignore : 'false',\n help : 'An email notification will be sent when the job has completed.',\n payload : {\n 'host' : window.location.host\n }\n });\n inputs.push({\n name : 'pja__' + output_id + '__DeleteIntermediatesAction',\n label : 'Output cleanup',\n type : 'boolean',\n value : String( Boolean( post_job_actions[ 'DeleteIntermediatesAction' + output_id ] ) ),\n ignore : 'false',\n help : 'Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs.'\n });\n for ( var i in node.output_terminals ) {\n inputs.push( _makeSection( i, datatypes ) );\n }\n }\n }\n\n return {\n Default: Default,\n Tool: Tool\n };\n});\n"]} \ No newline at end of file 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[ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], function( Utils, Form, ToolFormBase ) {\n\n /** Default form wrapper for non-tool modules in the workflow editor. */\n var Default = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n var node = options.node;\n this.form = new Form( Utils.merge( options, {\n onchange: function() {\n Utils.request({\n type : 'POST',\n url : Galaxy.root + 'api/workflows/build_module',\n data : {\n id : node.id,\n type : node.type,\n content_id : node.content_id,\n inputs : self.form.data.create()\n },\n success : function( data ) {\n node.update_field_data( data );\n }\n } );\n }\n } ) );\n _addLabelAnnotation( this.form );\n this.form.render();\n }\n });\n\n /** Tool form wrapper for the workflow editor. */\n var Tool = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n var node = options.node;\n this.form = new ToolFormBase( Utils.merge( options, {\n text_enable : 'Set in Advance',\n text_disable : 'Set at Runtime',\n narrow : true,\n initial_errors : true,\n cls : 'ui-portlet-narrow',\n initialmodel : function( process, form ) {\n self._customize( form );\n process.resolve();\n },\n buildmodel : function( process, form ) {\n form.model.get( 'postchange' )( process, form );\n },\n postchange : function( process, form ) {\n var options = form.model.attributes;\n var current_state = {\n tool_id : options.id,\n tool_version : options.version,\n type : 'tool',\n inputs : $.extend( true, {}, form.data.create() )\n }\n Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Sending current state.', current_state );\n Utils.request({\n type : 'POST',\n url : Galaxy.root + 'api/workflows/build_module',\n data : current_state,\n success : function( data ) {\n form.model.set( data.config_form );\n self._customize( form );\n form.update( data.config_form );\n form.errors( data.config_form );\n // This hasn't modified the workflow, just returned\n // module information for the tool to update the workflow\n // state stored on the client with. User needs to save\n // for this to take effect.\n node.update_field_data( data );\n Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Received new model.', data );\n process.resolve();\n },\n error : function( response ) {\n Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Refresh request failed.', response );\n process.reject();\n }\n });\n }\n }));\n },\n\n _customize: function( form ) {\n var options = form.model.attributes;\n Utils.deepeach( options.inputs, function( input ) {\n if ( input.type ) {\n if ( [ 'data', 'data_collection' ].indexOf( input.type ) != -1 ) {\n input.type = 'hidden';\n input.info = 'Data input \\'' + input.name + '\\' (' + Utils.textify( input.extensions ) + ')';\n input.value = { '__class__': 'RuntimeValue' };\n } else if ( !input.fixed ) {\n input.collapsible_value = { '__class__': 'RuntimeValue' };\n input.is_workflow = ( input.options && input.options.length == 0 ) ||\n ( [ 'integer', 'float' ].indexOf( input.type ) != -1 );\n }\n }\n });\n Utils.deepeach( options.inputs, function( input ) {\n input.type == 'conditional' && ( input.test_param.collapsible_value = undefined );\n });\n _addSections( form );\n _addLabelAnnotation( form );\n }\n });\n\n /** Augments the module form definition by adding label and annotation fields */\n function _addLabelAnnotation ( form ) {\n var options = form.model.attributes;\n var workflow = options.workflow;\n var node = options.node;\n options.inputs.unshift({\n type : 'text',\n name : '__annotation',\n label : 'Annotation',\n fixed : true,\n value : node.annotation,\n area : true,\n help : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'\n });\n options.inputs.unshift({\n type : 'text',\n name : '__label',\n label : 'Label',\n value : node.label,\n help : 'Add a step label.',\n fixed : true,\n onchange: function( new_label ) {\n var duplicate = false;\n for ( var i in workflow.nodes ) {\n var n = workflow.nodes[ i ];\n if ( n.label && n.label == new_label && n.id != node.id ) {\n duplicate = true;\n break;\n }\n }\n var input_id = form.data.match( '__label' );\n var input_element = form.element_list[ input_id ];\n input_element.model.set( 'error_text', duplicate && 'Duplicate label. Please fix this before saving the workflow.' );\n form.trigger( 'change' );\n }\n });\n }\n\n /** Builds all sub sections */\n function _addSections( form ) {\n var options = form.model.attributes;\n var inputs = options.inputs;\n var datatypes = options.datatypes;\n var node = options.node;\n var workflow = options.workflow;\n var post_job_actions = node.post_job_actions;\n var output_id = node.output_terminals && Object.keys( node.output_terminals )[ 0 ];\n\n /** Visit input nodes and enrich by name/value pairs from server data */\n function visit( head, head_list ) {\n head_list = head_list || [];\n head_list.push( head );\n for ( var i in head.inputs ) {\n var input = head.inputs[ i ];\n var action = input.action;\n if ( action ) {\n input.name = 'pja__' + output_id + '__' + input.action;\n if ( input.pja_arg ) {\n input.name += '__' + input.pja_arg;\n }\n if ( input.payload ) {\n for ( var p_id in input.payload ) {\n input.payload[ input.name + '__' + p_id ] = input.payload[ p_id ];\n delete input.payload[ p_id ];\n }\n }\n var d = post_job_actions[ input.action + output_id ];\n if ( d ) {\n for ( var j in head_list ) {\n head_list[ j ].expanded = true;\n }\n if ( input.pja_arg ) {\n input.value = d.action_arguments && d.action_arguments[ input.pja_arg ] || input.value;\n } else {\n input.value = 'true';\n }\n }\n }\n input.inputs && visit( input, head_list.slice( 0 ) );\n }\n }\n\n /** Builds sub section with step actions/annotation */\n function _makeSection( output_id, datatypes ) {\n var extensions = [];\n var input_terminal_names = [];\n for (var key in datatypes ) {\n extensions.push( { 0 : datatypes[ key ], 1 : datatypes[ key ] } );\n }\n for ( key in node.input_terminals ){\n input_terminal_names.push( node.input_terminals[ key ].name );\n }\n extensions.sort( function( a, b ) {\n return a.label > b.label ? 1 : a.label < b.label ? -1 : 0;\n });\n extensions.unshift({\n 0 : 'Sequences',\n 1 : 'Sequences'\n });\n extensions.unshift({\n 0 : 'Roadmaps',\n 1 : 'Roadmaps'\n });\n extensions.unshift({\n 0 : 'Leave unchanged',\n 1 : '__empty__'\n });\n var output;\n var input_config = {\n title : 'Configure Output: \\'' + output_id + '\\'',\n type : 'section',\n flat : true,\n inputs : [{\n label : 'Label',\n type : 'text',\n value : ( output = node.getWorkflowOutput( output_id ) ) && output.label || '',\n help : 'This will provide a short name to describe the output - this must be unique across workflows.',\n onchange : function( new_value ) {\n workflow.attemptUpdateOutputLabel( node, output_id, new_value );\n }\n },{\n action : 'RenameDatasetAction',\n pja_arg : 'newname',\n label : 'Rename dataset',\n type : 'text',\n value : '',\n ignore : '',\n help : 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' + input_terminal_names.join(', ') + '.'\n },{\n action : 'ChangeDatatypeAction',\n pja_arg : 'newtype',\n label : 'Change datatype',\n type : 'select',\n ignore : '__empty__',\n value : '__empty__',\n options : extensions,\n help : 'This action will change the datatype of the output to the indicated value.'\n },{\n action : 'TagDatasetAction',\n pja_arg : 'tags',\n label : 'Add Tags',\n type : 'text',\n value : '',\n ignore : '',\n help : 'This action will set tags for the dataset.'\n },{\n action : 'RemoveTagDatasetAction',\n pja_arg : 'tags',\n label : 'Remove Tags',\n type : 'text',\n value : '',\n ignore : '',\n help : 'This action will remove tags for the dataset.'\n },{\n title : 'Assign columns',\n type : 'section',\n flat : true,\n inputs : [{\n action : 'ColumnSetAction',\n pja_arg : 'chromCol',\n label : 'Chrom column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'startCol',\n label : 'Start column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'endCol',\n label : 'End column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'strandCol',\n label : 'Strand column',\n type : 'integer',\n value : '',\n ignore : ''\n },{\n action : 'ColumnSetAction',\n pja_arg : 'nameCol',\n label : 'Name column',\n type : 'integer',\n value : '',\n ignore : ''\n }],\n help : 'This action will set column assignments in the output dataset. Blank fields are ignored.'\n }]\n };\n visit( input_config );\n return input_config;\n }\n\n if ( output_id ) {\n inputs.push({\n name : 'pja__' + output_id + '__EmailAction',\n label : 'Email notification',\n type : 'boolean',\n value : String( Boolean( post_job_actions[ 'EmailAction' + output_id ] ) ),\n ignore : 'false',\n help : 'An email notification will be sent when the job has completed.',\n payload : {\n 'host' : window.location.host\n }\n });\n inputs.push({\n name : 'pja__' + output_id + '__DeleteIntermediatesAction',\n label : 'Output cleanup',\n type : 'boolean',\n value : String( Boolean( post_job_actions[ 'DeleteIntermediatesAction' + output_id ] ) ),\n ignore : 'false',\n help : 'Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs.'\n });\n for ( var i in node.output_terminals ) {\n inputs.push( _makeSection( i, datatypes ) );\n }\n }\n }\n\n return {\n Default: Default,\n Tool: Tool\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/reports_webapp/run_stats.js.map b/static/maps/reports_webapp/run_stats.js.map index 92e22b71abd..cec0396f6fa 100644 --- a/static/maps/reports_webapp/run_stats.js.map +++ b/static/maps/reports_webapp/run_stats.js.map @@ -1 +1 @@ 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days_in_month(month, year) {\n return new Date(year, month, 0).getDate();\n}\n\nfunction date_by_subtracting_days(date, days) {\n return new Date(\n date.getFullYear(), \n date.getMonth(), \n date.getDate() - days,\n date.getHours(),\n date.getMinutes(),\n date.getSeconds(),\n date.getMilliseconds()\n );\n}\n\nfunction date_by_subtracting_hours(date, hours) {\n return new Date(\n date.getFullYear(), \n date.getMonth(), \n date.getDate(),\n date.getHours() - hours,\n date.getMinutes(),\n date.getSeconds(),\n date.getMilliseconds()\n );\n}\n\n// Gets the utc time without minutes and seconds\nfunction get_utc_time_hours() {\n var date = new Date();\n return new Date(\n date.getUTCFullYear(),\n date.getUTCMonth(),\n date.getUTCDate(),\n date.getUTCHours(),\n 0, 0\n );\n}\n\n// Refreshes the page for more up to date information\nfunction refresh() {\n window.location.reload(true);\n}\n\n// This is commented out until we make Reports more responsive.\n// setTimeout(refresh, 60000); //1 minute = 60000 ms\n\nfunction create_chart( inp_data, name, time, title ) {\n // Initialize starting variables\n var data = inp_data;\n\n var hours_array = []\n var now = get_utc_time_hours()\n for(var i = 0; i < 24; i++) {\n hours_array.push(date_by_subtracting_hours(now, i));\n }\n\n var days_array = []\n var now = get_utc_time_hours()\n for(var i = 0; i < 30; i++) {\n days_array.push(date_by_subtracting_days(now, i));\n }\n\n var margin = {top: 60, right: 30, bottom: 50, left: 60};\n var width = 300;\n var barWidth = 0;\n if(time == \"hours\") {\n barWidth = width / 24;\n } else if(time == \"days\") {\n barWidth = width / 30;\n }\n var chart_width = width + margin.left + margin.right;\n\n var chart_zoom = 1.75;\n var height = 150;\n if(d3.max(data) != 0) {\n var zoom = height / d3.max(data);\n } else {\n var zoom = 1.0;\n }\n var chart_height = height + margin.top + margin.bottom;\n\n // Function for zooming in and out of charts\n function click() {\n var classes = d3.select(this).attr(\"class\");\n classes = classes.split(\" \");\n d3.selectAll(\".\" + classes[0]).filter(\".\" + classes[1])\n .style(\"cursor\", \"zoom-in\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height)\n .attr(\"width\", chart_width);\n\n d3.select(this)\n .style(\"cursor\", \"default\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height*chart_zoom)\n .attr(\"width\", chart_width*chart_zoom);\n }\n\n // Initialize all chart containers to have the correct height\n $(\".charts\").css(\"height\", chart_height * (chart_zoom));\n\n // Create the chart object\n var chart = d3.select(\"#\" + name)\n .attr(\"width\", chart_width)\n .attr(\"height\", chart_height)\n .attr(\"preserveAspectRatio\", \"xMidYMin\")\n .attr(\"viewBox\", \"0 0 \" + chart_width + \" \" + chart_height)\n .on(\"click\", click);\n\n // Create bars on the chart and assosciate data with it\n var bar = chart.selectAll(\"g\")\n .data(data)\n .enter().append(\"g\")\n .attr(\"transform\", function(d, i) {\n // Place the bar in the correct place\n var curr_margin = +margin.left;\n curr_margin += +(i * barWidth);\n return \"translate(\" + curr_margin + \",\" + margin.top + \")\";\n })\n .on(\"mouseenter\", function(d) {\n // Show tool tip\n var i = 1;\n var size = d;\n\n while( size >= 10) {\n size = size / 10;\n i++;\n }\n\n var wdth = (i * 4) + 10;\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"transform\", \"translate( \" + (margin.left - 5) + \", \" + ((height - (d * zoom)) + +margin.top + 10) + \" )\" )\n .attr(\"visibility\", \"visible\")\n .text(d);\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .select(\"rect\")\n .attr(\"transform\", \"translate( \" + ((+margin.left) - wdth) + \", \" + ((height - (d * zoom)) + +margin.top) + \" )\" )\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .attr(\"fill\",\"#ebd9b2\");\n })\n .on(\"mouseleave\", function(d) {\n // Remove tool tip\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"visibility\", \"hidden\");\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"rect\")\n .attr(\"width\", \"0\")\n .attr(\"height\", \"0\")\n .attr(\"fill\",\"\")\n .text(d);\n });\n\n // Add a title to the chart\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"title\")\n .attr(\"text-anchor\", \"end\")\n .attr(\"transform\", function(e) {\n return \"translate( \" + width + \",15 )\";\n })\n .text(title);\n\n // Add an x axis line to the chart\n chart.append(\"g\")\n .attr(\"class\", \"axis\")\n .append(\"path\")\n .attr(\"class\", \"x\")\n .attr(\"d\", function(d) {\n var m_x = margin.left;\n var m_y = +margin.top + height;\n var l_x = m_x + width;\n var l_y = m_y;\n\n return \"M\" + m_x + \" \" + m_y + \" L \" + l_x + \" \" + l_y;\n });\n\n // Declare how high the y axis goes\n var y = d3.scale.linear()\n .range([height, 0]);\n\n // Create a yAxis object\n var yAxis = d3.svg.axis()\n .scale(y)\n .orient(\"left\")\n .tickFormat( function(d) { return d3.round( d*d3.max(data), 0 ) });\n\n // Put the y axis on the chart\n chart.append(\"g\")\n .attr(\"class\", \"y axis\")\n .attr(\"id\", (\"y_\" + name))\n .attr(\"text-anchor\", \"end\")\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + margin.top + \")\")\n .call(yAxis)\n .select(\".domain\");\n\n // Put a title for y axis on chart\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#y_\" + name).node()\n var left_pad = +margin.left - axis.getBoundingClientRect().width - 5;\n var top_pad = +margin.top + (axis.getBoundingClientRect().height/2) - 30\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")rotate(-90)\";\n\n return trans;\n })\n .text(\"Number of Jobs\");\n\n // Add color to the chart's bars\n bar.append(\"rect\")\n .attr(\"y\", function(d) { return height - (d * zoom); })\n .attr(\"height\", function(d) { return (d * zoom); })\n .attr(\"width\", barWidth - 1);\n\n // Append x axis\n if(time == \"hours\") {\n // Append hour lines\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", 3)\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( \" + (barWidth/2) + \", \" + height + \")\"\n });\n\n // Append hour numbers\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"transform\", \"translate( 10, \" + (height + 10) + \" )\")\n .text(function(d, i) {\n var time = \"0000\"\n\n if( hours_array[i].getHours() < 10 ) {\n time = \"0\" + String(hours_array[i].getHours());\n } else {\n time = hours_array[i].getHours();\n }\n\n return time;\n });\n\n // Append day lines\n var curr_day = \"\";\n var first = false;\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", function(d, i) {\n var _y2 = 0;\n\n if(hours_array[i].getDate() != curr_day) {\n if(!first) {\n _y2 = 27;\n first = true;\n } else {\n _y2 = 20;\n }\n \n curr_day = hours_array[i].getDate();\n }\n\n return _y2;\n })\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( 0, \" + height + \")\";\n });\n\n // Append day numbers\n curr_day = \"\";\n curr_day_text = \"\";\n first = false;\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"pointer-events\", \"none\")\n .text(function(d, i) {\n var time = \"\";\n var locale = \"en-us\";\n\n if(hours_array[i].getDate() != curr_day_text) {\n time = String(hours_array[i].toLocaleString(locale, { month: \"long\" })); \n time += \" \" + String(hours_array[i].getDate())\n\n curr_day_text = hours_array[i].getDate();\n }\n\n return time;\n })\n .attr(\"transform\", function(d, i) {\n var text_height = height;\n var this_width = d3.select(this).node().getBBox().width;\n\n if(hours_array[i].getDate() != curr_day) {\n if(!first) {\n text_height += 26;\n first = true;\n } else {\n text_height += 18;\n }\n \n curr_day = hours_array[i].getDate();\n }\n\n return \"translate( \" + (this_width + 2) + \", \" + (text_height) + \" )\"\n });\n } else if(time == \"days\") {\n // Append day lines\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", 3)\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( \" + (barWidth/2) + \", \" + height + \")\"\n });\n\n // Append day numbers\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"transform\", \"translate( 9, \" + (height + 10) + \" )\")\n .text(function(d, i) {\n var time = \"0000\"\n\n if( days_array[i].getDate() < 10 ) {\n time = \"0\" + String(days_array[i].getDate());\n } else {\n time = days_array[i].getDate();\n }\n\n return time;\n });\n\n // Append month lines\n var curr_month = \"\";\n var first = false;\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", function(d, i) {\n var _y2 = 0;\n\n if(days_array[i].getMonth() != curr_month) {\n if(!first) {\n _y2 = 27;\n first = true;\n } else {\n _y2 = 20;\n }\n \n curr_month = days_array[i].getMonth();\n }\n\n return _y2;\n })\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( 0, \" + height + \")\";\n });\n\n // Append month numbers\n curr_month = \"\";\n curr_month_text = \"\";\n first = false;\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,100,0)\")\n .attr(\"pointer-events\", \"none\")\n .text(function(d, i) {\n var time = \"\";\n var locale = \"en-us\";\n\n if(days_array[i].getMonth() != curr_month_text) {\n time = String(days_array[i].toLocaleString(locale, { month: \"long\" })); \n time += \" \" + String(days_array[i].getFullYear())\n\n curr_month_text = days_array[i].getMonth();\n }\n\n return time;\n })\n .attr(\"transform\", function(d, i) {\n var text_height = height;\n var this_width = d3.select(this).node().getBBox().width;\n\n if(days_array[i].getMonth() != curr_month) {\n if(!first) {\n text_height += 26;\n first = true;\n } else {\n text_height += 18;\n }\n \n curr_month = days_array[i].getMonth();\n }\n\n return \"translate( \" + (this_width + 2) + \", \" + (text_height) + \" )\"\n });\n }\n\n // Put an invisible tool tip on the chart\n chart.append(\"g\")\n .attr(\"class\", \"tool_tip\")\n .append(\"rect\");\n chart.select(\".tool_tip\")\n .append(\"text\");\n\n // Initialize initial zoomed charts\n if(name == \"jc_dy_chart\" || name == \"jc_hr_chart\") {\n d3.select(\"#\" + name)\n .attr(\"height\", chart_height * chart_zoom)\n .attr(\"width\", chart_width * chart_zoom)\n .style(\"cursor\", \"default\");\n }\n}\n\n//============================================================================================================\n\nfunction create_histogram( inp_data, name, title ) {\n // Initialize initial variables\n // inp_data is an array of numbers that are the amount of minutes per run\n var data = inp_data;\n\n var chart_zoom = 1.75;\n var margin = {top: 60, right: 30, bottom: 50, left: 60};\n\n var height = 150;\n var chart_height = height + margin.top + margin.bottom;\n\n var width = 300;\n var chart_width = width + margin.left + margin.right;\n\n // Cereate x axis metadata\n // Used for x axis, histogram creation, and bar initialization\n var x = d3.scale.linear()\n .domain([0, d3.max(data)])\n .range([0, width]);\n\n // Generate a histogram using twenty uniformly-spaced bins.\n var data = d3.layout.histogram()\n .bins(x.ticks(20))(data);\n\n // Create an array of the sizes of the bars\n var lengths = [];\n for(var i = 0; i < data.length; i ++) {\n lengths.push(data[i].length)\n }\n\n // Find the amount needed to magnify the bars\n if(d3.max(data) != 0) {\n var zoom = height / d3.max(lengths);\n } else {\n var zoom = 1.0;\n }\n\n // Create y axis metadata\n // Used for y axis and bar initialization\n var y = d3.scale.linear()\n .domain([0, d3.max(data, function(d) { return d.y; })])\n .range([height, 0]);\n\n // Function for zooming in and out of charts\n function click() {\n var classes = d3.select(this).attr(\"class\");\n classes = classes.split(\" \");\n d3.selectAll(\".\" + classes[0]).filter(\".\" + classes[1])\n .style(\"cursor\", \"zoom-in\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height)\n .attr(\"width\", chart_width);\n\n d3.select(this)\n .style(\"cursor\", \"default\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height*chart_zoom)\n .attr(\"width\", chart_width*chart_zoom);\n }\n\n // Formatter for x axis times (converting minutes to HH:MM).\n var formatMinutes = function(d) {\n var hours = Math.floor( d / 60 ),\n minutes = Math.floor(d - (hours * 60))\n\n if(hours < 10) {\n hours = \"0\" + hours\n }\n if(minutes < 10) {\n minutes = \"0\" + minutes\n }\n\n return hours + \":\" + minutes;\n };\n\n // Create a chart object\n var chart = d3.select(\"#\" + name)\n .attr(\"viewBox\", \"0 0 \" + chart_width + \" \" + chart_height)\n .attr(\"width\", chart_width)\n .attr(\"height\", chart_height)\n .attr(\"preserveAspectRatio\", \"xMidYMin\")\n .on(\"click\", click);\n\n // Put title on chart\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"title\")\n .attr(\"transform\", function(e) {\n return \"translate( \" + width + \",15 )\";\n })\n .text(title);\n\n // Put bars on chart\n var bar = chart.selectAll(\".bar\")\n .data(data)\n .enter().append(\"g\")\n .attr(\"class\", \"bar\")\n .attr(\"transform\", function(d) {\n return \"translate(\" + (+x(d.x) + +margin.left) + \",\" + (+y(d.y) + +margin.top) + \")\"; })\n .on(\"mouseenter\", function(d) {\n // Show tool tip\n var i = 0,\n size = d.length;\n\n while( size >= 1) {\n size = size / 10;\n i++;\n }\n var wdth = (i * 4) + 10;\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"transform\", \"translate( \" + (margin.left - 5) + \", \" + (height - (d.length * zoom) + +margin.top + 10) + \" )\" )\n .attr(\"visibility\", \"visible\")\n .text(d.length);\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .select(\"rect\")\n .attr(\"transform\", \"translate( \" + ((+margin.left) - wdth) + \", \" + (height - (d.length * zoom) + +margin.top) + \" )\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .attr(\"fill\",\"#ebd9b2\");\n })\n .on(\"mouseleave\", function(d) {\n // Remove tool tip\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"visibility\", \"hidden\");\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"rect\")\n .attr(\"width\", \"0\")\n .attr(\"height\", \"0\")\n .attr(\"fill\",\"\")\n });\n\n // Create bar width\n var bar_x;\n if(data[0] == undefined) {\n bar_x = 1;\n } else {\n bar_x = x(data[0].dx);\n }\n\n // Add color to bar\n bar.append(\"rect\")\n .attr(\"x\", 1)\n .attr(\"width\", bar_x - 1)\n .attr(\"height\", function(d) { return height - y(d.y); });\n\n // Create x axis\n var xAxis = d3.svg.axis()\n .scale(x)\n .orient(\"bottom\")\n .tickFormat(formatMinutes);\n\n // Add x axis to chart\n chart.append(\"g\")\n .attr(\"class\", \"x axis\")\n .attr(\"id\", \"x_\" + name)\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + (+height + +margin.top) + \")\")\n .call(xAxis);\n\n // Add a title to the x axis\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#x_\" + name).node()\n var left_pad = +margin.left + (axis.getBoundingClientRect().width/2) + 30;\n var top_pad = +margin.top + height + axis.getBoundingClientRect().height + 10\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")\";\n\n return trans;\n })\n .text(\"ETA - hrs:mins\");\n\n // Create y axis\n var yAxis = d3.svg.axis()\n .scale(y)\n .orient(\"left\");\n\n // Add y axis to chart\n chart.append(\"g\")\n .attr(\"class\", \"y axis\")\n .attr(\"id\", (\"y_\" + name))\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + margin.top + \")\")\n .call(yAxis);\n\n // Add a title to the y axis\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#y_\" + name).node()\n var left_pad = +margin.left - axis.getBoundingClientRect().width - 5;\n var top_pad = +margin.top + (axis.getBoundingClientRect().height/2) - 30\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")rotate(-90)\";\n\n return trans;\n })\n .text(\"Number of Jobs\");\n\n // Put an invisible tool tip on the chart\n chart.append(\"g\")\n .attr(\"class\", \"tool_tip\")\n .append(\"rect\");\n chart.select(\".tool_tip\")\n .append(\"text\");\n}\n"]} \ No newline at end of file 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days_in_month(month, year) {\n return new Date(year, month, 0).getDate();\n}\n\nfunction date_by_subtracting_days(date, days) {\n return new Date(\n date.getFullYear(), \n date.getMonth(), \n date.getDate() - days,\n date.getHours(),\n date.getMinutes(),\n date.getSeconds(),\n date.getMilliseconds()\n );\n}\n\nfunction date_by_subtracting_hours(date, hours) {\n return new Date(\n date.getFullYear(), \n date.getMonth(), \n date.getDate(),\n date.getHours() - hours,\n date.getMinutes(),\n date.getSeconds(),\n date.getMilliseconds()\n );\n}\n\n// Gets the utc time without minutes and seconds\nfunction get_utc_time_hours() {\n var date = new Date();\n return new Date(\n date.getUTCFullYear(),\n date.getUTCMonth(),\n date.getUTCDate(),\n date.getUTCHours(),\n 0, 0\n );\n}\n\n// Refreshes the page for more up to date information\nfunction refresh() {\n window.location.reload(true);\n}\n\n// This is commented out until we make Reports more responsive.\n// setTimeout(refresh, 60000); //1 minute = 60000 ms\n\nfunction create_chart( inp_data, name, time, title ) {\n // Initialize starting variables\n var data = inp_data;\n\n var hours_array = []\n var now = get_utc_time_hours()\n for(var i = 0; i < 24; i++) {\n hours_array.push(date_by_subtracting_hours(now, i));\n }\n\n var days_array = []\n var now = get_utc_time_hours()\n for(var i = 0; i < 30; i++) {\n days_array.push(date_by_subtracting_days(now, i));\n }\n\n var margin = {top: 60, right: 30, bottom: 50, left: 60};\n var width = 300;\n var barWidth = 0;\n if(time == \"hours\") {\n barWidth = width / 24;\n } else if(time == \"days\") {\n barWidth = width / 30;\n }\n var chart_width = width + margin.left + margin.right;\n\n var chart_zoom = 1.75;\n var height = 150;\n if(d3.max(data) != 0) {\n var zoom = height / d3.max(data);\n } else {\n var zoom = 1.0;\n }\n var chart_height = height + margin.top + margin.bottom;\n\n // Function for zooming in and out of charts\n function click() {\n var classes = d3.select(this).attr(\"class\");\n classes = classes.split(\" \");\n d3.selectAll(\".\" + classes[0]).filter(\".\" + classes[1])\n .style(\"cursor\", \"zoom-in\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height)\n .attr(\"width\", chart_width);\n\n d3.select(this)\n .style(\"cursor\", \"default\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height*chart_zoom)\n .attr(\"width\", chart_width*chart_zoom);\n }\n\n // Initialize all chart containers to have the correct height\n $(\".charts\").css(\"height\", chart_height * (chart_zoom));\n\n // Create the chart object\n var chart = d3.select(\"#\" + name)\n .attr(\"width\", chart_width)\n .attr(\"height\", chart_height)\n .attr(\"preserveAspectRatio\", \"xMidYMin\")\n .attr(\"viewBox\", \"0 0 \" + chart_width + \" \" + chart_height)\n .on(\"click\", click);\n\n // Create bars on the chart and assosciate data with it\n var bar = chart.selectAll(\"g\")\n .data(data)\n .enter().append(\"g\")\n .attr(\"transform\", function(d, i) {\n // Place the bar in the correct place\n var curr_margin = +margin.left;\n curr_margin += +(i * barWidth);\n return \"translate(\" + curr_margin + \",\" + margin.top + \")\";\n })\n .on(\"mouseenter\", function(d) {\n // Show tool tip\n var i = 1;\n var size = d;\n\n while( size >= 10) {\n size = size / 10;\n i++;\n }\n\n var wdth = (i * 4) + 10;\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"transform\", \"translate( \" + (margin.left - 5) + \", \" + ((height - (d * zoom)) + +margin.top + 10) + \" )\" )\n .attr(\"visibility\", \"visible\")\n .text(d);\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .select(\"rect\")\n .attr(\"transform\", \"translate( \" + ((+margin.left) - wdth) + \", \" + ((height - (d * zoom)) + +margin.top) + \" )\" )\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .attr(\"fill\",\"#ebd9b2\");\n })\n .on(\"mouseleave\", function(d) {\n // Remove tool tip\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"visibility\", \"hidden\");\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"rect\")\n .attr(\"width\", \"0\")\n .attr(\"height\", \"0\")\n .attr(\"fill\",\"\")\n .text(d);\n });\n\n // Add a title to the chart\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"title\")\n .attr(\"text-anchor\", \"end\")\n .attr(\"transform\", function(e) {\n return \"translate( \" + width + \",15 )\";\n })\n .text(title);\n\n // Add an x axis line to the chart\n chart.append(\"g\")\n .attr(\"class\", \"axis\")\n .append(\"path\")\n .attr(\"class\", \"x\")\n .attr(\"d\", function(d) {\n var m_x = margin.left;\n var m_y = +margin.top + height;\n var l_x = m_x + width;\n var l_y = m_y;\n\n return \"M\" + m_x + \" \" + m_y + \" L \" + l_x + \" \" + l_y;\n });\n\n // Declare how high the y axis goes\n var y = d3.scale.linear()\n .range([height, 0]);\n\n // Create a yAxis object\n var yAxis = d3.svg.axis()\n .scale(y)\n .orient(\"left\")\n .tickFormat( function(d) { return d3.round( d*d3.max(data), 0 ) });\n\n // Put the y axis on the chart\n chart.append(\"g\")\n .attr(\"class\", \"y axis\")\n .attr(\"id\", (\"y_\" + name))\n .attr(\"text-anchor\", \"end\")\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + margin.top + \")\")\n .call(yAxis)\n .select(\".domain\");\n\n // Put a title for y axis on chart\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#y_\" + name).node()\n var left_pad = +margin.left - axis.getBoundingClientRect().width - 5;\n var top_pad = +margin.top + (axis.getBoundingClientRect().height/2) - 30\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")rotate(-90)\";\n\n return trans;\n })\n .text(\"Number of Jobs\");\n\n // Add color to the chart's bars\n bar.append(\"rect\")\n .attr(\"y\", function(d) { return height - (d * zoom); })\n .attr(\"height\", function(d) { return (d * zoom); })\n .attr(\"width\", barWidth - 1);\n\n // Append x axis\n if(time == \"hours\") {\n // Append hour lines\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", 3)\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( \" + (barWidth/2) + \", \" + height + \")\"\n });\n\n // Append hour numbers\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"transform\", \"translate( 10, \" + (height + 10) + \" )\")\n .text(function(d, i) {\n var time = \"0000\"\n\n if( hours_array[i].getHours() < 10 ) {\n time = \"0\" + String(hours_array[i].getHours());\n } else {\n time = hours_array[i].getHours();\n }\n\n return time;\n });\n\n // Append day lines\n var curr_day = \"\";\n var first = false;\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", function(d, i) {\n var _y2 = 0;\n\n if(hours_array[i].getDate() != curr_day) {\n if(!first) {\n _y2 = 27;\n first = true;\n } else {\n _y2 = 20;\n }\n \n curr_day = hours_array[i].getDate();\n }\n\n return _y2;\n })\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( 0, \" + height + \")\";\n });\n\n // Append day numbers\n curr_day = \"\";\n curr_day_text = \"\";\n first = false;\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"pointer-events\", \"none\")\n .text(function(d, i) {\n var time = \"\";\n var locale = \"en-us\";\n\n if(hours_array[i].getDate() != curr_day_text) {\n time = String(hours_array[i].toLocaleString(locale, { month: \"long\" })); \n time += \" \" + String(hours_array[i].getDate())\n\n curr_day_text = hours_array[i].getDate();\n }\n\n return time;\n })\n .attr(\"transform\", function(d, i) {\n var text_height = height;\n var this_width = d3.select(this).node().getBBox().width;\n\n if(hours_array[i].getDate() != curr_day) {\n if(!first) {\n text_height += 26;\n first = true;\n } else {\n text_height += 18;\n }\n \n curr_day = hours_array[i].getDate();\n }\n\n return \"translate( \" + (this_width + 2) + \", \" + (text_height) + \" )\"\n });\n } else if(time == \"days\") {\n // Append day lines\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", 3)\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( \" + (barWidth/2) + \", \" + height + \")\"\n });\n\n // Append day numbers\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"transform\", \"translate( 9, \" + (height + 10) + \" )\")\n .text(function(d, i) {\n var time = \"0000\"\n\n if( days_array[i].getDate() < 10 ) {\n time = \"0\" + String(days_array[i].getDate());\n } else {\n time = days_array[i].getDate();\n }\n\n return time;\n });\n\n // Append month lines\n var curr_month = \"\";\n var first = false;\n bar.append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", function(d, i) {\n var _y2 = 0;\n\n if(days_array[i].getMonth() != curr_month) {\n if(!first) {\n _y2 = 27;\n first = true;\n } else {\n _y2 = 20;\n }\n \n curr_month = days_array[i].getMonth();\n }\n\n return _y2;\n })\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( 0, \" + height + \")\";\n });\n\n // Append month numbers\n curr_month = \"\";\n curr_month_text = \"\";\n first = false;\n bar.append(\"text\")\n .attr(\"fill\", \"rgb(0,100,0)\")\n .attr(\"pointer-events\", \"none\")\n .text(function(d, i) {\n var time = \"\";\n var locale = \"en-us\";\n\n if(days_array[i].getMonth() != curr_month_text) {\n time = String(days_array[i].toLocaleString(locale, { month: \"long\" })); \n time += \" \" + String(days_array[i].getFullYear())\n\n curr_month_text = days_array[i].getMonth();\n }\n\n return time;\n })\n .attr(\"transform\", function(d, i) {\n var text_height = height;\n var this_width = d3.select(this).node().getBBox().width;\n\n if(days_array[i].getMonth() != curr_month) {\n if(!first) {\n text_height += 26;\n first = true;\n } else {\n text_height += 18;\n }\n \n curr_month = days_array[i].getMonth();\n }\n\n return \"translate( \" + (this_width + 2) + \", \" + (text_height) + \" )\"\n });\n }\n\n // Put an invisible tool tip on the chart\n chart.append(\"g\")\n .attr(\"class\", \"tool_tip\")\n .append(\"rect\");\n chart.select(\".tool_tip\")\n .append(\"text\");\n\n // Initialize initial zoomed charts\n if(name == \"jc_dy_chart\" || name == \"jc_hr_chart\") {\n d3.select(\"#\" + name)\n .attr(\"height\", chart_height * chart_zoom)\n .attr(\"width\", chart_width * chart_zoom)\n .style(\"cursor\", \"default\");\n }\n}\n\n//============================================================================================================\n\nfunction create_histogram( inp_data, name, title ) {\n // Initialize initial variables\n // inp_data is an array of numbers that are the amount of minutes per run\n var data = inp_data;\n\n var chart_zoom = 1.75;\n var margin = {top: 60, right: 30, bottom: 50, left: 60};\n\n var height = 150;\n var chart_height = height + margin.top + margin.bottom;\n\n var width = 300;\n var chart_width = width + margin.left + margin.right;\n\n // Cereate x axis metadata\n // Used for x axis, histogram creation, and bar initialization\n var x = d3.scale.linear()\n .domain([0, d3.max(data)])\n .range([0, width]);\n\n // Generate a histogram using twenty uniformly-spaced bins.\n var data = d3.layout.histogram()\n .bins(x.ticks(20))(data);\n\n // Create an array of the sizes of the bars\n var lengths = [];\n for(var i = 0; i < data.length; i ++) {\n lengths.push(data[i].length)\n }\n\n // Find the amount needed to magnify the bars\n if(d3.max(data) != 0) {\n var zoom = height / d3.max(lengths);\n } else {\n var zoom = 1.0;\n }\n\n // Create y axis metadata\n // Used for y axis and bar initialization\n var y = d3.scale.linear()\n .domain([0, d3.max(data, function(d) { return d.y; })])\n .range([height, 0]);\n\n // Function for zooming in and out of charts\n function click() {\n var classes = d3.select(this).attr(\"class\");\n classes = classes.split(\" \");\n d3.selectAll(\".\" + classes[0]).filter(\".\" + classes[1])\n .style(\"cursor\", \"zoom-in\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height)\n .attr(\"width\", chart_width);\n\n d3.select(this)\n .style(\"cursor\", \"default\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height*chart_zoom)\n .attr(\"width\", chart_width*chart_zoom);\n }\n\n // Formatter for x axis times (converting minutes to HH:MM).\n var formatMinutes = function(d) {\n var hours = Math.floor( d / 60 ),\n minutes = Math.floor(d - (hours * 60))\n\n if(hours < 10) {\n hours = \"0\" + hours\n }\n if(minutes < 10) {\n minutes = \"0\" + minutes\n }\n\n return hours + \":\" + minutes;\n };\n\n // Create a chart object\n var chart = d3.select(\"#\" + name)\n .attr(\"viewBox\", \"0 0 \" + chart_width + \" \" + chart_height)\n .attr(\"width\", chart_width)\n .attr(\"height\", chart_height)\n .attr(\"preserveAspectRatio\", \"xMidYMin\")\n .on(\"click\", click);\n\n // Put title on chart\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"title\")\n .attr(\"transform\", function(e) {\n return \"translate( \" + width + \",15 )\";\n })\n .text(title);\n\n // Put bars on chart\n var bar = chart.selectAll(\".bar\")\n .data(data)\n .enter().append(\"g\")\n .attr(\"class\", \"bar\")\n .attr(\"transform\", function(d) {\n return \"translate(\" + (+x(d.x) + +margin.left) + \",\" + (+y(d.y) + +margin.top) + \")\"; })\n .on(\"mouseenter\", function(d) {\n // Show tool tip\n var i = 0,\n size = d.length;\n\n while( size >= 1) {\n size = size / 10;\n i++;\n }\n var wdth = (i * 4) + 10;\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"transform\", \"translate( \" + (margin.left - 5) + \", \" + (height - (d.length * zoom) + +margin.top + 10) + \" )\" )\n .attr(\"visibility\", \"visible\")\n .text(d.length);\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .select(\"rect\")\n .attr(\"transform\", \"translate( \" + ((+margin.left) - wdth) + \", \" + (height - (d.length * zoom) + +margin.top) + \" )\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .attr(\"fill\",\"#ebd9b2\");\n })\n .on(\"mouseleave\", function(d) {\n // Remove tool tip\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"text\")\n .attr(\"visibility\", \"hidden\");\n\n d3.select(d3.event.path[1]).select(\".tool_tip\")\n .select(\"rect\")\n .attr(\"width\", \"0\")\n .attr(\"height\", \"0\")\n .attr(\"fill\",\"\")\n });\n\n // Create bar width\n var bar_x;\n if(data[0] == undefined) {\n bar_x = 1;\n } else {\n bar_x = x(data[0].dx);\n }\n\n // Add color to bar\n bar.append(\"rect\")\n .attr(\"x\", 1)\n .attr(\"width\", bar_x - 1)\n .attr(\"height\", function(d) { return height - y(d.y); });\n\n // Create x axis\n var xAxis = d3.svg.axis()\n .scale(x)\n .orient(\"bottom\")\n .tickFormat(formatMinutes);\n\n // Add x axis to chart\n chart.append(\"g\")\n .attr(\"class\", \"x axis\")\n .attr(\"id\", \"x_\" + name)\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + (+height + +margin.top) + \")\")\n .call(xAxis);\n\n // Add a title to the x axis\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#x_\" + name).node()\n var left_pad = +margin.left + (axis.getBoundingClientRect().width/2) + 30;\n var top_pad = +margin.top + height + axis.getBoundingClientRect().height + 10\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")\";\n\n return trans;\n })\n .text(\"ETA - hrs:mins\");\n\n // Create y axis\n var yAxis = d3.svg.axis()\n .scale(y)\n .orient(\"left\");\n\n // Add y axis to chart\n chart.append(\"g\")\n .attr(\"class\", \"y axis\")\n .attr(\"id\", (\"y_\" + name))\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + margin.top + \")\")\n .call(yAxis);\n\n // Add a title to the y axis\n chart.append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#y_\" + name).node()\n var left_pad = +margin.left - axis.getBoundingClientRect().width - 5;\n var top_pad = +margin.top + (axis.getBoundingClientRect().height/2) - 30\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")rotate(-90)\";\n\n return trans;\n })\n .text(\"Number of Jobs\");\n\n // Put an invisible tool tip on the chart\n chart.append(\"g\")\n .attr(\"class\", \"tool_tip\")\n .append(\"rect\");\n chart.select(\".tool_tip\")\n .append(\"text\");\n}\n"]} \ No newline at end of file diff --git a/static/maps/utils/ajax-queue.js.map b/static/maps/utils/ajax-queue.js.map index 7128e6aa9d0..74e06299e9e 100644 --- a/static/maps/utils/ajax-queue.js.map +++ b/static/maps/utils/ajax-queue.js.map @@ -1 +1 @@ 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Useful to prevent build up of duplicate\n * async calls.\n * Both the array initialFunctions sent to constructor and any added later with\n * add() should be objects (NOT functions) of the form:\n * { name: some unique id,\n * fn: the deferring fn or ajax call }\n */\nfunction NamedAjaxQueue( initialFunctions ){\n var self = this;\n self.names = {};\n AjaxQueue.call( this, initialFunctions );\n return self;\n}\nNamedAjaxQueue.prototype = new AjaxQueue();\nNamedAjaxQueue.prototype.constructor = NamedAjaxQueue;\n\n/** add the obj.fn to the queue if obj.name hasn't been used before */\nNamedAjaxQueue.prototype.add = function add( obj ){\n //console.debug( 'NamedAjaxQueue.adding:', obj )\n //console.debug( 'NamedAjaxQueue.prototype.add:', obj );\n if( !( obj.hasOwnProperty( 'name' ) && obj.hasOwnProperty( 'fn' ) ) ){\n throw new Error( 'NamedAjaxQueue.add requires an object with both \"name\" and \"fn\": ' + JSON.stringify( obj ) );\n }\n if( this.names.hasOwnProperty( obj.name ) ){\n //console.warn( 'name has been used:', obj.name );\n return;\n }\n this.names[ obj.name ] = true;\n //console.debug( '\\t names: ', this.names )\n return AjaxQueue.prototype.add.call( this, obj.fn );\n //console.debug( '\\t queue: ', this.queue.length );\n};\n\n/** override to remove names */\nNamedAjaxQueue.prototype.clear = function clear(){\n this.names = {};\n return this;\n};\n\n/** shortcut constructor / fire and forget\n * @returns {Deferred} the queue's main deferred\n */\nNamedAjaxQueue.create = function create( initialFunctions ){\n return new NamedAjaxQueue( initialFunctions ).deferred;\n};\n\n\n//=============================================================================\n return {\n AjaxQueue : AjaxQueue,\n NamedAjaxQueue : NamedAjaxQueue\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["utils/ajax-queue.js"],"names":["define","AjaxQueue","initialFunctions","self","this","deferred","jQuery","Deferred","queue","responses","numToProcess","running","init","NamedAjaxQueue","call","prototype","forEach","fn","add","index","length","push","fnIndex","xhr","done","response","notify","total","always","stop","start","causeFail","msg","reject","resolve","fail","progress","create","constructor","obj","hasOwnProperty","Error","JSON","stringify","names","clear"],"mappings":"aAAAA,UACG,WAWH,SAASC,EAAWC,GAChB,IAAAC,EAAAC,KAgBA,OAdAD,EAAAE,SAAAC,OAAAC,WAEAJ,EAAAK,SAEAL,EAAAM,aAEAN,EAAAO,aAAA,EAEAP,EAAAQ,SAAA,EAGAR,EAAKS,KAAMV,OAAXC,EAAAA,QAGOA,EAwGX,SAAAU,EAASA,GACL,IAAAV,EAAIA,KAGJ,OAFAA,EAAAA,SACAF,EAAAA,KAAUa,KAAMZ,GAChBC,EAsCIF,OA/IRA,EAAAc,UAAAH,KAAA,SAAAV,GACAD,IAAAA,EAAUc,KACNb,EAAWc,QAAX,SAAAC,GACAf,EAAAA,IAAAA,MAKJD,EAAAc,UAAAG,IAAA,SAAAD,GAEI,IAAAd,EAAAC,KACAe,EAAIhB,KAAOK,MAAXY,OAqBC,OArBDhB,KAAAM,cACiBF,EAGjBJ,KAAKI,MAAMa,KAAM,WAAjB,IAAAC,EAAWD,EACPE,EAAID,IAEJC,EAAAC,KAAA,SAAAC,GACAF,EAAIC,SAAME,QAAUD,KAAUH,EAAAK,MAAAxB,EAAAO,aAAAe,SAAAA,MAI9BF,EAAAK,OAAA,SAAAH,GACAF,EAAIK,UAAQP,KAAUI,GAClBtB,EAAKM,MAAAA,OACLN,EAAIA,MAAKK,OAATL,GAECA,EAFD0B,WAXRzB,MAqBJH,EAAAc,UAAAe,MAAA,WAKK,OAJL7B,KAAAA,MAAUc,SACNX,KAAIO,SAAWS,EACXhB,KAAAI,MAAKG,OAALP,IAEHA,MAQLH,EAAUc,UAAUc,KAAO,SAAeE,EAAWC,GAWjD,OAVA5B,KAAAO,SAAA,EACAP,KAAAI,SACAuB,EAEI3B,KAAAC,SAAA4B,OAAAD,GAEH5B,KAHDC,SAGO6B,QAAA9B,KAAAK,WAENL,KAAAM,aAAA,EACDN,KAAAC,SAAKK,OAALH,WACAH,MAKJH,EAAAc,UAAAS,KAAA,SAAAP,GACAhB,OAAAA,KAAUc,SAAUS,KAAOP,IAG3BhB,EAAAc,UAAAoB,KAAA,SAAAlB,GACAhB,OAAAA,KAAUc,SAAUoB,KAAOlB,IAG3BhB,EAAAc,UAAAa,OAAA,SAAAX,GACAhB,OAAAA,KAAUc,SAAUa,OAASX,IAG7BhB,EAAAc,UAAAqB,SAAA,SAAAnB,GACAhB,OAAAA,KAAUc,SAAUqB,SAAWnB,IAO/BhB,EAAUoC,OAAS,SAAiBnC,GAApCD,OAAAA,IAAUoC,EAASnC,GAAiBA,UAsBpCW,EAAAA,UAAeE,IAAYd,EAC3BY,EAAAA,UAAeE,YAAUuB,EAGzBzB,EAAAA,UAAeE,IAAUG,SAAeA,GAGpC,IAAAqB,EAAOA,eAAIC,UAAJD,EAAgCA,eAAoB,MACvD,MAAA,IAAME,MAAIA,oEAAOC,KAAsEA,UAAKC,IAEhG,IAAAvC,KAAIwC,MAAKA,eAAMJ,EAAgBD,MAM/B,OAFAnC,KAAAwC,MAAKA,EAAOL,OAAZ,EAEAtC,EAAOA,UAAUc,IAAUG,KAAIJ,KAAMyB,EAAMA,KAK/C1B,EAAAA,UAAeE,MAAU8B,WAErB,OADAzC,KAAAwC,SACAxC,MAMJS,EAAAA,OAAewB,SAAkBA,GAC7B,OAAA,IAAOxB,EAAIA,GAAJR,WAOHQ,UAAkBA,EAFtBA,eAAAA","file":"../../scripts/utils/ajax-queue.js","sourcesContent":["define([\n], function(){\n//ASSUMES: jquery\n//=============================================================================\n/** @class AjaxQueue\n * Class that allows queueing functions that return jQuery promises (such\n * as ajax calls). 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Useful to prevent build up of duplicate\n * async calls.\n * Both the array initialFunctions sent to constructor and any added later with\n * add() should be objects (NOT functions) of the form:\n * { name: some unique id,\n * fn: the deferring fn or ajax call }\n */\nfunction NamedAjaxQueue( initialFunctions ){\n var self = this;\n self.names = {};\n AjaxQueue.call( this, initialFunctions );\n return self;\n}\nNamedAjaxQueue.prototype = new AjaxQueue();\nNamedAjaxQueue.prototype.constructor = NamedAjaxQueue;\n\n/** add the obj.fn to the queue if obj.name hasn't been used before */\nNamedAjaxQueue.prototype.add = function add( obj ){\n //console.debug( 'NamedAjaxQueue.adding:', obj )\n //console.debug( 'NamedAjaxQueue.prototype.add:', obj );\n if( !( obj.hasOwnProperty( 'name' ) && obj.hasOwnProperty( 'fn' ) ) ){\n throw new Error( 'NamedAjaxQueue.add requires an object with both \"name\" and \"fn\": ' + JSON.stringify( obj ) );\n }\n if( this.names.hasOwnProperty( obj.name ) ){\n 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load required libraries\nrequire([\n 'utils/utils',\n], function(mod_utils)\n{\n // load css\n mod_utils.cssLoadFile(\"static/style/circster.css\");\n});\n\ndefine([\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/visualization\",\n \"utils/config\",\n 'mvc/ui/icon-button',\n 'libs/farbtastic'\n], function(_, d3, visualization, config, mod_icon_btn) {\n\n/**\n * Utility class for working with SVG.\n */\nvar SVGUtils = Backbone.Model.extend({\n\n /**\n * Returns true if element is visible.\n */\n is_visible: function(svg_elt, svg) {\n var eltBRect = svg_elt.getBoundingClientRect(),\n svgBRect = $('svg')[0].getBoundingClientRect();\n\n if (// To the left of screen?\n eltBRect.right < 0 ||\n // To the right of screen?\n eltBRect.left > svgBRect.right ||\n // Above screen?\n eltBRect.bottom < 0 ||\n // Below screen?\n eltBRect.top > svgBRect.bottom) {\n return false;\n }\n return true;\n }\n});\n\n/**\n * Mixin for using ticks.\n */\nvar UsesTicks = {\n drawTicks: function(parent_elt, data, dataHandler, textTransform, horizontal) {\n // Set up group elements for chroms and for each tick.\n var ticks = parent_elt.append(\"g\")\n .selectAll(\"g\")\n .data(data)\n .enter().append(\"g\")\n .selectAll(\"g\")\n .data(dataHandler)\n .enter().append(\"g\")\n .attr(\"class\", \"tick\")\n .attr(\"transform\", function(d) {\n return \"rotate(\" + (d.angle * 180 / Math.PI - 90) + \")\" +\n \"translate(\" + d.radius + \",0)\";\n });\n\n // Add line + text for ticks.\n var tick_coords = [],\n text_coords = [],\n text_anchor = function(d) {\n return d.angle > Math.PI ? \"end\" : null;\n };\n if (horizontal) {\n tick_coords = [0, 0, 0, -4];\n text_coords = [4, 0, \"\", \".35em\"];\n text_anchor = null;\n }\n else {\n tick_coords = [1, 0, 4, 0];\n text_coords = [0, 4, \".35em\", \"\"];\n\n }\n\n ticks.append(\"line\")\n .attr(\"x1\", tick_coords[0])\n .attr(\"y1\", tick_coords[1])\n .attr(\"x2\", tick_coords[2])\n .attr(\"y1\", tick_coords[3])\n .style(\"stroke\", \"#000\");\n\n return ticks.append(\"text\")\n .attr(\"x\", text_coords[0])\n .attr(\"y\", text_coords[1])\n .attr(\"dx\", text_coords[2])\n .attr(\"dy\", text_coords[3])\n .attr(\"text-anchor\", text_anchor)\n .attr(\"transform\", textTransform)\n .text(function(d) { return d.label; });\n },\n\n /**\n * Format number for display at a tick.\n */\n formatNum: function(num, sigDigits) {\n // Use default of 2 sig. digits.\n if (sigDigits === undefined)\n sigDigits = 2;\n\n // Verify input number\n if (num === null)\n return null;\n\n // Calculate return value\n var rval = null;\n if (Math.abs(num) < 1) {\n rval = num.toPrecision(sigDigits);\n }\n else {\n // Use round to turn string from toPrecision() back into a number.\n var roundedNum = Math.round(num.toPrecision(sigDigits));\n\n // Use abbreviations.\n num = Math.abs(num);\n if (num < 1000) {\n rval = roundedNum;\n }\n else if (num < 1000000) {\n // Use K.\n rval = Math.round((roundedNum/1000).toPrecision(3)).toFixed(0) + 'K';\n }\n else if (num < 1000000000) {\n // Use M.\n rval = Math.round((roundedNum/1000000).toPrecision(3)).toFixed(0) + 'M';\n }\n }\n\n return rval;\n }\n};\n\n/**\n * A label track.\n */\nvar CircsterLabelTrack = Backbone.Model.extend({});\n\n/**\n * Renders a full circster visualization.\n */\nvar CircsterView = Backbone.View.extend({\n className: 'circster',\n\n initialize: function(options) {\n this.genome = options.genome;\n this.label_arc_height = 50;\n this.scale = 1;\n this.circular_views = null;\n this.chords_views = null;\n\n // When tracks added to/removed from model, update view.\n this.model.get('drawables').on('add', this.add_track, this);\n this.model.get('drawables').on('remove', this.remove_track, this);\n\n // When config settings change, update view.\n var vis_config = this.model.get('config');\n vis_config.get('arc_dataset_height').on('change:value', this.update_track_bounds, this);\n vis_config.get('track_gap').on('change:value', this.update_track_bounds, this);\n },\n\n // HACKs: using track_type for circular/chord distinction in the functions below for now.\n\n /**\n * Returns tracks to be rendered using circular view.\n */\n get_circular_tracks: function() {\n return this.model.get('drawables').filter(function(track) {\n return track.get('track_type') !== 'DiagonalHeatmapTrack';\n });\n },\n\n /**\n * Returns tracks to be rendered using chords view.\n */\n get_chord_tracks: function() {\n return this.model.get('drawables').filter(function(track) {\n return track.get('track_type') === 'DiagonalHeatmapTrack';\n });\n },\n\n /**\n * Returns a list of circular tracks' radius bounds.\n */\n get_tracks_bounds: function() {\n var circular_tracks = this.get_circular_tracks(),\n dataset_arc_height = this.model.get('config').get_value('arc_dataset_height'),\n track_gap = this.model.get('config').get_value('track_gap'),\n // Subtract 20 to make sure chrom labels are on screen.\n min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20,\n // Compute radius start based on model, will be centered\n // and fit entirely inside element by default.\n radius_start = min_dimension / 2 -\n circular_tracks.length * (dataset_arc_height + track_gap) +\n // Add track_gap back in because no gap is needed for last track.\n track_gap -\n this.label_arc_height,\n\n // Compute range of track starting radii.\n tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap);\n\n // Map from track start to bounds.\n var self = this;\n return _.map(tracks_start_radii, function(radius) {\n return [radius, radius + dataset_arc_height];\n });\n },\n\n /**\n * Renders circular tracks, chord tracks, and label tracks.\n */\n render: function() {\n var self = this,\n width = self.$el.width(),\n height = self.$el.height(),\n circular_tracks = this.get_circular_tracks(),\n chords_tracks = this.get_chord_tracks(),\n total_gap = self.model.get('config').get_value('total_gap'),\n tracks_bounds = this.get_tracks_bounds(),\n\n // Set up SVG element.\n svg = d3.select(self.$el[0])\n .append(\"svg\")\n .attr(\"width\", width)\n .attr(\"height\", height)\n .attr(\"pointer-events\", \"all\")\n // Set up zooming, dragging.\n .append('svg:g')\n .call(d3.behavior.zoom().on('zoom', function() {\n // Do zoom, drag.\n var scale = d3.event.scale;\n svg.attr(\"transform\",\n \"translate(\" + d3.event.translate + \")\" +\n \" scale(\" + scale + \")\");\n\n // Propagate scale changes to views.\n if (self.scale !== scale) {\n // Use timeout to wait for zooming/dragging to stop before rendering more detail.\n if (self.zoom_drag_timeout) {\n clearTimeout(self.zoom_drag_timeout);\n }\n self.zoom_drag_timeout = setTimeout(function() {\n // Render more detail in tracks' visible elements.\n // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds\n // are not updated when new data is fetched--and fetching more detailed quantitative\n // data is not that useful.\n /*\n _.each(self.circular_views, function(view) {\n view.update_scale(scale);\n });\n */\n }, 400);\n }\n }))\n .attr(\"transform\", \"translate(\" + width / 2 + \",\" + height / 2 + \")\")\n .append('svg:g').attr('class', 'tracks');\n\n // -- Render circular tracks. --\n\n // Create a view for each track in the visualization and render.\n this.circular_views = circular_tracks.map(function(track, index) {\n var view = new CircsterBigWigTrackView({\n el: svg.append('g')[0],\n track: track,\n radius_bounds: tracks_bounds[index],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render chords tracks. --\n\n this.chords_views = chords_tracks.map(function(track) {\n var view = new CircsterChromInteractionsTrackView({\n el: svg.append('g')[0],\n track: track,\n radius_bounds: tracks_bounds[0],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render label track. --\n\n // Track bounds are:\n // (a) outer radius of last circular track;\n // (b)\n var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1],\n track_bounds = [\n outermost_radius,\n outermost_radius + this.label_arc_height\n ];\n this.label_track_view = new CircsterChromLabelTrackView({\n el: svg.append('g')[0],\n track: new CircsterLabelTrack(),\n radius_bounds: track_bounds,\n genome: self.genome,\n total_gap: total_gap\n });\n\n this.label_track_view.render();\n },\n\n /**\n * Render a single track on the outside of the current visualization.\n */\n add_track: function(new_track) {\n var total_gap = this.model.get('config').get_value('total_gap');\n\n if (new_track.get('track_type') === 'DiagonalHeatmapTrack') {\n // Added chords track.\n var innermost_radius_bounds = this.circular_views[0].radius_bounds,\n new_view = new CircsterChromInteractionsTrackView({\n el: d3.select('g.tracks').append('g')[0],\n track: new_track,\n radius_bounds: innermost_radius_bounds,\n genome: this.genome,\n total_gap: total_gap\n });\n new_view.render();\n this.chords_views.push(new_view);\n }\n else {\n // Added circular track.\n\n // Recompute and update circular track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n\n // Render new track.\n var track_index = this.circular_views.length,\n track_view = new CircsterBigWigTrackView({\n el: d3.select('g.tracks').append('g')[0],\n track: new_track,\n radius_bounds: new_track_bounds[track_index],\n genome: this.genome,\n total_gap: total_gap\n });\n track_view.render();\n this.circular_views.push(track_view);\n\n // Update label track.\n /*\n FIXME: should never have to update label track because vis always expands to fit area\n within label track.\n var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];\n track_bounds[1] = track_bounds[0];\n this.label_track_view.update_radius_bounds(track_bounds);\n */\n }\n },\n\n /**\n * Remove a track from the view.\n */\n remove_track: function(track, tracks, options) {\n // -- Remove track from view. --\n var track_view = this.circular_views[options.index];\n this.circular_views.splice(options.index, 1);\n track_view.$el.remove();\n\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n },\n\n update_track_bounds: function() {\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n\n }\n});\n\n/**\n * Renders a track in a Circster visualization.\n */\nvar CircsterTrackView = Backbone.View.extend({\n tagName: 'g',\n\n /* ----------------------- Public Methods ------------------------- */\n\n initialize: function(options) {\n this.bg_stroke = '#ddd';\n // Fill color when loading data.\n this.loading_bg_fill = '#ffc';\n // Fill color when data has been loaded.\n this.bg_fill = '#ddd';\n this.total_gap = options.total_gap;\n this.track = options.track;\n this.radius_bounds = options.radius_bounds;\n this.genome = options.genome;\n this.chroms_layout = this._chroms_layout();\n this.data_bounds = [];\n this.scale = 1;\n this.parent_elt = d3.select(this.$el[0]);\n },\n\n /**\n * Get fill color from config.\n */\n get_fill_color: function() {\n var color = this.track.get('config').get_value('block_color');\n if (!color) { color = this.track.get('config').get_value('color'); }\n return color;\n },\n\n /**\n * Render track's data by adding SVG elements to parent.\n */\n render: function() {\n // -- Create track group element. --\n var track_parent_elt = this.parent_elt;\n\n // -- Render background arcs. --\n var genome_arcs = this.chroms_layout,\n arc_gen = d3.svg.arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]),\n\n // Attach data to group element.\n chroms_elts = track_parent_elt.selectAll('g')\n .data(genome_arcs).enter().append('svg:g'),\n\n // Draw chrom arcs/paths.\n chroms_paths = chroms_elts.append('path')\n .attr(\"d\", arc_gen)\n .attr('class', 'chrom-background')\n .style(\"stroke\", this.bg_stroke)\n .style(\"fill\", this.loading_bg_fill);\n\n // Append titles to paths.\n chroms_paths.append(\"title\").text(function(d) { return d.data.chrom; });\n\n // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --\n\n var self = this,\n data_manager = self.track.get('data_manager'),\n // If track has a data manager, get deferred that resolves when data is ready.\n data_ready_deferred = (data_manager ? data_manager.data_is_ready() : true );\n\n // When data is ready, render track.\n $.when(data_ready_deferred).then(function() {\n $.when(self._render_data(track_parent_elt)).then(function() {\n chroms_paths.style(\"fill\", self.bg_fill);\n\n // Render labels after data is available so that data attributes are available.\n self.render_labels();\n });\n });\n },\n\n /**\n * Render track labels.\n */\n render_labels: function() {},\n\n /**\n * Update radius bounds.\n */\n update_radius_bounds: function(radius_bounds) {\n // Update bounds.\n this.radius_bounds = radius_bounds;\n\n // -- Update background arcs. --\n var new_d = d3.svg.arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]);\n\n this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d);\n\n this._transition_chrom_data();\n\n this._transition_labels();\n },\n\n /**\n * Update view scale. This fetches more data if scale is increased.\n */\n update_scale: function(new_scale) {\n // -- Update scale and return if new scale is less than old scale. --\n\n var old_scale = this.scale;\n this.scale = new_scale;\n if (new_scale <= old_scale) {\n return;\n }\n\n // -- Scale increased, so render visible data with more detail. --\n\n var self = this,\n utils = new SVGUtils();\n\n // Select all chrom data and filter to operate on those that are visible.\n this.parent_elt.selectAll('path.chrom-data').filter(function(d, i) {\n return utils.is_visible(this);\n }).each(function(d, i) {\n // -- Now operating on a single path element representing chromosome data. --\n\n var path_elt = d3.select(this),\n chrom = path_elt.attr('chrom'),\n chrom_region = self.genome.get_chrom_region(chrom),\n data_manager = self.track.get('data_manager'),\n data_deferred;\n\n // If can't get more detailed data, return.\n if (!data_manager.can_get_more_detailed_data(chrom_region)) {\n return;\n }\n\n // -- Get more detailed data. --\n data_deferred = self.track.get('data_manager').get_more_detailed_data(chrom_region, 'Coverage', 0, new_scale);\n\n // When more data is available, use new data to redraw path.\n $.when(data_deferred).then(function(data) {\n // Remove current data path.\n path_elt.remove();\n\n // Update data bounds with new data.\n self._update_data_bounds();\n\n // Find chromosome arc to draw data on.\n var chrom_arc = _.find(self.chroms_layout, function(layout) {\n return layout.data.chrom === chrom;\n });\n\n // Add new data path and apply preferences.\n var color = self.get_fill_color();\n self._render_chrom_data(self.parent_elt, chrom_arc, data).style('stroke', color).style('fill', color);\n });\n });\n\n return self;\n },\n\n /* ----------------------- Internal Methods ------------------------- */\n\n /**\n * Transitions chrom data to new values (e.g new radius or data bounds).\n */\n _transition_chrom_data: function() {\n var track = this.track,\n chrom_arcs = this.chroms_layout,\n chrom_data_paths = this.parent_elt.selectAll('g>path.chrom-data'),\n num_paths = chrom_data_paths[0].length;\n\n if (num_paths > 0) {\n var self = this;\n $.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) {\n // Map chrom data to path data, filtering out null values.\n var path_data = _.reject( _.map(genome_wide_data, function(chrom_data, i) {\n var rval = null,\n path_fn = self._get_path_function(chrom_arcs[i], chrom_data);\n if (path_fn) {\n rval = path_fn(chrom_data.data);\n }\n return rval;\n }), function(p_data) { return p_data === null; } );\n\n // Transition each path for data and color.\n var color = track.get('config').get_value('color');\n chrom_data_paths.each(function(path, index) {\n d3.select(this).transition().duration(1000)\n .style('stroke', color).style('fill', color)\n .attr('d', path_data[index]);\n });\n });\n }\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {},\n\n /**\n * Update data bounds. If there are new_bounds, use them; otherwise use\n * default data bounds.\n */\n _update_data_bounds: function(new_bounds) {\n var old_bounds = this.data_bounds;\n this.data_bounds = new_bounds ||\n this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome));\n this._transition_chrom_data();\n },\n\n /**\n * Render data as elements attached to svg.\n */\n _render_data: function(svg) {\n var self = this,\n chrom_arcs = this.chroms_layout,\n track = this.track,\n rendered_deferred = $.Deferred();\n\n // When genome-wide data is available, render data.\n $.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) {\n // Set bounds.\n self.data_bounds = self.get_data_bounds(genome_wide_data);\n\n // Set min, max value in config so that they can be adjusted. Make this silent\n // because these attributes are watched for changes and the viz is updated\n // accordingly (set up in initialize). Because we are setting up, we don't want\n // the watch to trigger events here.\n track.get('config').set_value('min_value', self.data_bounds[0], {silent: true});\n track.get('config').set_value('max_value', self.data_bounds[1], {silent: true});\n\n // Merge chroms layout with data.\n var layout_and_data = _.zip(chrom_arcs, genome_wide_data);\n\n // Render each chromosome's data.\n _.each(layout_and_data, function(chrom_info) {\n var chrom_arc = chrom_info[0],\n data = chrom_info[1];\n return self._render_chrom_data(svg, chrom_arc, data);\n });\n\n // Apply prefs to all track data.\n var color = self.get_fill_color();\n self.parent_elt.selectAll('path.chrom-data').style('stroke', color).style('fill', color);\n\n rendered_deferred.resolve(svg);\n });\n\n return rendered_deferred;\n },\n\n /**\n * Render a chromosome data and attach elements to svg.\n */\n _render_chrom_data: function(svg, chrom_arc, data) {},\n\n /**\n * Returns data for creating a path for the given data using chrom_arc and data bounds.\n */\n _get_path_function: function(chrom_arc, chrom_data) {},\n\n /**\n * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle\n * separated by gaps.\n */\n _chroms_layout: function() {\n // Setup chroms layout using pie.\n var chroms_info = this.genome.get_chroms_info(),\n pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null),\n init_arcs = pie_layout(chroms_info),\n gap_per_chrom = 2 * Math.PI * this.total_gap / chroms_info.length,\n chrom_arcs = _.map(init_arcs, function(arc, index) {\n // For short chroms, endAngle === startAngle.\n var new_endAngle = arc.endAngle - gap_per_chrom;\n arc.endAngle = (new_endAngle > arc.startAngle ? new_endAngle : arc.startAngle);\n return arc;\n });\n return chrom_arcs;\n }\n});\n\n/**\n * Render chromosome labels.\n */\nvar CircsterChromLabelTrackView = CircsterTrackView.extend({\n\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n // Use a single arc for rendering data.\n this.innerRadius = this.radius_bounds[0];\n this.radius_bounds[0] = this.radius_bounds[1];\n this.bg_stroke = '#fff';\n this.bg_fill = '#fff';\n\n // Minimum arc distance for labels to be applied.\n this.min_arc_len = 0.05;\n },\n\n /**\n * Render labels.\n */\n _render_data: function(svg) {\n // -- Add chromosome label where it will fit; an alternative labeling mechanism\n // would be nice for small chromosomes. --\n var self = this,\n chrom_arcs = svg.selectAll('g');\n\n chrom_arcs.selectAll('path')\n .attr('id', function(d) { return 'label-' + d.data.chrom; });\n\n chrom_arcs.append(\"svg:text\")\n .filter(function(d) {\n return d.endAngle - d.startAngle > self.min_arc_len;\n })\n .attr('text-anchor', 'middle')\n .append(\"svg:textPath\")\n .attr(\"class\", \"chrom-label\")\n .attr(\"xlink:href\", function(d) { return \"#label-\" + d.data.chrom; })\n .attr('startOffset', '25%')\n .text(function(d) {\n return d.data.chrom;\n });\n\n // -- Add ticks to denote chromosome length. --\n\n /** Returns an array of tick angles and labels, given a chrom arc. */\n var chromArcTicks = function(d) {\n var k = (d.endAngle - d.startAngle) / d.value,\n ticks = d3.range(0, d.value, 25000000).map(function(v, i) {\n return {\n radius: self.innerRadius,\n angle: v * k + d.startAngle,\n label: i === 0 ? 0 : (i % 3 ? null : self.formatNum(v))\n };\n });\n\n // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled.\n if (ticks.length < 4) {\n ticks[ticks.length-1].label = self.formatNum(\n Math.round( ( ticks[ticks.length-1].angle - d.startAngle ) / k )\n );\n }\n\n return ticks;\n };\n\n /** Rotate and move text as needed. */\n var textTransform = function(d) {\n return d.angle > Math.PI ? \"rotate(180)translate(-16)\" : null;\n };\n\n // Filter chroms for only those large enough for display.\n var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > self.min_arc_len; });\n\n this.drawTicks(this.parent_elt, visibleChroms, chromArcTicks, textTransform);\n }\n});\n_.extend(CircsterChromLabelTrackView.prototype, UsesTicks);\n\n/**\n * View for quantitative track in Circster.\n */\nvar CircsterQuantitativeTrackView = CircsterTrackView.extend({\n\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n\n // When config settings change, update view.\n var track_config = this.track.get('config');\n track_config.get('min_value').on('change:value', this._update_min_max, this);\n track_config.get('max_value').on('change:value', this._update_min_max, this);\n track_config.get('color').on('change:value', this._transition_chrom_data, this);\n },\n\n /**\n * Update track when min and/or max are changed.\n */\n _update_min_max: function() {\n var track_config = this.track.get('config'),\n new_bounds = [track_config.get_value('min_value'), track_config.get_value('max_value')];\n this._update_data_bounds(new_bounds);\n\n // FIXME: this works to update tick/text bounds, but there's probably a better way to do this\n // by updating the data itself.\n this.parent_elt.selectAll('.min_max').text(function(d, i) {\n return new_bounds[i];\n });\n },\n\n /**\n * Returns quantile for an array of numbers.\n */\n _quantile: function(numbers, quantile) {\n numbers.sort(d3.ascending);\n return d3.quantile(numbers, quantile);\n },\n\n /**\n * Renders quantitative data with the form [x, value] and assumes data is equally spaced across\n * chromosome. Attachs a dict with track and chrom name information to DOM element.\n */\n _render_chrom_data: function(svg, chrom_arc, chrom_data) {\n var path_data = this._get_path_function(chrom_arc, chrom_data);\n\n if (!path_data) { return null; }\n\n // There is path data, so render as path.\n var parent = svg.datum(chrom_data.data),\n path = parent.append('path')\n .attr('class', 'chrom-data')\n .attr('chrom', chrom_arc.data.chrom)\n .attr('d', path_data);\n\n return path;\n },\n\n /**\n * Returns function for creating a path across the chrom arc.\n */\n _get_path_function: function(chrom_arc, chrom_data) {\n // If no chrom data, return null.\n if (typeof chrom_data === \"string\" || !chrom_data.data || chrom_data.data.length === 0) {\n return null;\n }\n\n // Radius scaler.\n var radius = d3.scale.linear()\n .domain(this.data_bounds)\n .range(this.radius_bounds)\n .clamp(true);\n\n // Scaler for placing data points across arc.\n var angle = d3.scale.linear()\n .domain([0, chrom_data.data.length])\n .range([chrom_arc.startAngle, chrom_arc.endAngle]);\n\n // Use line generator to create area.\n var line = d3.svg.line.radial()\n .interpolate(\"linear\")\n .radius(function(d) { return radius(d[1]); })\n .angle(function(d, i) { return angle(i); });\n\n return d3.svg.area.radial()\n .interpolate(line.interpolate())\n .innerRadius(radius(0))\n .outerRadius(line.radius())\n .angle(line.angle());\n },\n\n /**\n * Render track min, max using ticks.\n */\n render_labels: function() {\n var self = this,\n // Keep counter of visible chroms.\n textTransform = function() {\n return \"rotate(90)\";\n };\n\n // FIXME:\n // (1) using min_max class below is needed for _update_min_max, which could be improved.\n // (2) showing config on tick click should be replaced by proper track config icon.\n\n // Draw min, max on first chrom only.\n var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],\n this._data_bounds_ticks_fn(), textTransform, true)\n .classed('min_max', true);\n\n // Show config when ticks are clicked on.\n _.each(ticks, function(tick) {\n $(tick).click(function() {\n var view = new config.ConfigSettingCollectionView({\n collection: self.track.get('config')\n });\n view.render_in_modal('Configure Track');\n });\n });\n\n\n\n /*\n // Filter for visible chroms, then for every third chrom so that labels attached to only every\n // third chrom.\n var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }),\n labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; });\n this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true);\n */\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {\n // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below\n // is copied from UseTicks mixin, so pull out and make generally available.\n\n // If there are no data bounds, nothing to transition.\n if (this.data_bounds.length === 0) { return; }\n\n // Transition labels to new radius bounds.\n var self = this,\n visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }),\n labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; }),\n new_data = _.flatten( _.map(labeledChroms, function(c) {\n return self._data_bounds_ticks_fn()(c);\n }));\n this.parent_elt.selectAll('g.tick').data(new_data).transition().attr(\"transform\", function(d) {\n return \"rotate(\" + (d.angle * 180 / Math.PI - 90) + \")\" +\n \"translate(\" + d.radius + \",0)\";\n });\n },\n\n /**\n * Get function for locating data bounds ticks.\n */\n _data_bounds_ticks_fn: function() {\n // Closure vars.\n var self = this;\n visibleChroms = 0;\n\n // Return function for locating ticks based on chrom arc data.\n return function(d) {\n // Set up data to display min, max ticks.\n return [\n {\n radius: self.radius_bounds[0],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[0])\n },\n {\n radius: self.radius_bounds[1],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[1])\n }\n ];\n };\n },\n\n /**\n * Returns an array with two values denoting the minimum and maximum\n * values for the track.\n */\n get_data_bounds: function(data) {}\n\n});\n_.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);\n\n/**\n * Bigwig track view in Circster.\n */\nvar CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({\n\n get_data_bounds: function(data) {\n // Set max across dataset by extracting all values, flattening them into a\n // single array, and getting third quartile.\n var values = _.flatten( _.map(data, function(d) {\n if (d) {\n // Each data point has the form [position, value], so return all values.\n return _.map(d.data, function(p) {\n // Null is used for a lack of data; resolve null to 0 for comparison.\n return parseInt(p[1], 10) || 0;\n });\n }\n else {\n return 0;\n }\n }) );\n\n // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0\n // for sparsely populated data, so use max in that case.\n return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ];\n }\n});\n\n/**\n * Chromosome interactions track view in Circster.\n */\nvar CircsterChromInteractionsTrackView = CircsterTrackView.extend({\n\n render: function() {\n var self = this;\n\n // When data is ready, render track.\n $.when(self.track.get('data_manager').data_is_ready()).then(function() {\n // When data has been fetched, render track.\n $.when(self.track.get('data_manager').get_genome_wide_data(self.genome)).then(function(genome_wide_data) {\n var chord_data = [],\n chroms_info = self.genome.get_chroms_info();\n // Convert chromosome data into chord data.\n _.each(genome_wide_data, function(chrom_data, index) {\n // Map each interaction into chord data.\n var cur_chrom = chroms_info[index].chrom;\n var chrom_chord_data = _.map(chrom_data.data, function(datum) {\n // Each datum is an interaction/chord.\n var source_angle = self._get_region_angle(cur_chrom, datum[1]),\n target_angle = self._get_region_angle(datum[3], datum[4]);\n return {\n source: {\n startAngle: source_angle,\n endAngle: source_angle + 0.01\n },\n target: {\n startAngle: target_angle,\n endAngle: target_angle + 0.01\n }\n };\n });\n\n chord_data = chord_data.concat(chrom_chord_data);\n });\n\n self.parent_elt.append(\"g\")\n .attr(\"class\", \"chord\")\n .selectAll(\"path\")\n .data(chord_data)\n .enter().append(\"path\")\n .style(\"fill\", self.get_fill_color())\n .attr(\"d\", d3.svg.chord().radius(self.radius_bounds[0]))\n .style(\"opacity\", 1);\n });\n });\n },\n\n update_radius_bounds: function(radius_bounds) {\n this.radius_bounds = radius_bounds;\n this.parent_elt.selectAll(\"path\").transition().attr(\"d\", d3.svg.chord().radius(this.radius_bounds[0]));\n },\n\n /**\n * Returns radians for a genomic position.\n */\n _get_region_angle: function(chrom, position) {\n // Find chrom angle data\n var chrom_angle_data = _.find(this.chroms_layout, function(chrom_layout) {\n return chrom_layout.data.chrom === chrom;\n });\n\n // Return angle at position.\n return chrom_angle_data.endAngle -\n (\n (chrom_angle_data.endAngle - chrom_angle_data.startAngle) *\n (chrom_angle_data.data.len - position) / chrom_angle_data.data.len\n );\n }\n\n});\n\n// circster app loader\nvar Circster = Backbone.View.extend(\n{\n initialize: function ()\n {\n // -- Configure visualization --\n var genome = new visualization.Genome(galaxy_config.app.genome),\n vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config);\n\n // Add Circster-specific config options.\n vis.get('config').add([\n { key: 'arc_dataset_height', label: 'Arc Dataset Height', type: 'int', value: 25, view: 'circster' },\n { key: 'track_gap', label: 'Gap Between Tracks', type: 'int', value: 5, view: 'circster' },\n { key: 'total_gap', label: 'Gap [0-1]', type: 'float', value: 0.4, view: 'circster', hidden: true }\n ]);\n\n var viz_view = new CircsterView(\n {\n // view pane\n el : $('#center .unified-panel-body'),\n genome : genome,\n model : vis\n });\n\n // Render vizualization\n viz_view.render();\n\n // setup title\n $('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + \" \" + galaxy_config.app.viz_config.dbkey);\n\n // setup menu\n var menu = mod_icon_btn.create_icon_buttons_menu([\n {\n icon_class: 'plus-button', title: 'Add tracks', on_click: function()\n {\n visualization.select_datasets({'dbkey': vis.get('dbkey')}, function(tracks)\n {\n vis.add_tracks(tracks);\n });\n }\n },\n {\n icon_class: 'gear', title: 'Settings', on_click: function()\n {\n var view = new config.ConfigSettingCollectionView({\n collection: vis.get('config')\n });\n view.render_in_modal('Configure Visualization');\n }\n },\n {\n icon_class: 'disk--arrow', title: 'Save', on_click: function()\n {\n // show saving dialog box\n Galaxy.modal.show({title: \"Saving...\", body: \"progress\" });\n\n // send to server\n $.ajax({\n url: Galaxy.root + \"visualization/save\",\n type: \"POST\",\n dataType: \"json\",\n data: {\n 'id' : vis.get('vis_id'),\n 'title' : vis.get('title'),\n 'dbkey' : vis.get('dbkey'),\n 'type' : 'trackster',\n 'vis_json' : JSON.stringify(vis)\n }\n }).success(function(vis_info) {\n Galaxy.modal.hide();\n vis.set('vis_id', vis_info.vis_id);\n }).error(function() {\n // show dialog\n Galaxy.modal.show({\n title : \"Could Not Save\",\n body : \"Could not save visualization. Please try again later.\",\n buttons : { \"Cancel\": function() { Galaxy.modal.hide(); } }\n });\n });\n }\n },\n {\n icon_class: 'cross-circle', title: 'Close', on_click: function()\n {\n window.location = Galaxy.root + \"visualizations/list\";\n }\n }], { tooltip_config: { placement: 'bottom' } });\n\n // add menu\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#center .unified-panel-header-inner\").append(menu.$el);\n\n // manual tooltip config because default gravity is S and cannot be changed\n $(\".menu-button\").tooltip( { placement: 'bottom' } );\n }\n});\n\n// Module exports.\nreturn {\n GalaxyApp: Circster\n};\n\n});\n"]} \ No newline at end of file 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load required libraries\nrequire([\n 'utils/utils',\n], function(mod_utils)\n{\n // load css\n mod_utils.cssLoadFile(\"static/style/circster.css\");\n});\n\ndefine([\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/visualization\",\n \"utils/config\",\n 'mvc/ui/icon-button',\n 'libs/farbtastic'\n], function(_, d3, visualization, config, mod_icon_btn) {\n\n/**\n * Utility class for working with SVG.\n */\nvar SVGUtils = Backbone.Model.extend({\n\n /**\n * Returns true if element is visible.\n */\n is_visible: function(svg_elt, svg) {\n var eltBRect = svg_elt.getBoundingClientRect(),\n svgBRect = $('svg')[0].getBoundingClientRect();\n\n if (// To the left of screen?\n eltBRect.right < 0 ||\n // To the right of screen?\n eltBRect.left > svgBRect.right ||\n // Above screen?\n eltBRect.bottom < 0 ||\n // Below screen?\n eltBRect.top > svgBRect.bottom) {\n return false;\n }\n return true;\n }\n});\n\n/**\n * Mixin for using ticks.\n */\nvar UsesTicks = {\n drawTicks: function(parent_elt, data, dataHandler, textTransform, horizontal) {\n // Set up group elements for chroms and for each tick.\n var ticks = parent_elt.append(\"g\")\n .selectAll(\"g\")\n .data(data)\n .enter().append(\"g\")\n .selectAll(\"g\")\n .data(dataHandler)\n .enter().append(\"g\")\n .attr(\"class\", \"tick\")\n .attr(\"transform\", function(d) {\n return \"rotate(\" + (d.angle * 180 / Math.PI - 90) + \")\" +\n \"translate(\" + d.radius + \",0)\";\n });\n\n // Add line + text for ticks.\n var tick_coords = [],\n text_coords = [],\n text_anchor = function(d) {\n return d.angle > Math.PI ? \"end\" : null;\n };\n if (horizontal) {\n tick_coords = [0, 0, 0, -4];\n text_coords = [4, 0, \"\", \".35em\"];\n text_anchor = null;\n }\n else {\n tick_coords = [1, 0, 4, 0];\n text_coords = [0, 4, \".35em\", \"\"];\n\n }\n\n ticks.append(\"line\")\n .attr(\"x1\", tick_coords[0])\n .attr(\"y1\", tick_coords[1])\n .attr(\"x2\", tick_coords[2])\n .attr(\"y1\", tick_coords[3])\n .style(\"stroke\", \"#000\");\n\n return ticks.append(\"text\")\n .attr(\"x\", text_coords[0])\n .attr(\"y\", text_coords[1])\n .attr(\"dx\", text_coords[2])\n .attr(\"dy\", text_coords[3])\n .attr(\"text-anchor\", text_anchor)\n .attr(\"transform\", textTransform)\n .text(function(d) { return d.label; });\n },\n\n /**\n * Format number for display at a tick.\n */\n formatNum: function(num, sigDigits) {\n // Use default of 2 sig. digits.\n if (sigDigits === undefined)\n sigDigits = 2;\n\n // Verify input number\n if (num === null)\n return null;\n\n // Calculate return value\n var rval = null;\n if (Math.abs(num) < 1) {\n rval = num.toPrecision(sigDigits);\n }\n else {\n // Use round to turn string from toPrecision() back into a number.\n var roundedNum = Math.round(num.toPrecision(sigDigits));\n\n // Use abbreviations.\n num = Math.abs(num);\n if (num < 1000) {\n rval = roundedNum;\n }\n else if (num < 1000000) {\n // Use K.\n rval = Math.round((roundedNum/1000).toPrecision(3)).toFixed(0) + 'K';\n }\n else if (num < 1000000000) {\n // Use M.\n rval = Math.round((roundedNum/1000000).toPrecision(3)).toFixed(0) + 'M';\n }\n }\n\n return rval;\n }\n};\n\n/**\n * A label track.\n */\nvar CircsterLabelTrack = Backbone.Model.extend({});\n\n/**\n * Renders a full circster visualization.\n */\nvar CircsterView = Backbone.View.extend({\n className: 'circster',\n\n initialize: function(options) {\n this.genome = options.genome;\n this.label_arc_height = 50;\n this.scale = 1;\n this.circular_views = null;\n this.chords_views = null;\n\n // When tracks added to/removed from model, update view.\n this.model.get('drawables').on('add', this.add_track, this);\n this.model.get('drawables').on('remove', this.remove_track, this);\n\n // When config settings change, update view.\n var vis_config = this.model.get('config');\n vis_config.get('arc_dataset_height').on('change:value', this.update_track_bounds, this);\n vis_config.get('track_gap').on('change:value', this.update_track_bounds, this);\n },\n\n // HACKs: using track_type for circular/chord distinction in the functions below for now.\n\n /**\n * Returns tracks to be rendered using circular view.\n */\n get_circular_tracks: function() {\n return this.model.get('drawables').filter(function(track) {\n return track.get('track_type') !== 'DiagonalHeatmapTrack';\n });\n },\n\n /**\n * Returns tracks to be rendered using chords view.\n */\n get_chord_tracks: function() {\n return this.model.get('drawables').filter(function(track) {\n return track.get('track_type') === 'DiagonalHeatmapTrack';\n });\n },\n\n /**\n * Returns a list of circular tracks' radius bounds.\n */\n get_tracks_bounds: function() {\n var circular_tracks = this.get_circular_tracks(),\n dataset_arc_height = this.model.get('config').get_value('arc_dataset_height'),\n track_gap = this.model.get('config').get_value('track_gap'),\n // Subtract 20 to make sure chrom labels are on screen.\n min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20,\n // Compute radius start based on model, will be centered\n // and fit entirely inside element by default.\n radius_start = min_dimension / 2 -\n circular_tracks.length * (dataset_arc_height + track_gap) +\n // Add track_gap back in because no gap is needed for last track.\n track_gap -\n this.label_arc_height,\n\n // Compute range of track starting radii.\n tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap);\n\n // Map from track start to bounds.\n var self = this;\n return _.map(tracks_start_radii, function(radius) {\n return [radius, radius + dataset_arc_height];\n });\n },\n\n /**\n * Renders circular tracks, chord tracks, and label tracks.\n */\n render: function() {\n var self = this,\n width = self.$el.width(),\n height = self.$el.height(),\n circular_tracks = this.get_circular_tracks(),\n chords_tracks = this.get_chord_tracks(),\n total_gap = self.model.get('config').get_value('total_gap'),\n tracks_bounds = this.get_tracks_bounds(),\n\n // Set up SVG element.\n svg = d3.select(self.$el[0])\n .append(\"svg\")\n .attr(\"width\", width)\n .attr(\"height\", height)\n .attr(\"pointer-events\", \"all\")\n // Set up zooming, dragging.\n .append('svg:g')\n .call(d3.behavior.zoom().on('zoom', function() {\n // Do zoom, drag.\n var scale = d3.event.scale;\n svg.attr(\"transform\",\n \"translate(\" + d3.event.translate + \")\" +\n \" scale(\" + scale + \")\");\n\n // Propagate scale changes to views.\n if (self.scale !== scale) {\n // Use timeout to wait for zooming/dragging to stop before rendering more detail.\n if (self.zoom_drag_timeout) {\n clearTimeout(self.zoom_drag_timeout);\n }\n self.zoom_drag_timeout = setTimeout(function() {\n // Render more detail in tracks' visible elements.\n // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds\n // are not updated when new data is fetched--and fetching more detailed quantitative\n // data is not that useful.\n /*\n _.each(self.circular_views, function(view) {\n view.update_scale(scale);\n });\n */\n }, 400);\n }\n }))\n .attr(\"transform\", \"translate(\" + width / 2 + \",\" + height / 2 + \")\")\n .append('svg:g').attr('class', 'tracks');\n\n // -- Render circular tracks. --\n\n // Create a view for each track in the visualization and render.\n this.circular_views = circular_tracks.map(function(track, index) {\n var view = new CircsterBigWigTrackView({\n el: svg.append('g')[0],\n track: track,\n radius_bounds: tracks_bounds[index],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render chords tracks. --\n\n this.chords_views = chords_tracks.map(function(track) {\n var view = new CircsterChromInteractionsTrackView({\n el: svg.append('g')[0],\n track: track,\n radius_bounds: tracks_bounds[0],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render label track. --\n\n // Track bounds are:\n // (a) outer radius of last circular track;\n // (b)\n var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1],\n track_bounds = [\n outermost_radius,\n outermost_radius + this.label_arc_height\n ];\n this.label_track_view = new CircsterChromLabelTrackView({\n el: svg.append('g')[0],\n track: new CircsterLabelTrack(),\n radius_bounds: track_bounds,\n genome: self.genome,\n total_gap: total_gap\n });\n\n this.label_track_view.render();\n },\n\n /**\n * Render a single track on the outside of the current visualization.\n */\n add_track: function(new_track) {\n var total_gap = this.model.get('config').get_value('total_gap');\n\n if (new_track.get('track_type') === 'DiagonalHeatmapTrack') {\n // Added chords track.\n var innermost_radius_bounds = this.circular_views[0].radius_bounds,\n new_view = new CircsterChromInteractionsTrackView({\n el: d3.select('g.tracks').append('g')[0],\n track: new_track,\n radius_bounds: innermost_radius_bounds,\n genome: this.genome,\n total_gap: total_gap\n });\n new_view.render();\n this.chords_views.push(new_view);\n }\n else {\n // Added circular track.\n\n // Recompute and update circular track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n\n // Render new track.\n var track_index = this.circular_views.length,\n track_view = new CircsterBigWigTrackView({\n el: d3.select('g.tracks').append('g')[0],\n track: new_track,\n radius_bounds: new_track_bounds[track_index],\n genome: this.genome,\n total_gap: total_gap\n });\n track_view.render();\n this.circular_views.push(track_view);\n\n // Update label track.\n /*\n FIXME: should never have to update label track because vis always expands to fit area\n within label track.\n var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];\n track_bounds[1] = track_bounds[0];\n this.label_track_view.update_radius_bounds(track_bounds);\n */\n }\n },\n\n /**\n * Remove a track from the view.\n */\n remove_track: function(track, tracks, options) {\n // -- Remove track from view. --\n var track_view = this.circular_views[options.index];\n this.circular_views.splice(options.index, 1);\n track_view.$el.remove();\n\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n },\n\n update_track_bounds: function() {\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n\n }\n});\n\n/**\n * Renders a track in a Circster visualization.\n */\nvar CircsterTrackView = Backbone.View.extend({\n tagName: 'g',\n\n /* ----------------------- Public Methods ------------------------- */\n\n initialize: function(options) {\n this.bg_stroke = '#ddd';\n // Fill color when loading data.\n this.loading_bg_fill = '#ffc';\n // Fill color when data has been loaded.\n this.bg_fill = '#ddd';\n this.total_gap = options.total_gap;\n this.track = options.track;\n this.radius_bounds = options.radius_bounds;\n this.genome = options.genome;\n this.chroms_layout = this._chroms_layout();\n this.data_bounds = [];\n this.scale = 1;\n this.parent_elt = d3.select(this.$el[0]);\n },\n\n /**\n * Get fill color from config.\n */\n get_fill_color: function() {\n var color = this.track.get('config').get_value('block_color');\n if (!color) { color = this.track.get('config').get_value('color'); }\n return color;\n },\n\n /**\n * Render track's data by adding SVG elements to parent.\n */\n render: function() {\n // -- Create track group element. --\n var track_parent_elt = this.parent_elt;\n\n // -- Render background arcs. --\n var genome_arcs = this.chroms_layout,\n arc_gen = d3.svg.arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]),\n\n // Attach data to group element.\n chroms_elts = track_parent_elt.selectAll('g')\n .data(genome_arcs).enter().append('svg:g'),\n\n // Draw chrom arcs/paths.\n chroms_paths = chroms_elts.append('path')\n .attr(\"d\", arc_gen)\n .attr('class', 'chrom-background')\n .style(\"stroke\", this.bg_stroke)\n .style(\"fill\", this.loading_bg_fill);\n\n // Append titles to paths.\n chroms_paths.append(\"title\").text(function(d) { return d.data.chrom; });\n\n // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --\n\n var self = this,\n data_manager = self.track.get('data_manager'),\n // If track has a data manager, get deferred that resolves when data is ready.\n data_ready_deferred = (data_manager ? data_manager.data_is_ready() : true );\n\n // When data is ready, render track.\n $.when(data_ready_deferred).then(function() {\n $.when(self._render_data(track_parent_elt)).then(function() {\n chroms_paths.style(\"fill\", self.bg_fill);\n\n // Render labels after data is available so that data attributes are available.\n self.render_labels();\n });\n });\n },\n\n /**\n * Render track labels.\n */\n render_labels: function() {},\n\n /**\n * Update radius bounds.\n */\n update_radius_bounds: function(radius_bounds) {\n // Update bounds.\n this.radius_bounds = radius_bounds;\n\n // -- Update background arcs. --\n var new_d = d3.svg.arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]);\n\n this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d);\n\n this._transition_chrom_data();\n\n this._transition_labels();\n },\n\n /**\n * Update view scale. This fetches more data if scale is increased.\n */\n update_scale: function(new_scale) {\n // -- Update scale and return if new scale is less than old scale. --\n\n var old_scale = this.scale;\n this.scale = new_scale;\n if (new_scale <= old_scale) {\n return;\n }\n\n // -- Scale increased, so render visible data with more detail. --\n\n var self = this,\n utils = new SVGUtils();\n\n // Select all chrom data and filter to operate on those that are visible.\n this.parent_elt.selectAll('path.chrom-data').filter(function(d, i) {\n return utils.is_visible(this);\n }).each(function(d, i) {\n // -- Now operating on a single path element representing chromosome data. --\n\n var path_elt = d3.select(this),\n chrom = path_elt.attr('chrom'),\n chrom_region = self.genome.get_chrom_region(chrom),\n data_manager = self.track.get('data_manager'),\n data_deferred;\n\n // If can't get more detailed data, return.\n if (!data_manager.can_get_more_detailed_data(chrom_region)) {\n return;\n }\n\n // -- Get more detailed data. --\n data_deferred = self.track.get('data_manager').get_more_detailed_data(chrom_region, 'Coverage', 0, new_scale);\n\n // When more data is available, use new data to redraw path.\n $.when(data_deferred).then(function(data) {\n // Remove current data path.\n path_elt.remove();\n\n // Update data bounds with new data.\n self._update_data_bounds();\n\n // Find chromosome arc to draw data on.\n var chrom_arc = _.find(self.chroms_layout, function(layout) {\n return layout.data.chrom === chrom;\n });\n\n // Add new data path and apply preferences.\n var color = self.get_fill_color();\n self._render_chrom_data(self.parent_elt, chrom_arc, data).style('stroke', color).style('fill', color);\n });\n });\n\n return self;\n },\n\n /* ----------------------- Internal Methods ------------------------- */\n\n /**\n * Transitions chrom data to new values (e.g new radius or data bounds).\n */\n _transition_chrom_data: function() {\n var track = this.track,\n chrom_arcs = this.chroms_layout,\n chrom_data_paths = this.parent_elt.selectAll('g>path.chrom-data'),\n num_paths = chrom_data_paths[0].length;\n\n if (num_paths > 0) {\n var self = this;\n $.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) {\n // Map chrom data to path data, filtering out null values.\n var path_data = _.reject( _.map(genome_wide_data, function(chrom_data, i) {\n var rval = null,\n path_fn = self._get_path_function(chrom_arcs[i], chrom_data);\n if (path_fn) {\n rval = path_fn(chrom_data.data);\n }\n return rval;\n }), function(p_data) { return p_data === null; } );\n\n // Transition each path for data and color.\n var color = track.get('config').get_value('color');\n chrom_data_paths.each(function(path, index) {\n d3.select(this).transition().duration(1000)\n .style('stroke', color).style('fill', color)\n .attr('d', path_data[index]);\n });\n });\n }\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {},\n\n /**\n * Update data bounds. If there are new_bounds, use them; otherwise use\n * default data bounds.\n */\n _update_data_bounds: function(new_bounds) {\n var old_bounds = this.data_bounds;\n this.data_bounds = new_bounds ||\n this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome));\n this._transition_chrom_data();\n },\n\n /**\n * Render data as elements attached to svg.\n */\n _render_data: function(svg) {\n var self = this,\n chrom_arcs = this.chroms_layout,\n track = this.track,\n rendered_deferred = $.Deferred();\n\n // When genome-wide data is available, render data.\n $.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) {\n // Set bounds.\n self.data_bounds = self.get_data_bounds(genome_wide_data);\n\n // Set min, max value in config so that they can be adjusted. Make this silent\n // because these attributes are watched for changes and the viz is updated\n // accordingly (set up in initialize). Because we are setting up, we don't want\n // the watch to trigger events here.\n track.get('config').set_value('min_value', self.data_bounds[0], {silent: true});\n track.get('config').set_value('max_value', self.data_bounds[1], {silent: true});\n\n // Merge chroms layout with data.\n var layout_and_data = _.zip(chrom_arcs, genome_wide_data);\n\n // Render each chromosome's data.\n _.each(layout_and_data, function(chrom_info) {\n var chrom_arc = chrom_info[0],\n data = chrom_info[1];\n return self._render_chrom_data(svg, chrom_arc, data);\n });\n\n // Apply prefs to all track data.\n var color = self.get_fill_color();\n self.parent_elt.selectAll('path.chrom-data').style('stroke', color).style('fill', color);\n\n rendered_deferred.resolve(svg);\n });\n\n return rendered_deferred;\n },\n\n /**\n * Render a chromosome data and attach elements to svg.\n */\n _render_chrom_data: function(svg, chrom_arc, data) {},\n\n /**\n * Returns data for creating a path for the given data using chrom_arc and data bounds.\n */\n _get_path_function: function(chrom_arc, chrom_data) {},\n\n /**\n * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle\n * separated by gaps.\n */\n _chroms_layout: function() {\n // Setup chroms layout using pie.\n var chroms_info = this.genome.get_chroms_info(),\n pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null),\n init_arcs = pie_layout(chroms_info),\n gap_per_chrom = 2 * Math.PI * this.total_gap / chroms_info.length,\n chrom_arcs = _.map(init_arcs, function(arc, index) {\n // For short chroms, endAngle === startAngle.\n var new_endAngle = arc.endAngle - gap_per_chrom;\n arc.endAngle = (new_endAngle > arc.startAngle ? new_endAngle : arc.startAngle);\n return arc;\n });\n return chrom_arcs;\n }\n});\n\n/**\n * Render chromosome labels.\n */\nvar CircsterChromLabelTrackView = CircsterTrackView.extend({\n\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n // Use a single arc for rendering data.\n this.innerRadius = this.radius_bounds[0];\n this.radius_bounds[0] = this.radius_bounds[1];\n this.bg_stroke = '#fff';\n this.bg_fill = '#fff';\n\n // Minimum arc distance for labels to be applied.\n this.min_arc_len = 0.05;\n },\n\n /**\n * Render labels.\n */\n _render_data: function(svg) {\n // -- Add chromosome label where it will fit; an alternative labeling mechanism\n // would be nice for small chromosomes. --\n var self = this,\n chrom_arcs = svg.selectAll('g');\n\n chrom_arcs.selectAll('path')\n .attr('id', function(d) { return 'label-' + d.data.chrom; });\n\n chrom_arcs.append(\"svg:text\")\n .filter(function(d) {\n return d.endAngle - d.startAngle > self.min_arc_len;\n })\n .attr('text-anchor', 'middle')\n .append(\"svg:textPath\")\n .attr(\"class\", \"chrom-label\")\n .attr(\"xlink:href\", function(d) { return \"#label-\" + d.data.chrom; })\n .attr('startOffset', '25%')\n .text(function(d) {\n return d.data.chrom;\n });\n\n // -- Add ticks to denote chromosome length. --\n\n /** Returns an array of tick angles and labels, given a chrom arc. */\n var chromArcTicks = function(d) {\n var k = (d.endAngle - d.startAngle) / d.value,\n ticks = d3.range(0, d.value, 25000000).map(function(v, i) {\n return {\n radius: self.innerRadius,\n angle: v * k + d.startAngle,\n label: i === 0 ? 0 : (i % 3 ? null : self.formatNum(v))\n };\n });\n\n // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled.\n if (ticks.length < 4) {\n ticks[ticks.length-1].label = self.formatNum(\n Math.round( ( ticks[ticks.length-1].angle - d.startAngle ) / k )\n );\n }\n\n return ticks;\n };\n\n /** Rotate and move text as needed. */\n var textTransform = function(d) {\n return d.angle > Math.PI ? \"rotate(180)translate(-16)\" : null;\n };\n\n // Filter chroms for only those large enough for display.\n var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > self.min_arc_len; });\n\n this.drawTicks(this.parent_elt, visibleChroms, chromArcTicks, textTransform);\n }\n});\n_.extend(CircsterChromLabelTrackView.prototype, UsesTicks);\n\n/**\n * View for quantitative track in Circster.\n */\nvar CircsterQuantitativeTrackView = CircsterTrackView.extend({\n\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n\n // When config settings change, update view.\n var track_config = this.track.get('config');\n track_config.get('min_value').on('change:value', this._update_min_max, this);\n track_config.get('max_value').on('change:value', this._update_min_max, this);\n track_config.get('color').on('change:value', this._transition_chrom_data, this);\n },\n\n /**\n * Update track when min and/or max are changed.\n */\n _update_min_max: function() {\n var track_config = this.track.get('config'),\n new_bounds = [track_config.get_value('min_value'), track_config.get_value('max_value')];\n this._update_data_bounds(new_bounds);\n\n // FIXME: this works to update tick/text bounds, but there's probably a better way to do this\n // by updating the data itself.\n this.parent_elt.selectAll('.min_max').text(function(d, i) {\n return new_bounds[i];\n });\n },\n\n /**\n * Returns quantile for an array of numbers.\n */\n _quantile: function(numbers, quantile) {\n numbers.sort(d3.ascending);\n return d3.quantile(numbers, quantile);\n },\n\n /**\n * Renders quantitative data with the form [x, value] and assumes data is equally spaced across\n * chromosome. Attachs a dict with track and chrom name information to DOM element.\n */\n _render_chrom_data: function(svg, chrom_arc, chrom_data) {\n var path_data = this._get_path_function(chrom_arc, chrom_data);\n\n if (!path_data) { return null; }\n\n // There is path data, so render as path.\n var parent = svg.datum(chrom_data.data),\n path = parent.append('path')\n .attr('class', 'chrom-data')\n .attr('chrom', chrom_arc.data.chrom)\n .attr('d', path_data);\n\n return path;\n },\n\n /**\n * Returns function for creating a path across the chrom arc.\n */\n _get_path_function: function(chrom_arc, chrom_data) {\n // If no chrom data, return null.\n if (typeof chrom_data === \"string\" || !chrom_data.data || chrom_data.data.length === 0) {\n return null;\n }\n\n // Radius scaler.\n var radius = d3.scale.linear()\n .domain(this.data_bounds)\n .range(this.radius_bounds)\n .clamp(true);\n\n // Scaler for placing data points across arc.\n var angle = d3.scale.linear()\n .domain([0, chrom_data.data.length])\n .range([chrom_arc.startAngle, chrom_arc.endAngle]);\n\n // Use line generator to create area.\n var line = d3.svg.line.radial()\n .interpolate(\"linear\")\n .radius(function(d) { return radius(d[1]); })\n .angle(function(d, i) { return angle(i); });\n\n return d3.svg.area.radial()\n .interpolate(line.interpolate())\n .innerRadius(radius(0))\n .outerRadius(line.radius())\n .angle(line.angle());\n },\n\n /**\n * Render track min, max using ticks.\n */\n render_labels: function() {\n var self = this,\n // Keep counter of visible chroms.\n textTransform = function() {\n return \"rotate(90)\";\n };\n\n // FIXME:\n // (1) using min_max class below is needed for _update_min_max, which could be improved.\n // (2) showing config on tick click should be replaced by proper track config icon.\n\n // Draw min, max on first chrom only.\n var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],\n this._data_bounds_ticks_fn(), textTransform, true)\n .classed('min_max', true);\n\n // Show config when ticks are clicked on.\n _.each(ticks, function(tick) {\n $(tick).click(function() {\n var view = new config.ConfigSettingCollectionView({\n collection: self.track.get('config')\n });\n view.render_in_modal('Configure Track');\n });\n });\n\n\n\n /*\n // Filter for visible chroms, then for every third chrom so that labels attached to only every\n // third chrom.\n var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }),\n labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; });\n this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true);\n */\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {\n // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below\n // is copied from UseTicks mixin, so pull out and make generally available.\n\n // If there are no data bounds, nothing to transition.\n if (this.data_bounds.length === 0) { return; }\n\n // Transition labels to new radius bounds.\n var self = this,\n visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }),\n labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; }),\n new_data = _.flatten( _.map(labeledChroms, function(c) {\n return self._data_bounds_ticks_fn()(c);\n }));\n this.parent_elt.selectAll('g.tick').data(new_data).transition().attr(\"transform\", function(d) {\n return \"rotate(\" + (d.angle * 180 / Math.PI - 90) + \")\" +\n \"translate(\" + d.radius + \",0)\";\n });\n },\n\n /**\n * Get function for locating data bounds ticks.\n */\n _data_bounds_ticks_fn: function() {\n // Closure vars.\n var self = this;\n visibleChroms = 0;\n\n // Return function for locating ticks based on chrom arc data.\n return function(d) {\n // Set up data to display min, max ticks.\n return [\n {\n radius: self.radius_bounds[0],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[0])\n },\n {\n radius: self.radius_bounds[1],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[1])\n }\n ];\n };\n },\n\n /**\n * Returns an array with two values denoting the minimum and maximum\n * values for the track.\n */\n get_data_bounds: function(data) {}\n\n});\n_.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);\n\n/**\n * Bigwig track view in Circster.\n */\nvar CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({\n\n get_data_bounds: function(data) {\n // Set max across dataset by extracting all values, flattening them into a\n // single array, and getting third quartile.\n var values = _.flatten( _.map(data, function(d) {\n if (d) {\n // Each data point has the form [position, value], so return all values.\n return _.map(d.data, function(p) {\n // Null is used for a lack of data; resolve null to 0 for comparison.\n return parseInt(p[1], 10) || 0;\n });\n }\n else {\n return 0;\n }\n }) );\n\n // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0\n // for sparsely populated data, so use max in that case.\n return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ];\n }\n});\n\n/**\n * Chromosome interactions track view in Circster.\n */\nvar CircsterChromInteractionsTrackView = CircsterTrackView.extend({\n\n render: function() {\n var self = this;\n\n // When data is ready, render track.\n $.when(self.track.get('data_manager').data_is_ready()).then(function() {\n // When data has been fetched, render track.\n $.when(self.track.get('data_manager').get_genome_wide_data(self.genome)).then(function(genome_wide_data) {\n var chord_data = [],\n chroms_info = self.genome.get_chroms_info();\n // Convert chromosome data into chord data.\n _.each(genome_wide_data, function(chrom_data, index) {\n // Map each interaction into chord data.\n var cur_chrom = chroms_info[index].chrom;\n var chrom_chord_data = _.map(chrom_data.data, function(datum) {\n // Each datum is an interaction/chord.\n var source_angle = self._get_region_angle(cur_chrom, datum[1]),\n target_angle = self._get_region_angle(datum[3], datum[4]);\n return {\n source: {\n startAngle: source_angle,\n endAngle: source_angle + 0.01\n },\n target: {\n startAngle: target_angle,\n endAngle: target_angle + 0.01\n }\n };\n });\n\n chord_data = chord_data.concat(chrom_chord_data);\n });\n\n self.parent_elt.append(\"g\")\n .attr(\"class\", \"chord\")\n .selectAll(\"path\")\n .data(chord_data)\n .enter().append(\"path\")\n .style(\"fill\", self.get_fill_color())\n .attr(\"d\", d3.svg.chord().radius(self.radius_bounds[0]))\n .style(\"opacity\", 1);\n });\n });\n },\n\n update_radius_bounds: function(radius_bounds) {\n this.radius_bounds = radius_bounds;\n this.parent_elt.selectAll(\"path\").transition().attr(\"d\", d3.svg.chord().radius(this.radius_bounds[0]));\n },\n\n /**\n * Returns radians for a genomic position.\n */\n _get_region_angle: function(chrom, position) {\n // Find chrom angle data\n var chrom_angle_data = _.find(this.chroms_layout, function(chrom_layout) {\n return chrom_layout.data.chrom === chrom;\n });\n\n // Return angle at position.\n return chrom_angle_data.endAngle -\n (\n (chrom_angle_data.endAngle - chrom_angle_data.startAngle) *\n (chrom_angle_data.data.len - position) / chrom_angle_data.data.len\n );\n }\n\n});\n\n// circster app loader\nvar Circster = Backbone.View.extend(\n{\n initialize: function ()\n {\n // -- Configure visualization --\n var genome = new visualization.Genome(galaxy_config.app.genome),\n vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config);\n\n // Add Circster-specific config options.\n vis.get('config').add([\n { key: 'arc_dataset_height', label: 'Arc Dataset Height', type: 'int', value: 25, view: 'circster' },\n { key: 'track_gap', label: 'Gap Between Tracks', type: 'int', value: 5, view: 'circster' },\n { key: 'total_gap', label: 'Gap [0-1]', type: 'float', value: 0.4, view: 'circster', hidden: true }\n ]);\n\n var viz_view = new CircsterView(\n {\n // view pane\n el : $('#center .unified-panel-body'),\n genome : genome,\n model : vis\n });\n\n // Render vizualization\n viz_view.render();\n\n // setup title\n $('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + \" \" + galaxy_config.app.viz_config.dbkey);\n\n // setup menu\n var menu = mod_icon_btn.create_icon_buttons_menu([\n {\n icon_class: 'plus-button', title: 'Add tracks', on_click: function()\n {\n visualization.select_datasets({'dbkey': vis.get('dbkey')}, function(tracks)\n {\n vis.add_tracks(tracks);\n });\n }\n },\n {\n icon_class: 'gear', title: 'Settings', on_click: function()\n {\n var view = new config.ConfigSettingCollectionView({\n collection: vis.get('config')\n });\n view.render_in_modal('Configure Visualization');\n }\n },\n {\n icon_class: 'disk--arrow', title: 'Save', on_click: function()\n {\n // show saving dialog box\n Galaxy.modal.show({title: \"Saving...\", body: \"progress\" });\n\n // send to server\n $.ajax({\n url: Galaxy.root + \"visualization/save\",\n type: \"POST\",\n dataType: \"json\",\n data: {\n 'id' : vis.get('vis_id'),\n 'title' : vis.get('title'),\n 'dbkey' : vis.get('dbkey'),\n 'type' : 'trackster',\n 'vis_json' : JSON.stringify(vis)\n }\n }).success(function(vis_info) {\n Galaxy.modal.hide();\n vis.set('vis_id', vis_info.vis_id);\n }).error(function() {\n // show dialog\n Galaxy.modal.show({\n title : \"Could Not Save\",\n body : \"Could not save visualization. Please try again later.\",\n buttons : { \"Cancel\": function() { Galaxy.modal.hide(); } }\n });\n });\n }\n },\n {\n icon_class: 'cross-circle', title: 'Close', on_click: function()\n {\n window.location = Galaxy.root + \"visualizations/list\";\n }\n }], { tooltip_config: { placement: 'bottom' } });\n\n // add menu\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#center .unified-panel-header-inner\").append(menu.$el);\n\n // manual tooltip config because default gravity is S and cannot be changed\n $(\".menu-button\").tooltip( { placement: 'bottom' } );\n }\n});\n\n// Module exports.\nreturn {\n GalaxyApp: Circster\n};\n\n});\n"]} \ No newline at end of file diff --git a/static/maps/viz/sweepster.js.map b/static/maps/viz/sweepster.js.map index 3897669c100..c7076d93105 100644 --- a/static/maps/viz/sweepster.js.map +++ b/static/maps/viz/sweepster.js.map @@ -1 +1 @@ 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* Visualization and components for Sweepster, a visualization for exploring a tool's parameter space via\n * genomic visualization.\n */\n\ndefine([\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/trackster/util\",\n \"viz/visualization\",\n \"viz/trackster/tracks\",\n \"mvc/tool/tools\",\n \"mvc/dataset/data\",\n \"utils/config\",\n \"mvc/ui/icon-button\"\n\n], function(_, d3, util, visualization, tracks, tools, data, config, mod_icon_btn) {\n\n/**\n * A collection of tool input settings. Object is useful for keeping a list of settings\n * for future use without changing the input's value and for preserving inputs order.\n */\nvar ToolInputsSettings = Backbone.Model.extend({\n defaults: {\n inputs: null,\n values: null\n }\n});\n\n/**\n * Tree for a tool's parameters.\n */\nvar ToolParameterTree = Backbone.Model.extend({\n defaults: {\n tool: null,\n tree_data: null\n },\n\n initialize: function(options) {\n // Set up tool parameters to work with tree.\n var self = this;\n this.get('tool').get('inputs').each(function(input) {\n // Listen for changes to input's attributes.\n input.on('change:min change:max change:num_samples', function(input) {\n if (input.get('in_ptree')) {\n self.set_tree_data();\n }\n }, self);\n input.on('change:in_ptree', function(input) {\n if (input.get('in_ptree')) {\n self.add_param(input);\n }\n else {\n self.remove_param(input);\n }\n self.set_tree_data();\n }, self);\n });\n\n // If there is a config, use it.\n if (options.config) {\n _.each(options.config, function(input_config) {\n var input = self.get('tool').get('inputs').find(function(input) {\n return input.get('name') === input_config.name;\n });\n self.add_param(input);\n input.set(input_config);\n });\n }\n },\n\n add_param: function(param) {\n // If parameter already present, do not add it.\n if (param.get('ptree_index')) { return; }\n\n param.set('in_ptree', true);\n param.set('ptree_index', this.get_tree_params().length);\n },\n\n remove_param: function(param) {\n // Remove param from tree.\n param.set('in_ptree', false);\n param.set('ptree_index', null);\n\n // Update ptree indices for remaining params.\n _(this.get_tree_params()).each(function(input, index) {\n // +1 to use 1-based indexing.\n input.set('ptree_index', index + 1);\n });\n },\n\n /**\n * Sets tree data using tool's inputs.\n */\n set_tree_data: function() {\n // Get samples for each parameter.\n var params_samples = _.map(this.get_tree_params(), function(param) {\n return {\n param: param,\n samples: param.get_samples()\n };\n });\n var node_id = 0,\n // Creates tree data recursively.\n create_tree_data = function(params_samples, index) {\n var param_samples = params_samples[index],\n param = param_samples.param,\n param_label = param.get('label'),\n settings = param_samples.samples;\n\n // Create leaves when last parameter setting is reached.\n if (params_samples.length - 1 === index) {\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting\n };\n });\n }\n\n // Recurse to handle other parameters.\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting,\n children: create_tree_data(params_samples, index + 1)\n };\n });\n };\n\n this.set('tree_data', {\n name: 'Root',\n id: node_id++,\n children: (params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null)\n });\n },\n\n get_tree_params: function() {\n // Filter and sort parameters to get list in tree.\n return _(this.get('tool').get('inputs').where( {in_ptree: true} ))\n .sortBy( function(input) { return input.get('ptree_index'); } );\n },\n\n /**\n * Returns number of leaves in tree.\n */\n get_num_leaves: function() {\n return this.get_tree_params().reduce(function(memo, param) { return memo * param.get_samples().length; }, 1);\n },\n\n /**\n * Returns array of ToolInputsSettings objects based on a node and its subtree.\n */\n get_node_settings: function(target_node) {\n // -- Get fixed settings from tool and parent nodes.\n\n // Start with tool's settings.\n var fixed_settings = this.get('tool').get_inputs_dict();\n\n // Get fixed settings using node's parents.\n var cur_node = target_node.parent;\n if (cur_node) {\n while(cur_node.depth !== 0) {\n fixed_settings[cur_node.param.get('name')] = cur_node.value;\n cur_node = cur_node.parent;\n }\n }\n\n // Walk subtree starting at clicked node to get full list of settings.\n var self = this,\n get_settings = function(node, settings) {\n // Add setting for this node. Root node does not have a param,\n // however.\n if (node.param) {\n settings[node.param.get('name')] = node.value;\n }\n\n if (!node.children) {\n // At leaf node, so return settings.\n return new ToolInputsSettings({\n inputs: self.get('tool').get('inputs'),\n values: settings\n });\n }\n else {\n // At interior node: return list of subtree settings.\n return _.flatten( _.map(node.children, function(c) { return get_settings(c, _.clone(settings)); }) );\n }\n },\n all_settings = get_settings(target_node, fixed_settings);\n\n // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.\n if (!_.isArray(all_settings)) { all_settings = [ all_settings ]; }\n\n return all_settings;\n },\n\n /**\n * Returns all nodes connected a particular node; this includes parents and children of the node.\n */\n get_connected_nodes: function(node) {\n var get_subtree_nodes = function(a_node) {\n if (!a_node.children) {\n return a_node;\n }\n else {\n // At interior node: return subtree nodes.\n return _.flatten( [a_node, _.map(a_node.children, function(c) { return get_subtree_nodes(c); })] );\n }\n };\n\n // Get node's parents.\n var parents = [],\n cur_parent = node.parent;\n while(cur_parent) {\n parents.push(cur_parent);\n cur_parent = cur_parent.parent;\n }\n\n return _.flatten([parents, get_subtree_nodes(node)]);\n },\n\n /**\n * Returns the leaf that corresponds to a settings collection.\n */\n get_leaf: function(settings) {\n var cur_node = this.get('tree_data'),\n find_child = function(children) {\n return _.find(children, function(child) {\n return settings[child.param.get('name')] === child.value;\n });\n };\n\n while (cur_node.children) {\n cur_node = find_child(cur_node.children);\n }\n return cur_node;\n },\n\n /**\n * Returns a list of parameters used in tree.\n */\n toJSON: function() {\n // FIXME: returning and jsonifying complete param causes trouble on the server side,\n // so just use essential attributes for now.\n return this.get_tree_params().map(function(param) {\n return {\n name: param.get('name'),\n min: param.get('min'),\n max: param.get('max'),\n num_samples: param.get('num_samples')\n };\n });\n }\n});\n\nvar SweepsterTrack = Backbone.Model.extend({\n defaults: {\n track: null,\n mode: 'Pack',\n settings: null,\n regions: null\n },\n\n initialize: function(options) {\n this.set('regions', options.regions);\n if (options.track) {\n // FIXME: find a better way to deal with needed URLs:\n var track_config = _.extend({\n data_url: Galaxy.root + 'dummy1',\n converted_datasets_state_url: Galaxy.root + 'dummy2'\n }, options.track);\n this.set('track', tracks.object_from_template(track_config, {}, null));\n }\n },\n\n same_settings: function(a_track) {\n var this_settings = this.get('settings'),\n other_settings = a_track.get('settings');\n for (var prop in this_settings) {\n if (!other_settings[prop] ||\n this_settings[prop] !== other_settings[prop]) {\n return false;\n }\n }\n return true;\n },\n\n toJSON: function() {\n return {\n track: this.get('track').to_dict(),\n settings: this.get('settings'),\n regions: this.get('regions')\n };\n }\n});\n\nvar TrackCollection = Backbone.Collection.extend({\n model: SweepsterTrack\n});\n\n/**\n * Sweepster visualization model.\n */\nvar SweepsterVisualization = visualization.Visualization.extend({\n defaults: _.extend({}, visualization.Visualization.prototype.defaults, {\n dataset: null,\n tool: null,\n parameter_tree: null,\n regions: null,\n tracks: null,\n default_mode: 'Pack'\n }),\n\n initialize: function(options) {\n this.set('dataset', new data.Dataset(options.dataset));\n this.set('tool', new tools.Tool(options.tool));\n this.set('regions', new visualization.GenomeRegionCollection(options.regions));\n this.set('tracks', new TrackCollection(options.tracks));\n\n var tool_with_samplable_inputs = this.get('tool');\n this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);\n // Remove complex parameters for now.\n tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional', 'text' ] );\n\n this.set('parameter_tree', new ToolParameterTree({\n tool: tool_with_samplable_inputs,\n config: options.tree_config\n }));\n },\n\n add_track: function(track) {\n this.get('tracks').add(track);\n },\n\n toJSON: function() {\n return {\n id: this.get('id'),\n title: 'Parameter exploration for dataset \\'' + this.get('dataset').get('name') + '\\'',\n type: 'sweepster',\n dataset_id: this.get('dataset').id,\n tool_id: this.get('tool').id,\n regions: this.get('regions').toJSON(),\n tree_config: this.get('parameter_tree').toJSON(),\n tracks: this.get('tracks').toJSON()\n };\n }\n});\n\n/**\n * --- Views ---\n */\n\n/**\n * Sweepster track view.\n */\nvar SweepsterTrackView = Backbone.View.extend({\n tagName: 'tr',\n\n TILE_LEN: 250,\n\n initialize: function(options) {\n this.canvas_manager = options.canvas_manager;\n this.render();\n this.model.on('change:track change:mode', this.draw_tiles, this);\n },\n\n render: function() {\n // Render settings icon and popup.\n // TODO: use template.\n var settings = this.model.get('settings'),\n values = settings.get('values'),\n settings_td = $('').addClass('settings').appendTo(this.$el),\n settings_div = $('').addClass('track-info').hide().appendTo(settings_td);\n settings_div.append( $('').css('font-weight', 'bold').text('Track Settings') );\n settings.get('inputs').each(function(input) {\n settings_div.append( input.get('label') + ': ' + values[input.get('name')] + '
');\n });\n var self = this,\n run_on_dataset_button = $('').appendTo(settings_div).text('Run on complete dataset').click(function() {\n settings_div.toggle();\n self.trigger('run_on_dataset', settings);\n });\n var icon_menu = mod_icon_btn.create_icon_buttons_menu([\n {\n title: 'Settings',\n icon_class: 'gear track-settings',\n on_click: function() {\n settings_div.toggle();\n }\n },\n {\n title: 'Remove',\n icon_class: 'cross-circle',\n on_click: function() {\n self.$el.remove();\n $('.tooltip').remove();\n // TODO: remove track from viz collection.\n }\n }\n ]);\n settings_td.prepend(icon_menu.$el);\n\n // Render tile placeholders.\n this.model.get('regions').each(function() {\n self.$el.append($('').addClass('tile').html(\n $(' ').attr('src', Galaxy.root + 'images/loading_large_white_bg.gif')\n ));\n });\n\n if (this.model.get('track')) {\n this.draw_tiles();\n }\n },\n\n /**\n * Draw tiles for regions.\n */\n draw_tiles: function() {\n var self = this,\n track = this.model.get('track'),\n regions = this.model.get('regions'),\n tile_containers = this.$el.find('td.tile');\n\n // Do nothing if track is not defined.\n if (!track) { return; }\n\n // When data is ready, draw tiles.\n $.when(track.data_manager.data_is_ready()).then(function(data_ok) {\n // Draw tile for each region.\n regions.each(function(region, index) {\n var resolution = region.length() / self.TILE_LEN,\n w_scale = 1/resolution,\n mode = self.model.get('mode');\n $.when(track.data_manager.get_data(region, mode, resolution, {})).then(function(tile_data) {\n var canvas = self.canvas_manager.new_canvas();\n canvas.width = self.TILE_LEN;\n canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width);\n track.draw_tile(tile_data, canvas.getContext('2d'), mode, region, w_scale);\n $(tile_containers[index]).empty().append(canvas);\n });\n });\n });\n }\n});\n\n/**\n * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as\n * it augments an existing input form row rather than creates a completely new HTML element.\n */\nvar ToolInputValOrSweepView = Backbone.View.extend({\n\n // Template for rendering sweep inputs:\n number_input_template: '
' +\n '\"> - ' +\n '\">' +\n ' samples: \">' +\n '',\n\n select_input_template: '<%= options %>',\n\n initialize: function(options) {\n this.$el = options.tool_row;\n this.render();\n },\n\n render: function() {\n var input = this.model,\n type = input.get('type'),\n single_input_row = this.$el.find('.form-row-input'),\n sweep_inputs_row = null;\n\n // Update tool inputs as single input changes.\n single_input_row.find(':input').change(function() {\n input.set('value', $(this).val());\n });\n\n // Add row for parameter sweep inputs.\n if (input instanceof tools.IntegerToolParameter) {\n sweep_inputs_row = $( _.template(this.number_input_template)(this.model.toJSON()) );\n }\n else if (input instanceof tools.SelectToolParameter) {\n var options = _.map(this.$el.find('select option'), function(option) {\n return $(option).val();\n }),\n options_text = options.join(', ');\n sweep_inputs_row = $( _.template(this.select_input_template)({\n options: options_text\n }) );\n }\n sweep_inputs_row.insertAfter(single_input_row);\n\n // Add buttons for adding/removing parameter.\n var self = this,\n menu = mod_icon_btn.create_icon_buttons_menu([\n {\n title: 'Add parameter to tree',\n icon_class: 'plus-button',\n on_click: function () {\n input.set('in_ptree', true);\n single_input_row.hide();\n sweep_inputs_row.show();\n $(this).hide();\n self.$el.find('.icon-button.toggle').show();\n }\n\n },\n {\n title: 'Remove parameter from tree',\n icon_class: 'toggle',\n on_click: function() {\n // Remove parameter from tree params where name matches clicked paramter.\n input.set('in_ptree', false);\n sweep_inputs_row.hide();\n single_input_row.show();\n $(this).hide();\n self.$el.find('.icon-button.plus-button').show();\n }\n }\n ],\n {\n\n });\n this.$el.prepend(menu.$el);\n\n // Show/hide input rows and icons depending on whether parameter is in the tree.\n if (input.get('in_ptree')) {\n single_input_row.hide();\n self.$el.find('.icon-button.plus-button').hide();\n }\n else {\n self.$el.find('.icon-button.toggle').hide();\n sweep_inputs_row.hide();\n }\n\n // Update input's min, max, number of samples as values change.\n _.each(['min', 'max', 'num_samples'], function(attr) {\n sweep_inputs_row.find('.' + attr).change(function() {\n input.set(attr, parseFloat( $(this).val() ));\n });\n });\n }\n});\n\nvar ToolParameterTreeDesignView = Backbone.View.extend({\n className: 'tree-design',\n\n initialize: function(options) {\n this.render();\n },\n\n render: function() {\n // Start with tool form view.\n var tool_form_view = new tools.ToolFormView({\n model: this.model.get('tool')\n });\n tool_form_view.render();\n this.$el.append(tool_form_view.$el);\n\n // Set up views for each tool input.\n var self = this,\n inputs = self.model.get('tool').get('inputs');\n this.$el.find('.form-row').not('.form-actions').each(function(i) {\n var input_view = new ToolInputValOrSweepView({\n model: inputs.at(i),\n tool_row: $(this)\n });\n });\n }\n});\n\n/**\n * Displays and updates parameter tree.\n */\nvar ToolParameterTreeView = Backbone.View.extend({\n className: 'tool-parameter-tree',\n\n initialize: function(options) {\n // When tree data changes, re-render.\n this.model.on('change:tree_data', this.render, this);\n },\n\n render: function() {\n // Start fresh.\n this.$el.children().remove();\n\n var tree_params = this.model.get_tree_params();\n if (!tree_params.length) {\n return;\n }\n\n // Set width, height based on params and samples.\n this.width = 100 * (2 + tree_params.length);\n this.height = 15 * this.model.get_num_leaves();\n\n var self = this;\n\n // Layout tree.\n var cluster = d3.layout.cluster()\n .size([this.height, this.width - 160]);\n\n var diagonal = d3.svg.diagonal()\n .projection(function(d) { return [d.y, d.x]; });\n\n // Layout nodes.\n var nodes = cluster.nodes(this.model.get('tree_data'));\n\n // Setup and add labels for tree levels.\n var param_depths = _.uniq(_.pluck(nodes, \"y\"));\n _.each(tree_params, function(param, index) {\n var x = param_depths[index+1],\n center_left = $('#center').position().left;\n self.$el.append( $('').addClass('label')\n .text(param.get('label'))\n .css('left', x + center_left) );\n });\n\n // Set up vis element.\n var vis = d3.select(this.$el[0])\n .append(\"svg\")\n .attr(\"width\", this.width)\n .attr(\"height\", this.height + 30)\n .append(\"g\")\n .attr(\"transform\", \"translate(40, 20)\");\n\n // Draw links.\n var link = vis.selectAll(\"path.link\")\n .data(cluster.links(nodes))\n .enter().append(\"path\")\n .attr(\"class\", \"link\")\n .attr(\"d\", diagonal);\n\n // Draw nodes.\n var node = vis.selectAll(\"g.node\")\n .data(nodes)\n .enter().append(\"g\")\n .attr(\"class\", \"node\")\n .attr(\"transform\", function(d) { return \"translate(\" + d.y + \",\" + d.x + \")\"; })\n .on('mouseover', function(a_node) {\n var connected_node_ids = _.pluck(self.model.get_connected_nodes(a_node), 'id');\n // TODO: probably can use enter() to do this more easily.\n node.filter(function(d) {\n return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;\n }).style('fill', '#f00');\n })\n .on('mouseout', function() {\n node.style('fill', '#000');\n });\n\n node.append(\"circle\")\n .attr(\"r\", 9);\n\n node.append(\"text\")\n .attr(\"dx\", function(d) { return d.children ? -12 : 12; })\n .attr(\"dy\", 3)\n .attr(\"text-anchor\", function(d) { return d.children ? \"end\" : \"start\"; })\n .text(function(d) { return d.name; });\n }\n});\n\n/**\n * Sweepster visualization view. View requires rendering in 3-panel setup for now.\n */\nvar SweepsterVisualizationView = Backbone.View.extend({\n className: 'Sweepster',\n\n helpText:\n '',\n\n initialize: function(options) {\n this.canvas_manager = new visualization.CanvasManager(this.$el.parents('body'));\n this.tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') });\n this.track_collection_container = $('Getting Started
' +\n '').addClass('tracks');\n\n // Handle node clicks for tree data.\n this.model.get('parameter_tree').on('change:tree_data', this.handle_node_clicks, this);\n\n // Each track must have a view so it has a canvas manager.\n var self = this;\n this.model.get('tracks').each(function(track) {\n track.get('track').view = self;\n });\n\n // Set block, reverse strand block colors; these colors will be used for all tracks.\n this.config = config.ConfigSettingCollection.from_models_and_saved_values(\n [\n { key: 'name', label: 'Name', type: 'text', default_value: '' },\n { key: 'a_color', label: 'A Color', type: 'color', default_value: \"#FF0000\" },\n { key: 'c_color', label: 'C Color', type: 'color', default_value: \"#00FF00\" },\n { key: 'g_color', label: 'G Color', type: 'color', default_value: \"#0000FF\" },\n { key: 't_color', label: 'T Color', type: 'color', default_value: \"#FF00FF\" },\n { key: 'n_color', label: 'N Color', type: 'color', default_value: \"#AAAAAA\" },\n { key: 'block_color', label: 'Block color', type: 'color' },\n { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },\n ], {}\n );\n },\n\n render: function() {\n // Render tree design view in left panel.\n var tree_design_view = new ToolParameterTreeDesignView({\n model: this.model.get('parameter_tree')\n });\n\n $('#left').append(tree_design_view.$el);\n\n // Render track collection container/view in right panel.\n var self = this,\n regions = self.model.get('regions'),\n tr = $('
').appendTo(this.track_collection_container);\n\n regions.each(function(region) {\n tr.append( $(' ').text(region.toString()) );\n });\n tr.children().first().attr('colspan', 2);\n\n var tracks_div = $(' ').addClass('tiles');\n $('#right').append( tracks_div.append(this.track_collection_container) );\n\n self.model.get('tracks').each(function(track) {\n self.add_track(track);\n });\n\n // -- Render help and tool parameter tree in center panel. --\n\n // Help includes text and a close button.\n var help_div = $(this.helpText).addClass('help'),\n close_button = mod_icon_btn.create_icon_buttons_menu([\n {\n title: 'Close',\n icon_class: 'cross-circle',\n on_click: function() {\n $('.tooltip').remove();\n help_div.remove();\n }\n }\n ]);\n\n help_div.prepend(close_button.$el.css('float', 'right'));\n $('#center').append(help_div);\n\n // Parameter tree:\n this.tool_param_tree_view.render();\n $('#center').append(this.tool_param_tree_view.$el);\n\n // Set up handler for tree node clicks.\n this.handle_node_clicks();\n\n // Set up visualization menu.\n var menu = mod_icon_btn.create_icon_buttons_menu(\n [\n // Save.\n /*\n { icon_class: 'disk--arrow', title: 'Save', on_click: function() {\n // Show saving dialog box\n show_modal(\"Saving...\", \"progress\");\n\n viz.save().success(function(vis_info) {\n hide_modal();\n viz.set({\n 'id': vis_info.vis_id,\n 'has_changes': false\n });\n })\n .error(function() {\n show_modal( \"Could Not Save\", \"Could not save visualization. Please try again later.\",\n { \"Close\" : hide_modal } );\n });\n } },\n */\n // Change track modes.\n {\n icon_class: 'chevron-expand',\n title: 'Set display mode'\n },\n // Close viz.\n {\n icon_class: 'cross-circle',\n title: 'Close',\n on_click: function() {\n window.location = \"${h.url_for( controller='visualization', action='list' )}\";\n }\n }\n ],\n {\n tooltip_config: {placement: 'bottom'}\n });\n\n // Create mode selection popup. Mode selection changes default mode and mode for all tracks.\n var modes = ['Squish', 'Pack'],\n mode_mapping = {};\n _.each(modes, function(mode) {\n mode_mapping[mode] = function() {\n self.model.set('default_mode', mode);\n self.model.get('tracks').each(function(track) {\n track.set('mode', mode);\n });\n };\n });\n\n make_popupmenu(menu.$el.find('.chevron-expand'), mode_mapping);\n\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#right .unified-panel-header-inner\").append(menu.$el);\n },\n\n get_base_color: function(base) {\n return this.config.get_value(base.toLowerCase() + '_color') ||\n this.config.get_value('n_color');\n },\n\n run_tool_on_dataset: function(settings) {\n var tool = this.model.get('tool'),\n tool_name = tool.get('name'),\n dataset = this.model.get('dataset');\n tool.set_input_values(settings.get('values'));\n $.when(tool.rerun(dataset)).then(function(outputs) {\n // TODO.\n });\n\n show_modal('Running ' + tool_name + ' on complete dataset',\n tool_name + ' is running on dataset \\'' +\n dataset.get('name') + '\\'. Outputs are in the dataset\\'s history.',\n {\n 'Ok': function() { hide_modal(); }\n });\n },\n\n /**\n * Add track to model and view.\n */\n add_track: function(pm_track) {\n var self = this,\n param_tree = this.model.get('parameter_tree');\n\n // Add track to model.\n self.model.add_track(pm_track);\n\n var track_view = new SweepsterTrackView({\n model: pm_track,\n canvas_manager: self.canvas_manager\n });\n track_view.on('run_on_dataset', self.run_tool_on_dataset, self);\n self.track_collection_container.append(track_view.$el);\n track_view.$el.hover(function() {\n var settings_leaf = param_tree.get_leaf(pm_track.get('settings').get('values'));\n var connected_node_ids = _.pluck(param_tree.get_connected_nodes(settings_leaf), 'id');\n\n // TODO: can do faster with enter?\n d3.select(self.tool_param_tree_view.$el[0]).selectAll(\"g.node\")\n .filter(function(d) {\n return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;\n }).style('fill', '#f00');\n },\n function() {\n d3.select(self.tool_param_tree_view.$el[0]).selectAll(\"g.node\").style('fill', '#000');\n });\n return pm_track;\n },\n\n /**\n * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of\n * the settings defined by the node's subtree and tracks are added for each run.\n */\n handle_node_clicks: function() {\n // When node clicked in tree, run tool and add tracks to model.\n var self = this,\n param_tree = this.model.get('parameter_tree'),\n regions = this.model.get('regions'),\n node = d3.select(this.tool_param_tree_view.$el[0]).selectAll(\"g.node\");\n node.on(\"click\", function(d, i) {\n // Get all settings corresponding to node.\n var tool = self.model.get('tool'),\n dataset = self.model.get('dataset'),\n all_settings = param_tree.get_node_settings(d),\n run_jobs_deferred = $.Deferred();\n\n // Do not allow 10+ jobs to be run.\n if (all_settings.length >= 10) {\n show_modal(\"Whoa there cowboy!\",\n \"You clicked on a node to try \" + self.model.get('tool').get('name') +\n \" with \" + all_settings.length +\n \" different combinations of settings. You can only run 10 jobs at a time.\",\n {\n \"Ok\": function() { hide_modal(); run_jobs_deferred.resolve(false); }\n });\n }\n else {\n run_jobs_deferred.resolve(true);\n }\n\n // Take action when deferred resolves.\n $.when(run_jobs_deferred).then(function(run_jobs) {\n if (!run_jobs) { return; }\n\n // Create and add tracks for each settings group.\n var new_tracks = _.map(all_settings, function(settings) {\n var pm_track = new SweepsterTrack({\n settings: settings,\n regions: regions,\n mode: self.model.get('default_mode')\n });\n self.add_track(pm_track);\n return pm_track;\n });\n\n // For each track, run tool using track's settings and update track.\n _.each(new_tracks, function(pm_track, index) {\n setTimeout(function() {\n // Set inputs and run tool.\n tool.set_input_values(pm_track.get('settings').get('values'));\n $.when(tool.rerun(dataset, regions)).then(function(output) {\n // HACKish: output is an HDA with track config attribute. To create a track\n // that works correctly with Backbone relational, it is necessary to\n // use a modified version of the track config.\n var dataset = output.first(),\n track_config = dataset.get('track_config');\n // Set dataset to be the tool's output.\n track_config.dataset = dataset;\n // Set tool to null so that it is not unpacked; unpacking it messes with\n // the tool parameters and parameter tree.\n track_config.tool = null;\n\n track_config.prefs = self.config.to_key_value_dict();\n\n // Create and add track for output dataset.\n var track_obj = tracks.object_from_template(track_config, self, null);\n track_obj.init_for_tool_data();\n\n pm_track.set('track', track_obj);\n });\n }, index * 10000);\n });\n });\n });\n }\n});\n\nreturn {\n SweepsterVisualization: SweepsterVisualization,\n SweepsterVisualizationView: SweepsterVisualizationView\n};\n\n});\n"]} \ No newline at end of file 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* Visualization and components for Sweepster, a visualization for exploring a tool's parameter space via\n * genomic visualization.\n */\n\ndefine([\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/trackster/util\",\n \"viz/visualization\",\n \"viz/trackster/tracks\",\n \"mvc/tool/tools\",\n \"mvc/dataset/data\",\n \"utils/config\",\n \"mvc/ui/icon-button\"\n\n], function(_, d3, util, visualization, tracks, tools, data, config, mod_icon_btn) {\n\n/**\n * A collection of tool input settings. Object is useful for keeping a list of settings\n * for future use without changing the input's value and for preserving inputs order.\n */\nvar ToolInputsSettings = Backbone.Model.extend({\n defaults: {\n inputs: null,\n values: null\n }\n});\n\n/**\n * Tree for a tool's parameters.\n */\nvar ToolParameterTree = Backbone.Model.extend({\n defaults: {\n tool: null,\n tree_data: null\n },\n\n initialize: function(options) {\n // Set up tool parameters to work with tree.\n var self = this;\n this.get('tool').get('inputs').each(function(input) {\n // Listen for changes to input's attributes.\n input.on('change:min change:max change:num_samples', function(input) {\n if (input.get('in_ptree')) {\n self.set_tree_data();\n }\n }, self);\n input.on('change:in_ptree', function(input) {\n if (input.get('in_ptree')) {\n self.add_param(input);\n }\n else {\n self.remove_param(input);\n }\n self.set_tree_data();\n }, self);\n });\n\n // If there is a config, use it.\n if (options.config) {\n _.each(options.config, function(input_config) {\n var input = self.get('tool').get('inputs').find(function(input) {\n return input.get('name') === input_config.name;\n });\n self.add_param(input);\n input.set(input_config);\n });\n }\n },\n\n add_param: function(param) {\n // If parameter already present, do not add it.\n if (param.get('ptree_index')) { return; }\n\n param.set('in_ptree', true);\n param.set('ptree_index', this.get_tree_params().length);\n },\n\n remove_param: function(param) {\n // Remove param from tree.\n param.set('in_ptree', false);\n param.set('ptree_index', null);\n\n // Update ptree indices for remaining params.\n _(this.get_tree_params()).each(function(input, index) {\n // +1 to use 1-based indexing.\n input.set('ptree_index', index + 1);\n });\n },\n\n /**\n * Sets tree data using tool's inputs.\n */\n set_tree_data: function() {\n // Get samples for each parameter.\n var params_samples = _.map(this.get_tree_params(), function(param) {\n return {\n param: param,\n samples: param.get_samples()\n };\n });\n var node_id = 0,\n // Creates tree data recursively.\n create_tree_data = function(params_samples, index) {\n var param_samples = params_samples[index],\n param = param_samples.param,\n param_label = param.get('label'),\n settings = param_samples.samples;\n\n // Create leaves when last parameter setting is reached.\n if (params_samples.length - 1 === index) {\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting\n };\n });\n }\n\n // Recurse to handle other parameters.\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting,\n children: create_tree_data(params_samples, index + 1)\n };\n });\n };\n\n this.set('tree_data', {\n name: 'Root',\n id: node_id++,\n children: (params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null)\n });\n },\n\n get_tree_params: function() {\n // Filter and sort parameters to get list in tree.\n return _(this.get('tool').get('inputs').where( {in_ptree: true} ))\n .sortBy( function(input) { return input.get('ptree_index'); } );\n },\n\n /**\n * Returns number of leaves in tree.\n */\n get_num_leaves: function() {\n return this.get_tree_params().reduce(function(memo, param) { return memo * param.get_samples().length; }, 1);\n },\n\n /**\n * Returns array of ToolInputsSettings objects based on a node and its subtree.\n */\n get_node_settings: function(target_node) {\n // -- Get fixed settings from tool and parent nodes.\n\n // Start with tool's settings.\n var fixed_settings = this.get('tool').get_inputs_dict();\n\n // Get fixed settings using node's parents.\n var cur_node = target_node.parent;\n if (cur_node) {\n while(cur_node.depth !== 0) {\n fixed_settings[cur_node.param.get('name')] = cur_node.value;\n cur_node = cur_node.parent;\n }\n }\n\n // Walk subtree starting at clicked node to get full list of settings.\n var self = this,\n get_settings = function(node, settings) {\n // Add setting for this node. Root node does not have a param,\n // however.\n if (node.param) {\n settings[node.param.get('name')] = node.value;\n }\n\n if (!node.children) {\n // At leaf node, so return settings.\n return new ToolInputsSettings({\n inputs: self.get('tool').get('inputs'),\n values: settings\n });\n }\n else {\n // At interior node: return list of subtree settings.\n return _.flatten( _.map(node.children, function(c) { return get_settings(c, _.clone(settings)); }) );\n }\n },\n all_settings = get_settings(target_node, fixed_settings);\n\n // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.\n if (!_.isArray(all_settings)) { all_settings = [ all_settings ]; }\n\n return all_settings;\n },\n\n /**\n * Returns all nodes connected a particular node; this includes parents and children of the node.\n */\n get_connected_nodes: function(node) {\n var get_subtree_nodes = function(a_node) {\n if (!a_node.children) {\n return a_node;\n }\n else {\n // At interior node: return subtree nodes.\n return _.flatten( [a_node, _.map(a_node.children, function(c) { return get_subtree_nodes(c); })] );\n }\n };\n\n // Get node's parents.\n var parents = [],\n cur_parent = node.parent;\n while(cur_parent) {\n parents.push(cur_parent);\n cur_parent = cur_parent.parent;\n }\n\n return _.flatten([parents, get_subtree_nodes(node)]);\n },\n\n /**\n * Returns the leaf that corresponds to a settings collection.\n */\n get_leaf: function(settings) {\n var cur_node = this.get('tree_data'),\n find_child = function(children) {\n return _.find(children, function(child) {\n return settings[child.param.get('name')] === child.value;\n });\n };\n\n while (cur_node.children) {\n cur_node = find_child(cur_node.children);\n }\n return cur_node;\n },\n\n /**\n * Returns a list of parameters used in tree.\n */\n toJSON: function() {\n // FIXME: returning and jsonifying complete param causes trouble on the server side,\n // so just use essential attributes for now.\n return this.get_tree_params().map(function(param) {\n return {\n name: param.get('name'),\n min: param.get('min'),\n max: param.get('max'),\n num_samples: param.get('num_samples')\n };\n });\n }\n});\n\nvar SweepsterTrack = Backbone.Model.extend({\n defaults: {\n track: null,\n mode: 'Pack',\n settings: null,\n regions: null\n },\n\n initialize: function(options) {\n this.set('regions', options.regions);\n if (options.track) {\n // FIXME: find a better way to deal with needed URLs:\n var track_config = _.extend({\n data_url: Galaxy.root + 'dummy1',\n converted_datasets_state_url: Galaxy.root + 'dummy2'\n }, options.track);\n this.set('track', tracks.object_from_template(track_config, {}, null));\n }\n },\n\n same_settings: function(a_track) {\n var this_settings = this.get('settings'),\n other_settings = a_track.get('settings');\n for (var prop in this_settings) {\n if (!other_settings[prop] ||\n this_settings[prop] !== other_settings[prop]) {\n return false;\n }\n }\n return true;\n },\n\n toJSON: function() {\n return {\n track: this.get('track').to_dict(),\n settings: this.get('settings'),\n regions: this.get('regions')\n };\n }\n});\n\nvar TrackCollection = Backbone.Collection.extend({\n model: SweepsterTrack\n});\n\n/**\n * Sweepster visualization model.\n */\nvar SweepsterVisualization = visualization.Visualization.extend({\n defaults: _.extend({}, visualization.Visualization.prototype.defaults, {\n dataset: null,\n tool: null,\n parameter_tree: null,\n regions: null,\n tracks: null,\n default_mode: 'Pack'\n }),\n\n initialize: function(options) {\n this.set('dataset', new data.Dataset(options.dataset));\n this.set('tool', new tools.Tool(options.tool));\n this.set('regions', new visualization.GenomeRegionCollection(options.regions));\n this.set('tracks', new TrackCollection(options.tracks));\n\n var tool_with_samplable_inputs = this.get('tool');\n this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);\n // Remove complex parameters for now.\n tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional', 'text' ] );\n\n this.set('parameter_tree', new ToolParameterTree({\n tool: tool_with_samplable_inputs,\n config: options.tree_config\n }));\n },\n\n add_track: function(track) {\n this.get('tracks').add(track);\n },\n\n toJSON: function() {\n return {\n id: this.get('id'),\n title: 'Parameter exploration for dataset \\'' + this.get('dataset').get('name') + '\\'',\n type: 'sweepster',\n dataset_id: this.get('dataset').id,\n tool_id: this.get('tool').id,\n regions: this.get('regions').toJSON(),\n tree_config: this.get('parameter_tree').toJSON(),\n tracks: this.get('tracks').toJSON()\n };\n }\n});\n\n/**\n * --- Views ---\n */\n\n/**\n * Sweepster track view.\n */\nvar SweepsterTrackView = Backbone.View.extend({\n tagName: 'tr',\n\n TILE_LEN: 250,\n\n initialize: function(options) {\n this.canvas_manager = options.canvas_manager;\n this.render();\n this.model.on('change:track change:mode', this.draw_tiles, this);\n },\n\n render: function() {\n // Render settings icon and popup.\n // TODO: use template.\n var settings = this.model.get('settings'),\n values = settings.get('values'),\n settings_td = $('').addClass('settings').appendTo(this.$el),\n settings_div = $('').addClass('track-info').hide().appendTo(settings_td);\n settings_div.append( $('').css('font-weight', 'bold').text('Track Settings') );\n settings.get('inputs').each(function(input) {\n settings_div.append( input.get('label') + ': ' + values[input.get('name')] + '
');\n });\n var self = this,\n run_on_dataset_button = $('').appendTo(settings_div).text('Run on complete dataset').click(function() {\n settings_div.toggle();\n self.trigger('run_on_dataset', settings);\n });\n var icon_menu = mod_icon_btn.create_icon_buttons_menu([\n {\n title: 'Settings',\n icon_class: 'gear track-settings',\n on_click: function() {\n settings_div.toggle();\n }\n },\n {\n title: 'Remove',\n icon_class: 'cross-circle',\n on_click: function() {\n self.$el.remove();\n $('.tooltip').remove();\n // TODO: remove track from viz collection.\n }\n }\n ]);\n settings_td.prepend(icon_menu.$el);\n\n // Render tile placeholders.\n this.model.get('regions').each(function() {\n self.$el.append($('').addClass('tile').html(\n $(' ').attr('src', Galaxy.root + 'images/loading_large_white_bg.gif')\n ));\n });\n\n if (this.model.get('track')) {\n this.draw_tiles();\n }\n },\n\n /**\n * Draw tiles for regions.\n */\n draw_tiles: function() {\n var self = this,\n track = this.model.get('track'),\n regions = this.model.get('regions'),\n tile_containers = this.$el.find('td.tile');\n\n // Do nothing if track is not defined.\n if (!track) { return; }\n\n // When data is ready, draw tiles.\n $.when(track.data_manager.data_is_ready()).then(function(data_ok) {\n // Draw tile for each region.\n regions.each(function(region, index) {\n var resolution = region.length() / self.TILE_LEN,\n w_scale = 1/resolution,\n mode = self.model.get('mode');\n $.when(track.data_manager.get_data(region, mode, resolution, {})).then(function(tile_data) {\n var canvas = self.canvas_manager.new_canvas();\n canvas.width = self.TILE_LEN;\n canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width);\n track.draw_tile(tile_data, canvas.getContext('2d'), mode, region, w_scale);\n $(tile_containers[index]).empty().append(canvas);\n });\n });\n });\n }\n});\n\n/**\n * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as\n * it augments an existing input form row rather than creates a completely new HTML element.\n */\nvar ToolInputValOrSweepView = Backbone.View.extend({\n\n // Template for rendering sweep inputs:\n number_input_template: '
' +\n '\"> - ' +\n '\">' +\n ' samples: \">' +\n '',\n\n select_input_template: '<%= options %>',\n\n initialize: function(options) {\n this.$el = options.tool_row;\n this.render();\n },\n\n render: function() {\n var input = this.model,\n type = input.get('type'),\n single_input_row = this.$el.find('.form-row-input'),\n sweep_inputs_row = null;\n\n // Update tool inputs as single input changes.\n single_input_row.find(':input').change(function() {\n input.set('value', $(this).val());\n });\n\n // Add row for parameter sweep inputs.\n if (input instanceof tools.IntegerToolParameter) {\n sweep_inputs_row = $( _.template(this.number_input_template)(this.model.toJSON()) );\n }\n else if (input instanceof tools.SelectToolParameter) {\n var options = _.map(this.$el.find('select option'), function(option) {\n return $(option).val();\n }),\n options_text = options.join(', ');\n sweep_inputs_row = $( _.template(this.select_input_template)({\n options: options_text\n }) );\n }\n sweep_inputs_row.insertAfter(single_input_row);\n\n // Add buttons for adding/removing parameter.\n var self = this,\n menu = mod_icon_btn.create_icon_buttons_menu([\n {\n title: 'Add parameter to tree',\n icon_class: 'plus-button',\n on_click: function () {\n input.set('in_ptree', true);\n single_input_row.hide();\n sweep_inputs_row.show();\n $(this).hide();\n self.$el.find('.icon-button.toggle').show();\n }\n\n },\n {\n title: 'Remove parameter from tree',\n icon_class: 'toggle',\n on_click: function() {\n // Remove parameter from tree params where name matches clicked paramter.\n input.set('in_ptree', false);\n sweep_inputs_row.hide();\n single_input_row.show();\n $(this).hide();\n self.$el.find('.icon-button.plus-button').show();\n }\n }\n ],\n {\n\n });\n this.$el.prepend(menu.$el);\n\n // Show/hide input rows and icons depending on whether parameter is in the tree.\n if (input.get('in_ptree')) {\n single_input_row.hide();\n self.$el.find('.icon-button.plus-button').hide();\n }\n else {\n self.$el.find('.icon-button.toggle').hide();\n sweep_inputs_row.hide();\n }\n\n // Update input's min, max, number of samples as values change.\n _.each(['min', 'max', 'num_samples'], function(attr) {\n sweep_inputs_row.find('.' + attr).change(function() {\n input.set(attr, parseFloat( $(this).val() ));\n });\n });\n }\n});\n\nvar ToolParameterTreeDesignView = Backbone.View.extend({\n className: 'tree-design',\n\n initialize: function(options) {\n this.render();\n },\n\n render: function() {\n // Start with tool form view.\n var tool_form_view = new tools.ToolFormView({\n model: this.model.get('tool')\n });\n tool_form_view.render();\n this.$el.append(tool_form_view.$el);\n\n // Set up views for each tool input.\n var self = this,\n inputs = self.model.get('tool').get('inputs');\n this.$el.find('.form-row').not('.form-actions').each(function(i) {\n var input_view = new ToolInputValOrSweepView({\n model: inputs.at(i),\n tool_row: $(this)\n });\n });\n }\n});\n\n/**\n * Displays and updates parameter tree.\n */\nvar ToolParameterTreeView = Backbone.View.extend({\n className: 'tool-parameter-tree',\n\n initialize: function(options) {\n // When tree data changes, re-render.\n this.model.on('change:tree_data', this.render, this);\n },\n\n render: function() {\n // Start fresh.\n this.$el.children().remove();\n\n var tree_params = this.model.get_tree_params();\n if (!tree_params.length) {\n return;\n }\n\n // Set width, height based on params and samples.\n this.width = 100 * (2 + tree_params.length);\n this.height = 15 * this.model.get_num_leaves();\n\n var self = this;\n\n // Layout tree.\n var cluster = d3.layout.cluster()\n .size([this.height, this.width - 160]);\n\n var diagonal = d3.svg.diagonal()\n .projection(function(d) { return [d.y, d.x]; });\n\n // Layout nodes.\n var nodes = cluster.nodes(this.model.get('tree_data'));\n\n // Setup and add labels for tree levels.\n var param_depths = _.uniq(_.pluck(nodes, \"y\"));\n _.each(tree_params, function(param, index) {\n var x = param_depths[index+1],\n center_left = $('#center').position().left;\n self.$el.append( $('').addClass('label')\n .text(param.get('label'))\n .css('left', x + center_left) );\n });\n\n // Set up vis element.\n var vis = d3.select(this.$el[0])\n .append(\"svg\")\n .attr(\"width\", this.width)\n .attr(\"height\", this.height + 30)\n .append(\"g\")\n .attr(\"transform\", \"translate(40, 20)\");\n\n // Draw links.\n var link = vis.selectAll(\"path.link\")\n .data(cluster.links(nodes))\n .enter().append(\"path\")\n .attr(\"class\", \"link\")\n .attr(\"d\", diagonal);\n\n // Draw nodes.\n var node = vis.selectAll(\"g.node\")\n .data(nodes)\n .enter().append(\"g\")\n .attr(\"class\", \"node\")\n .attr(\"transform\", function(d) { return \"translate(\" + d.y + \",\" + d.x + \")\"; })\n .on('mouseover', function(a_node) {\n var connected_node_ids = _.pluck(self.model.get_connected_nodes(a_node), 'id');\n // TODO: probably can use enter() to do this more easily.\n node.filter(function(d) {\n return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;\n }).style('fill', '#f00');\n })\n .on('mouseout', function() {\n node.style('fill', '#000');\n });\n\n node.append(\"circle\")\n .attr(\"r\", 9);\n\n node.append(\"text\")\n .attr(\"dx\", function(d) { return d.children ? -12 : 12; })\n .attr(\"dy\", 3)\n .attr(\"text-anchor\", function(d) { return d.children ? \"end\" : \"start\"; })\n .text(function(d) { return d.name; });\n }\n});\n\n/**\n * Sweepster visualization view. View requires rendering in 3-panel setup for now.\n */\nvar SweepsterVisualizationView = Backbone.View.extend({\n className: 'Sweepster',\n\n helpText:\n '',\n\n initialize: function(options) {\n this.canvas_manager = new visualization.CanvasManager(this.$el.parents('body'));\n this.tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') });\n this.track_collection_container = $('Getting Started
' +\n '').addClass('tracks');\n\n // Handle node clicks for tree data.\n this.model.get('parameter_tree').on('change:tree_data', this.handle_node_clicks, this);\n\n // Each track must have a view so it has a canvas manager.\n var self = this;\n this.model.get('tracks').each(function(track) {\n track.get('track').view = self;\n });\n\n // Set block, reverse strand block colors; these colors will be used for all tracks.\n this.config = config.ConfigSettingCollection.from_models_and_saved_values(\n [\n { key: 'name', label: 'Name', type: 'text', default_value: '' },\n { key: 'a_color', label: 'A Color', type: 'color', default_value: \"#FF0000\" },\n { key: 'c_color', label: 'C Color', type: 'color', default_value: \"#00FF00\" },\n { key: 'g_color', label: 'G Color', type: 'color', default_value: \"#0000FF\" },\n { key: 't_color', label: 'T Color', type: 'color', default_value: \"#FF00FF\" },\n { key: 'n_color', label: 'N Color', type: 'color', default_value: \"#AAAAAA\" },\n { key: 'block_color', label: 'Block color', type: 'color' },\n { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },\n ], {}\n );\n },\n\n render: function() {\n // Render tree design view in left panel.\n var tree_design_view = new ToolParameterTreeDesignView({\n model: this.model.get('parameter_tree')\n });\n\n $('#left').append(tree_design_view.$el);\n\n // Render track collection container/view in right panel.\n var self = this,\n regions = self.model.get('regions'),\n tr = $('
').appendTo(this.track_collection_container);\n\n regions.each(function(region) {\n tr.append( $(' ').text(region.toString()) );\n });\n tr.children().first().attr('colspan', 2);\n\n var tracks_div = $(' ').addClass('tiles');\n $('#right').append( tracks_div.append(this.track_collection_container) );\n\n self.model.get('tracks').each(function(track) {\n self.add_track(track);\n });\n\n // -- Render help and tool parameter tree in center panel. --\n\n // Help includes text and a close button.\n var help_div = $(this.helpText).addClass('help'),\n close_button = mod_icon_btn.create_icon_buttons_menu([\n {\n title: 'Close',\n icon_class: 'cross-circle',\n on_click: function() {\n $('.tooltip').remove();\n help_div.remove();\n }\n }\n ]);\n\n help_div.prepend(close_button.$el.css('float', 'right'));\n $('#center').append(help_div);\n\n // Parameter tree:\n this.tool_param_tree_view.render();\n $('#center').append(this.tool_param_tree_view.$el);\n\n // Set up handler for tree node clicks.\n this.handle_node_clicks();\n\n // Set up visualization menu.\n var menu = mod_icon_btn.create_icon_buttons_menu(\n [\n // Save.\n /*\n { icon_class: 'disk--arrow', title: 'Save', on_click: function() {\n // Show saving dialog box\n show_modal(\"Saving...\", \"progress\");\n\n viz.save().success(function(vis_info) {\n hide_modal();\n viz.set({\n 'id': vis_info.vis_id,\n 'has_changes': false\n });\n })\n .error(function() {\n show_modal( \"Could Not Save\", \"Could not save visualization. Please try again later.\",\n { \"Close\" : hide_modal } );\n });\n } },\n */\n // Change track modes.\n {\n icon_class: 'chevron-expand',\n title: 'Set display mode'\n },\n // Close viz.\n {\n icon_class: 'cross-circle',\n title: 'Close',\n on_click: function() {\n window.location = \"${h.url_for( controller='visualization', action='list' )}\";\n }\n }\n ],\n {\n tooltip_config: {placement: 'bottom'}\n });\n\n // Create mode selection popup. Mode selection changes default mode and mode for all tracks.\n var modes = ['Squish', 'Pack'],\n mode_mapping = {};\n _.each(modes, function(mode) {\n mode_mapping[mode] = function() {\n self.model.set('default_mode', mode);\n self.model.get('tracks').each(function(track) {\n track.set('mode', mode);\n });\n };\n });\n\n make_popupmenu(menu.$el.find('.chevron-expand'), mode_mapping);\n\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#right .unified-panel-header-inner\").append(menu.$el);\n },\n\n get_base_color: function(base) {\n return this.config.get_value(base.toLowerCase() + '_color') ||\n this.config.get_value('n_color');\n },\n\n run_tool_on_dataset: function(settings) {\n var tool = this.model.get('tool'),\n tool_name = tool.get('name'),\n dataset = this.model.get('dataset');\n tool.set_input_values(settings.get('values'));\n $.when(tool.rerun(dataset)).then(function(outputs) {\n // TODO.\n });\n\n show_modal('Running ' + tool_name + ' on complete dataset',\n tool_name + ' is running on dataset \\'' +\n dataset.get('name') + '\\'. Outputs are in the dataset\\'s history.',\n {\n 'Ok': function() { hide_modal(); }\n });\n },\n\n /**\n * Add track to model and view.\n */\n add_track: function(pm_track) {\n var self = this,\n param_tree = this.model.get('parameter_tree');\n\n // Add track to model.\n self.model.add_track(pm_track);\n\n var track_view = new SweepsterTrackView({\n model: pm_track,\n canvas_manager: self.canvas_manager\n });\n track_view.on('run_on_dataset', self.run_tool_on_dataset, self);\n self.track_collection_container.append(track_view.$el);\n track_view.$el.hover(function() {\n var settings_leaf = param_tree.get_leaf(pm_track.get('settings').get('values'));\n var connected_node_ids = _.pluck(param_tree.get_connected_nodes(settings_leaf), 'id');\n\n // TODO: can do faster with enter?\n d3.select(self.tool_param_tree_view.$el[0]).selectAll(\"g.node\")\n .filter(function(d) {\n return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;\n }).style('fill', '#f00');\n },\n function() {\n d3.select(self.tool_param_tree_view.$el[0]).selectAll(\"g.node\").style('fill', '#000');\n });\n return pm_track;\n },\n\n /**\n * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of\n * the settings defined by the node's subtree and tracks are added for each run.\n */\n handle_node_clicks: function() {\n // When node clicked in tree, run tool and add tracks to model.\n var self = this,\n param_tree = this.model.get('parameter_tree'),\n regions = this.model.get('regions'),\n node = d3.select(this.tool_param_tree_view.$el[0]).selectAll(\"g.node\");\n node.on(\"click\", function(d, i) {\n // Get all settings corresponding to node.\n var tool = self.model.get('tool'),\n dataset = self.model.get('dataset'),\n all_settings = param_tree.get_node_settings(d),\n run_jobs_deferred = $.Deferred();\n\n // Do not allow 10+ jobs to be run.\n if (all_settings.length >= 10) {\n show_modal(\"Whoa there cowboy!\",\n \"You clicked on a node to try \" + self.model.get('tool').get('name') +\n \" with \" + all_settings.length +\n \" different combinations of settings. You can only run 10 jobs at a time.\",\n {\n \"Ok\": function() { hide_modal(); run_jobs_deferred.resolve(false); }\n });\n }\n else {\n run_jobs_deferred.resolve(true);\n }\n\n // Take action when deferred resolves.\n $.when(run_jobs_deferred).then(function(run_jobs) {\n if (!run_jobs) { return; }\n\n // Create and add tracks for each settings group.\n var new_tracks = _.map(all_settings, function(settings) {\n var pm_track = new SweepsterTrack({\n settings: settings,\n regions: regions,\n mode: self.model.get('default_mode')\n });\n self.add_track(pm_track);\n return pm_track;\n });\n\n // For each track, run tool using track's settings and update track.\n _.each(new_tracks, function(pm_track, index) {\n setTimeout(function() {\n // Set inputs and run tool.\n tool.set_input_values(pm_track.get('settings').get('values'));\n $.when(tool.rerun(dataset, regions)).then(function(output) {\n // HACKish: output is an HDA with track config attribute. To create a track\n // that works correctly with Backbone relational, it is necessary to\n // use a modified version of the track config.\n var dataset = output.first(),\n track_config = dataset.get('track_config');\n // Set dataset to be the tool's output.\n track_config.dataset = dataset;\n // Set tool to null so that it is not unpacked; unpacking it messes with\n // the tool parameters and parameter tree.\n track_config.tool = null;\n\n track_config.prefs = self.config.to_key_value_dict();\n\n // Create and add track for output dataset.\n var track_obj = tracks.object_from_template(track_config, self, null);\n track_obj.init_for_tool_data();\n\n pm_track.set('track', track_obj);\n });\n }, index * 10000);\n });\n });\n });\n }\n});\n\nreturn {\n SweepsterVisualization: SweepsterVisualization,\n SweepsterVisualizationView: SweepsterVisualizationView\n};\n\n});\n"]} \ No newline at end of file diff --git a/static/maps/viz/visualization.js.map b/static/maps/viz/visualization.js.map index f9d8ebae972..f68019cc7c0 100644 --- a/static/maps/viz/visualization.js.map +++ b/static/maps/viz/visualization.js.map @@ -1 +1 @@ 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[\"libs/underscore\", \"mvc/dataset/data\", \"viz/trackster/util\", \"utils/config\", \"mvc/grid/grid-view\", \"mvc/ui/ui-tabs\", \"mvc/ui/ui-misc\"], function(_, data_mod, util_mod, config_mod, GridView, Tabs, Ui) {\n\n/**\n * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes\n * to include in the representation; to_json_mappers defines mappers for returned objects.\n */\nvar CustomToJSON = {\n /**\n * Returns JSON representation of object using to_json_keys and to_json_mappers.\n */\n toJSON: function() {\n var self = this,\n json = {};\n _.each(self.constructor.to_json_keys, function(k) {\n var val = self.get(k);\n if (k in self.constructor.to_json_mappers) {\n val = self.constructor.to_json_mappers[k](val, self);\n }\n json[k] = val;\n });\n return json;\n }\n};\n\n/**\n * Model, view, and controller objects for Galaxy visualization framework.\n *\n * Models have no references to views, instead using events to indicate state\n * changes; this is advantageous because multiple views can use the same object\n * and models can be used without views.\n */\n\n/**\n * Use a popup grid to select datasets from histories or libraries. After datasets are selected,\n * track definitions are obtained from the server and the success_fn is called with the list of\n * definitions for selected datasets.\n */\nvar select_datasets = function(filters, success_fn) {\n // history dataset selection tab\n var history_grid = new GridView({\n url_base : Galaxy.root + 'visualization/list_history_datasets',\n filters : filters,\n dict_format : true,\n embedded : true\n });\n\n // library dataset selection tab\n var library_grid = new GridView( {\n url_base : Galaxy.root + 'visualization/list_library_datasets',\n dict_format : true,\n embedded : true\n });\n\n // build tabs\n var tabs = new Tabs.View();\n tabs.add({ id : 'histories',\n title : 'Histories',\n $el : $( '' ).append( history_grid.$el )\n });\n tabs.add({ id : 'libraries',\n title : 'Libraries',\n $el : $( '' ).append( library_grid.$el )\n });\n\n // modal\n Galaxy.modal.show({\n title : 'Select datasets for new tracks',\n body : tabs.$el,\n closing_events : true,\n buttons : {\n 'Cancel': function() {\n Galaxy.modal.hide();\n },\n 'Add': function() {\n var requests = [];\n tabs.$('input.grid-row-select-checkbox[name=id]:checked').each(function() {\n window.console.log( $(this).val() );\n requests[requests.length] = $.ajax({\n url : Galaxy.root + 'api/datasets/' + $(this).val(),\n dataType : 'json',\n data : {\n data_type : 'track_config',\n hda_ldda : tabs.current() == 'histories' ? 'hda' : 'ldda'\n }\n });\n });\n // To preserve order, wait until there are definitions for all tracks and then add\n // them sequentially.\n $.when.apply($, requests).then(function() {\n // jQuery always returns an Array for arguments, so need to look at first element\n // to determine whether multiple requests were made and consequently how to\n // map arguments to track definitions.\n var track_defs = ( arguments[0] instanceof Array ?\n $.map(arguments, function(arg) { return arg[0]; }) :\n [ arguments[0] ] );\n success_fn(track_defs);\n });\n Galaxy.modal.hide();\n }\n }\n });\n};\n\n// --------- Models ---------\n\n/**\n * Canvas manager is used to create canvases for browsers as well as providing a pattern cache\n */\nvar CanvasManager = function(default_font) {\n this.default_font = default_font !== undefined ? default_font : \"9px Monaco, Lucida Console, monospace\";\n\n this.dummy_canvas = this.new_canvas();\n this.dummy_context = this.dummy_canvas.getContext('2d');\n this.dummy_context.font = this.default_font;\n\n this.char_width_px = this.dummy_context.measureText(\"A\").width;\n\n this.patterns = {};\n\n // FIXME: move somewhere to make this more general\n this.load_pattern( 'right_strand', \"/visualization/strand_right.png\" );\n this.load_pattern( 'left_strand', \"/visualization/strand_left.png\" );\n this.load_pattern( 'right_strand_inv', \"/visualization/strand_right_inv.png\" );\n this.load_pattern( 'left_strand_inv', \"/visualization/strand_left_inv.png\" );\n};\n\n_.extend( CanvasManager.prototype, {\n load_pattern: function( key, path ) {\n var patterns = this.patterns,\n dummy_context = this.dummy_context,\n image = new Image();\n image.src = Galaxy.root + \"static/images\" + path;\n image.onload = function() {\n patterns[key] = dummy_context.createPattern( image, \"repeat\" );\n };\n },\n get_pattern: function( key ) {\n return this.patterns[key];\n },\n new_canvas: function() {\n var canvas = $(\"\")[0];\n // Keep a reference back to the manager\n canvas.manager = this;\n return canvas;\n }\n});\n\n/**\n * Generic cache that handles key/value pairs. Keys can be any object that can be\n * converted to a String and compared.\n */\nvar Cache = Backbone.Model.extend({\n defaults: {\n num_elements: 20,\n // Objects in cache; indexes into cache are strings of keys.\n obj_cache: null,\n // key_ary contains keys for objects in cache.\n key_ary: null\n },\n\n initialize: function(options) {\n this.clear();\n },\n\n /**\n * Get an element from the cache using its key.\n */\n get_elt: function(key) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n index = _.indexOf(key_ary, function(k) {\n return k.toString() === key_str;\n });\n\n // Update cache.\n if (index !== -1) {\n // Object is in cache, so update it.\n if (obj_cache[key_str].stale) {\n // Object is stale: remove key and object.\n key_ary.splice(index, 1);\n delete obj_cache[key_str];\n }\n else {\n // Move key to back because it is most recently used.\n this.move_key_to_end(key, index);\n }\n }\n\n return obj_cache[key_str];\n },\n\n /**\n * Put an element into the cache.\n */\n set_elt: function(key, value) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n num_elements = this.attributes.num_elements;\n\n // Update keys, objects.\n if (!obj_cache[key_str]) {\n // Add object to cache.\n\n if (key_ary.length >= num_elements) {\n // Cache full, so remove first element.\n var deleted_key = key_ary.shift();\n delete obj_cache[deleted_key.toString()];\n }\n\n // Add key.\n key_ary.push(key);\n }\n\n // Add object.\n obj_cache[key_str] = value;\n return value;\n },\n\n /**\n * Move key to end of cache. Keys are removed from the front, so moving a key to the end\n * delays the key's removal.\n */\n move_key_to_end: function(key, index) {\n this.attributes.key_ary.splice(index, 1);\n this.attributes.key_ary.push(key);\n },\n\n /**\n * Clear all elements from the cache.\n */\n clear: function() {\n this.attributes.obj_cache = {};\n this.attributes.key_ary = [];\n },\n\n /** Returns the number of elements in the cache. */\n size: function() {\n return this.attributes.key_ary.length;\n },\n\n /** Returns key most recently added to cache. */\n most_recently_added: function() {\n return this.size() === 0 ? null :\n // Most recent key is at the end of key array.\n this.attributes.key_ary[this.attributes.key_ary.length - 1];\n }\n});\n\n/**\n * Data manager for genomic data. Data is connected to and queryable by genomic regions.\n */\nvar GenomeDataManager = Cache.extend({\n defaults: _.extend({}, Cache.prototype.defaults, {\n dataset: null,\n genome: null,\n init_data: null,\n min_region_size: 200,\n filters_manager: null,\n data_type: \"data\",\n data_mode_compatible: function(entry, mode) { return true; },\n can_subset: function(entry) { return false; }\n }),\n\n /**\n * Initialization.\n */\n initialize: function(options) {\n Cache.prototype.initialize.call(this);\n\n // Set initial entries in data manager.\n var initial_entries = this.get('init_data');\n if (initial_entries) {\n this.add_data(initial_entries);\n }\n },\n\n /**\n * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type.\n * If necessary, manager size is increased to hold all data.\n */\n add_data: function(entries) {\n // Increase size to accomodate all entries.\n if (this.get('num_elements') < entries.length) {\n this.set('num_elements', entries.length);\n }\n\n // Put data into manager.\n var self = this;\n _.each(entries, function(entry) {\n self.set_data(entry.region, entry);\n });\n },\n\n /**\n * Returns deferred that resolves to true when dataset is ready (or false if dataset\n * cannot be used).\n */\n data_is_ready: function() {\n var dataset = this.get('dataset'),\n ready_deferred = $.Deferred(),\n // If requesting raw data, query dataset state; if requesting (converted) data,\n // need to query converted datasets state.\n query_type = (this.get('data_type') === 'raw_data' ? 'state' :\n this.get('data_type') === 'data' ? 'converted_datasets_state' : \"error\" ),\n ss_deferred = new util_mod.ServerStateDeferred({\n ajax_settings: {\n url: this.get('dataset').url(),\n data: {\n hda_ldda: dataset.get('hda_ldda'),\n data_type: query_type\n },\n dataType: \"json\"\n },\n interval: 5000,\n success_fn: function(response) { return response !== \"pending\"; }\n });\n\n $.when(ss_deferred.go()).then(function(response) {\n ready_deferred.resolve(response === \"ok\" || response === \"data\" );\n });\n return ready_deferred;\n },\n\n /**\n * Perform a feature search from server; returns Deferred object that resolves when data is available.\n */\n search_features: function(query) {\n var dataset = this.get('dataset'),\n params = {\n query: query,\n hda_ldda: dataset.get('hda_ldda'),\n data_type: 'features'\n };\n return $.getJSON(dataset.url(), params);\n },\n\n /**\n * Load data from server and manages data entries. Adds a Deferred to manager\n * for region; when data becomes available, replaces Deferred with data.\n * Returns the Deferred that resolves when data is available.\n */\n load_data: function(region, mode, resolution, extra_params) {\n // Setup data request params.\n var dataset = this.get('dataset'),\n params = {\n \"data_type\": this.get('data_type'),\n \"chrom\": region.get('chrom'),\n \"low\": region.get('start'),\n \"high\": region.get('end'),\n \"mode\": mode,\n \"resolution\": resolution,\n \"hda_ldda\": dataset.get('hda_ldda')\n };\n\n $.extend(params, extra_params);\n\n // Add track filters to params.\n var filters_manager = this.get('filters_manager');\n if (filters_manager) {\n var filter_names = [];\n var filters = filters_manager.filters;\n for (var i = 0; i < filters.length; i++) {\n filter_names.push(filters[i].name);\n }\n params.filter_cols = JSON.stringify(filter_names);\n }\n\n // Do request.\n var manager = this,\n entry = $.getJSON(dataset.url(), params, function (result) {\n // Add region to the result.\n result.region = region;\n manager.set_data(region, result);\n });\n\n this.set_data(region, entry);\n return entry;\n },\n\n /**\n * Get data from dataset.\n */\n get_data: function(region, mode, resolution, extra_params) {\n // Look for entry and return if it's a deferred or if data available is compatible with mode.\n var entry = this.get_elt(region);\n if ( entry &&\n ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) {\n return entry;\n }\n\n //\n // Look in cache for data that can be used.\n // TODO: this logic could be improved if the visualization knew whether\n // the data was \"index\" or \"data.\"\n //\n var key_ary = this.get('key_ary'),\n obj_cache = this.get('obj_cache'),\n entry_region, is_subregion;\n for (var i = 0; i < key_ary.length; i++) {\n entry_region = key_ary[i];\n\n if (entry_region.contains(region)) {\n is_subregion = true;\n\n // This entry has data in the requested range. Return if data\n // is compatible and can be subsetted.\n entry = obj_cache[entry_region.toString()];\n if ( util_mod.is_deferred(entry) ||\n ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) {\n this.move_key_to_end(entry_region, i);\n\n // If there's data, subset it.\n if ( !util_mod.is_deferred(entry) ) {\n var subset_entry = this.subset_entry(entry, region);\n this.set_data(region, subset_entry);\n entry = subset_entry;\n }\n\n return entry;\n }\n }\n }\n\n // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be\n // subsetted. For these cases, do not increase length because region will never be found (and\n // an infinite loop will occur.)\n // If needed, extend region to make it minimum size.\n if (!is_subregion && region.length() < this.attributes.min_region_size) {\n // IDEA: alternative heuristic is to find adjacent cache entry to region and use that to extend.\n // This would prevent bad extensions when zooming in/out while still preserving the behavior\n // below.\n\n // Use copy of region to avoid changing actual region.\n region = region.copy();\n\n // Use heuristic to extend region: extend relative to last data request.\n var last_request = this.most_recently_added();\n if (!last_request || (region.get('start') > last_request.get('start'))) {\n // This request is after the last request, so extend right.\n region.set('end', region.get('start') + this.attributes.min_region_size);\n }\n else {\n // This request is after the last request, so extend left.\n region.set('start', region.get('end') - this.attributes.min_region_size);\n }\n\n // Trim region to avoid invalid coordinates.\n region.set('genome', this.attributes.genome);\n region.trim();\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Alias for set_elt for readbility.\n */\n set_data: function(region, entry) {\n this.set_elt(region, entry);\n },\n\n /** \"Deep\" data request; used as a parameter for DataManager.get_more_data() */\n DEEP_DATA_REQ: \"deep\",\n\n /** \"Broad\" data request; used as a parameter for DataManager.get_more_data() */\n BROAD_DATA_REQ: \"breadth\",\n\n /**\n * Gets more data for a region using either a depth-first or a breadth-first approach.\n */\n get_more_data: function(region, mode, resolution, extra_params, req_type) {\n var cur_data = this._mark_stale(region);\n if (!(cur_data && this.get('data_mode_compatible')(cur_data, mode))) {\n console.log('ERROR: problem with getting more data: current data is not compatible');\n return;\n }\n\n //\n // Set parameters based on request type.\n //\n var query_low = region.get('start');\n if (req_type === this.DEEP_DATA_REQ) {\n // Use same interval but set start_val to skip data that's already in cur_data.\n $.extend(extra_params, {start_val: cur_data.data.length + 1});\n }\n else if (req_type === this.BROAD_DATA_REQ) {\n // To get past an area of extreme feature depth, set query low to be after either\n // (a) the maximum high or HACK/FIXME (b) the end of the last feature returned.\n query_low = (cur_data.max_high ? cur_data.max_high : cur_data.data[cur_data.data.length - 1][2]) + 1;\n }\n var query_region = region.copy().set('start', query_low);\n\n //\n // Get additional data, append to current data, and set new data. Use a custom deferred object\n // to signal when new data is available.\n //\n var data_manager = this,\n new_data_request = this.load_data(query_region, mode, resolution, extra_params),\n new_data_available = $.Deferred();\n // load_data sets cache to new_data_request, but use custom deferred object so that signal and data\n // is all data, not just new data.\n this.set_data(region, new_data_available);\n $.when(new_data_request).then(function(result) {\n // Update data and message.\n if (result.data) {\n result.data = cur_data.data.concat(result.data);\n if (result.max_low) {\n result.max_low = cur_data.max_low;\n }\n if (result.message) {\n // HACK: replace number in message with current data length. Works but is ugly.\n result.message = result.message.replace(/[0-9]+/, result.data.length);\n }\n }\n data_manager.set_data(region, result);\n new_data_available.resolve(result);\n });\n return new_data_available;\n },\n\n /**\n * Returns true if more detailed data can be obtained for entry.\n */\n can_get_more_detailed_data: function(region) {\n var cur_data = this.get_elt(region);\n\n // Can only get more detailed data for bigwig data that has less than 8000 data points.\n // Summary tree returns *way* too much data, and 8000 data points ~ 500KB.\n return (cur_data.dataset_type === 'bigwig' && cur_data.data.length < 8000);\n },\n\n /**\n * Returns more detailed data for an entry.\n */\n get_more_detailed_data: function(region, mode, resolution, detail_multiplier, extra_params) {\n // Mark current entry as stale.\n var cur_data = this._mark_stale(region);\n if (!cur_data) {\n console.log(\"ERROR getting more detailed data: no current data\");\n return;\n }\n\n if (!extra_params) { extra_params = {}; }\n\n // Use additional parameters to get more detailed data.\n if (cur_data.dataset_type === 'bigwig') {\n // FIXME: constant should go somewhere.\n extra_params.num_samples = 1000 * detail_multiplier;\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Marks cache data as stale.\n */\n _mark_stale: function(region) {\n var entry = this.get_elt(region);\n if (!entry) {\n console.log(\"ERROR: no data to mark as stale: \", this.get('dataset'), region.toString());\n }\n entry.stale = true;\n return entry;\n },\n\n /**\n * Returns an array of data with each entry representing one chromosome/contig\n * of data or, if data is not available, returns a Deferred that resolves to the\n * data when it becomes available.\n */\n get_genome_wide_data: function(genome) {\n // -- Get all data. --\n\n var self = this,\n all_data_available = true,\n\n // Map chromosome info into genome data.\n gw_data = _.map(genome.get('chroms_info').chrom_info, function(chrom_info) {\n var chrom_data = self.get_elt(\n new GenomeRegion({\n chrom: chrom_info.chrom,\n start: 0,\n end: chrom_info.len\n })\n );\n\n // Set flag if data is not available.\n if (!chrom_data) { all_data_available = false; }\n\n return chrom_data;\n });\n\n // -- If all data is available, return it. --\n if (all_data_available) {\n return gw_data;\n }\n\n // -- All data is not available, so load from server. --\n\n var deferred = $.Deferred();\n $.getJSON(this.get('dataset').url(), { data_type: 'genome_data' }, function(genome_wide_data) {\n self.add_data(genome_wide_data.data);\n deferred.resolve(genome_wide_data.data);\n });\n\n return deferred;\n },\n\n /**\n * Returns entry with only data in the subregion.\n */\n subset_entry: function(entry, subregion) {\n // Dictionary from entry type to function for subsetting data.\n var subset_fns = {\n bigwig: function(data, subregion) {\n return _.filter(data, function(data_point) {\n return data_point[0] >= subregion.get('start') &&\n data_point[0] <= subregion.get('end');\n });\n },\n refseq: function(data, subregion) {\n var seq_start = subregion.get('start') - entry.region.get('start');\n return entry.data.slice(seq_start, seq_start + subregion.length());\n }\n };\n\n // Subset entry if there is a function for subsetting and regions are not the same.\n var subregion_data = entry.data;\n if (!entry.region.same(subregion) && entry.dataset_type in subset_fns) {\n subregion_data = subset_fns[entry.dataset_type](entry.data, subregion);\n }\n\n // Return entry with subregion's data.\n return {\n region: subregion,\n data: subregion_data,\n dataset_type: entry.dataset_type\n };\n }\n});\n\nvar GenomeReferenceDataManager = GenomeDataManager.extend({\n initialize: function(options) {\n // Use generic object in place of dataset and set urlRoot to fetch data.\n var dataset_placeholder = new Backbone.Model();\n dataset_placeholder.urlRoot = options.data_url;\n this.set('dataset', dataset_placeholder);\n },\n\n load_data: function(region, mode, resolution, extra_params) {\n // Fetch data if region is not too large.\n return ( region.length() <= 100000 ?\n GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params) :\n { data: null, region: region } );\n }\n});\n\n/**\n * A genome build.\n */\nvar Genome = Backbone.Model.extend({\n defaults: {\n name: null,\n key: null,\n chroms_info: null\n },\n\n initialize: function(options) {\n this.id = options.dbkey;\n },\n\n /**\n * Shorthand for getting to chromosome information.\n */\n get_chroms_info: function() {\n return this.attributes.chroms_info.chrom_info;\n },\n\n /**\n * Returns a GenomeRegion object denoting a complete chromosome.\n */\n get_chrom_region: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) {\n return chrom_info.chrom === chr_name;\n });\n return new GenomeRegion({\n chrom: chrom_info.chrom,\n end: chrom_info.len\n });\n },\n\n /** Returns the length of a chromosome. */\n get_chrom_len: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n return _.find(this.get_chroms_info(), function(chrom_info) {\n return chrom_info.chrom === chr_name;\n }).len;\n }\n});\n\n/**\n * A genomic region.\n */\nvar GenomeRegion = Backbone.Model.extend({\n defaults: {\n chrom: null,\n start: 0,\n end: 0,\n str_val: null,\n genome: null\n },\n\n /**\n * Returns true if this region is the same as a given region.\n * It does not test the genome right now.\n */\n same: function(region) {\n return this.attributes.chrom === region.get('chrom') &&\n this.attributes.start === region.get('start') &&\n this.attributes.end === region.get('end');\n },\n\n /**\n * If from_str specified, use it to initialize attributes.\n */\n initialize: function(options) {\n if (options.from_str) {\n var pieces = options.from_str.split(':'),\n chrom = pieces[0],\n start_end = pieces[1].split('-');\n this.set({\n chrom: chrom,\n start: parseInt(start_end[0], 10),\n end: parseInt(start_end[1], 10)\n });\n }\n\n // Keep a copy of region's string value for fast lookup.\n this.attributes.str_val = this.get('chrom') + \":\" + this.get('start') + \"-\" + this.get('end');\n\n // Set str_val on attribute change.\n this.on('change', function() {\n this.attributes.str_val = this.get('chrom') + \":\" + this.get('start') + \"-\" + this.get('end');\n }, this);\n },\n\n copy: function() {\n return new GenomeRegion({\n chrom: this.get('chrom'),\n start: this.get('start'),\n end: this.get('end')\n });\n },\n\n length: function() {\n return this.get('end') - this.get('start');\n },\n\n /** Returns region in canonical form chrom:start-end */\n toString: function() {\n return this.attributes.str_val;\n },\n\n toJSON: function() {\n return {\n chrom: this.get('chrom'),\n start: this.get('start'),\n end: this.get('end')\n };\n },\n\n /**\n * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region;\n * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.\n */\n compute_overlap: function(a_region) {\n var first_chrom = this.get('chrom'), second_chrom = a_region.get('chrom'),\n first_start = this.get('start'), second_start = a_region.get('start'),\n first_end = this.get('end'), second_end = a_region.get('end'),\n overlap;\n\n // Compare chroms.\n if (first_chrom && second_chrom && first_chrom !== second_chrom) {\n return GenomeRegion.overlap_results.DIF_CHROMS;\n }\n\n // Compare regions.\n if (first_start < second_start) {\n if (first_end < second_start) {\n overlap = GenomeRegion.overlap_results.BEFORE;\n }\n else if (first_end < second_end) {\n overlap = GenomeRegion.overlap_results.OVERLAP_START;\n }\n else { // first_end >= second_end\n overlap = GenomeRegion.overlap_results.CONTAINS;\n }\n }\n else if (first_start > second_start) {\n if (first_start > second_end) {\n overlap = GenomeRegion.overlap_results.AFTER;\n }\n else if (first_end <= second_end) {\n overlap = GenomeRegion.overlap_results.CONTAINED_BY;\n }\n else {\n overlap = GenomeRegion.overlap_results.OVERLAP_END;\n }\n }\n else { // first_start === second_start\n overlap = (first_end >= second_end ?\n GenomeRegion.overlap_results.CONTAINS :\n GenomeRegion.overlap_results.CONTAINED_BY);\n }\n\n return overlap;\n },\n\n /**\n * Trim a region to match genome's constraints.\n */\n trim: function(genome) {\n // Assume that all chromosome/contigs start at 0.\n if (this.attributes.start < 0) {\n this.attributes.start = 0;\n }\n\n // Only try to trim the end if genome is set.\n if (this.attributes.genome) {\n var chrom_len = this.attributes.genome.get_chrom_len(this.attributes.chrom);\n if (this.attributes.end > chrom_len) {\n this.attributes.end = chrom_len - 1;\n }\n }\n\n return this;\n },\n\n /**\n * Returns true if this region contains a given region.\n */\n contains: function(a_region) {\n return this.compute_overlap(a_region) === GenomeRegion.overlap_results.CONTAINS;\n },\n\n /**\n * Returns true if regions overlap.\n */\n overlaps: function(a_region) {\n return _.intersection( [this.compute_overlap(a_region)],\n [GenomeRegion.overlap_results.DIF_CHROMS, GenomeRegion.overlap_results.BEFORE, GenomeRegion.overlap_results.AFTER] ).length === 0;\n }\n},\n{\n overlap_results: {\n DIF_CHROMS: 1000,\n BEFORE: 1001,\n CONTAINS: 1002,\n OVERLAP_START: 1003,\n OVERLAP_END: 1004,\n CONTAINED_BY: 1005,\n AFTER: 1006\n }\n});\n\nvar GenomeRegionCollection = Backbone.Collection.extend({\n model: GenomeRegion\n});\n\n/**\n * A genome browser bookmark.\n */\nvar BrowserBookmark = Backbone.Model.extend({\n defaults: {\n region: null,\n note: ''\n },\n\n initialize: function(options) {\n this.set('region', new GenomeRegion(options.region));\n }\n});\n\n/**\n * Bookmarks collection.\n */\nvar BrowserBookmarkCollection = Backbone.Collection.extend({\n model: 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[\"libs/underscore\", \"mvc/dataset/data\", \"viz/trackster/util\", \"utils/config\", \"mvc/grid/grid-view\", \"mvc/ui/ui-tabs\", \"mvc/ui/ui-misc\"], function(_, data_mod, util_mod, config_mod, GridView, Tabs, Ui) {\n\n/**\n * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes\n * to include in the representation; to_json_mappers defines mappers for returned objects.\n */\nvar CustomToJSON = {\n /**\n * Returns JSON representation of object using to_json_keys and to_json_mappers.\n */\n toJSON: function() {\n var self = this,\n json = {};\n _.each(self.constructor.to_json_keys, function(k) {\n var val = self.get(k);\n if (k in self.constructor.to_json_mappers) {\n val = self.constructor.to_json_mappers[k](val, self);\n }\n json[k] = val;\n });\n return json;\n }\n};\n\n/**\n * Model, view, and controller objects for Galaxy visualization framework.\n *\n * Models have no references to views, instead using events to indicate state\n * changes; this is advantageous because multiple views can use the same object\n * and models can be used without views.\n */\n\n/**\n * Use a popup grid to select datasets from histories or libraries. After datasets are selected,\n * track definitions are obtained from the server and the success_fn is called with the list of\n * definitions for selected datasets.\n */\nvar select_datasets = function(filters, success_fn) {\n // history dataset selection tab\n var history_grid = new GridView({\n url_base : Galaxy.root + 'visualization/list_history_datasets',\n filters : filters,\n dict_format : true,\n embedded : true\n });\n\n // library dataset selection tab\n var library_grid = new GridView( {\n url_base : Galaxy.root + 'visualization/list_library_datasets',\n dict_format : true,\n embedded : true\n });\n\n // build tabs\n var tabs = new Tabs.View();\n tabs.add({ id : 'histories',\n title : 'Histories',\n $el : $( '' ).append( history_grid.$el )\n });\n tabs.add({ id : 'libraries',\n title : 'Libraries',\n $el : $( '' ).append( library_grid.$el )\n });\n\n // modal\n Galaxy.modal.show({\n title : 'Select datasets for new tracks',\n body : tabs.$el,\n closing_events : true,\n buttons : {\n 'Cancel': function() {\n Galaxy.modal.hide();\n },\n 'Add': function() {\n var requests = [];\n tabs.$('input.grid-row-select-checkbox[name=id]:checked').each(function() {\n window.console.log( $(this).val() );\n requests[requests.length] = $.ajax({\n url : Galaxy.root + 'api/datasets/' + $(this).val(),\n dataType : 'json',\n data : {\n data_type : 'track_config',\n hda_ldda : tabs.current() == 'histories' ? 'hda' : 'ldda'\n }\n });\n });\n // To preserve order, wait until there are definitions for all tracks and then add\n // them sequentially.\n $.when.apply($, requests).then(function() {\n // jQuery always returns an Array for arguments, so need to look at first element\n // to determine whether multiple requests were made and consequently how to\n // map arguments to track definitions.\n var track_defs = ( arguments[0] instanceof Array ?\n $.map(arguments, function(arg) { return arg[0]; }) :\n [ arguments[0] ] );\n success_fn(track_defs);\n });\n Galaxy.modal.hide();\n }\n }\n });\n};\n\n// --------- Models ---------\n\n/**\n * Canvas manager is used to create canvases for browsers as well as providing a pattern cache\n */\nvar CanvasManager = function(default_font) {\n this.default_font = default_font !== undefined ? default_font : \"9px Monaco, Lucida Console, monospace\";\n\n this.dummy_canvas = this.new_canvas();\n this.dummy_context = this.dummy_canvas.getContext('2d');\n this.dummy_context.font = this.default_font;\n\n this.char_width_px = this.dummy_context.measureText(\"A\").width;\n\n this.patterns = {};\n\n // FIXME: move somewhere to make this more general\n this.load_pattern( 'right_strand', \"/visualization/strand_right.png\" );\n this.load_pattern( 'left_strand', \"/visualization/strand_left.png\" );\n this.load_pattern( 'right_strand_inv', \"/visualization/strand_right_inv.png\" );\n this.load_pattern( 'left_strand_inv', \"/visualization/strand_left_inv.png\" );\n};\n\n_.extend( CanvasManager.prototype, {\n load_pattern: function( key, path ) {\n var patterns = this.patterns,\n dummy_context = this.dummy_context,\n image = new Image();\n image.src = Galaxy.root + \"static/images\" + path;\n image.onload = function() {\n patterns[key] = dummy_context.createPattern( image, \"repeat\" );\n };\n },\n get_pattern: function( key ) {\n return this.patterns[key];\n },\n new_canvas: function() {\n var canvas = $(\"\")[0];\n // Keep a reference back to the manager\n canvas.manager = this;\n return canvas;\n }\n});\n\n/**\n * Generic cache that handles key/value pairs. Keys can be any object that can be\n * converted to a String and compared.\n */\nvar Cache = Backbone.Model.extend({\n defaults: {\n num_elements: 20,\n // Objects in cache; indexes into cache are strings of keys.\n obj_cache: null,\n // key_ary contains keys for objects in cache.\n key_ary: null\n },\n\n initialize: function(options) {\n this.clear();\n },\n\n /**\n * Get an element from the cache using its key.\n */\n get_elt: function(key) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n index = _.indexOf(key_ary, function(k) {\n return k.toString() === key_str;\n });\n\n // Update cache.\n if (index !== -1) {\n // Object is in cache, so update it.\n if (obj_cache[key_str].stale) {\n // Object is stale: remove key and object.\n key_ary.splice(index, 1);\n delete obj_cache[key_str];\n }\n else {\n // Move key to back because it is most recently used.\n this.move_key_to_end(key, index);\n }\n }\n\n return obj_cache[key_str];\n },\n\n /**\n * Put an element into the cache.\n */\n set_elt: function(key, value) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n num_elements = this.attributes.num_elements;\n\n // Update keys, objects.\n if (!obj_cache[key_str]) {\n // Add object to cache.\n\n if (key_ary.length >= num_elements) {\n // Cache full, so remove first element.\n var deleted_key = key_ary.shift();\n delete obj_cache[deleted_key.toString()];\n }\n\n // Add key.\n key_ary.push(key);\n }\n\n // Add object.\n obj_cache[key_str] = value;\n return value;\n },\n\n /**\n * Move key to end of cache. Keys are removed from the front, so moving a key to the end\n * delays the key's removal.\n */\n move_key_to_end: function(key, index) {\n this.attributes.key_ary.splice(index, 1);\n this.attributes.key_ary.push(key);\n },\n\n /**\n * Clear all elements from the cache.\n */\n clear: function() {\n this.attributes.obj_cache = {};\n this.attributes.key_ary = [];\n },\n\n /** Returns the number of elements in the cache. */\n size: function() {\n return this.attributes.key_ary.length;\n },\n\n /** Returns key most recently added to cache. */\n most_recently_added: function() {\n return this.size() === 0 ? null :\n // Most recent key is at the end of key array.\n this.attributes.key_ary[this.attributes.key_ary.length - 1];\n }\n});\n\n/**\n * Data manager for genomic data. Data is connected to and queryable by genomic regions.\n */\nvar GenomeDataManager = Cache.extend({\n defaults: _.extend({}, Cache.prototype.defaults, {\n dataset: null,\n genome: null,\n init_data: null,\n min_region_size: 200,\n filters_manager: null,\n data_type: \"data\",\n data_mode_compatible: function(entry, mode) { return true; },\n can_subset: function(entry) { return false; }\n }),\n\n /**\n * Initialization.\n */\n initialize: function(options) {\n Cache.prototype.initialize.call(this);\n\n // Set initial entries in data manager.\n var initial_entries = this.get('init_data');\n if (initial_entries) {\n this.add_data(initial_entries);\n }\n },\n\n /**\n * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type.\n * If necessary, manager size is increased to hold all data.\n */\n add_data: function(entries) {\n // Increase size to accomodate all entries.\n if (this.get('num_elements') < entries.length) {\n this.set('num_elements', entries.length);\n }\n\n // Put data into manager.\n var self = this;\n _.each(entries, function(entry) {\n self.set_data(entry.region, entry);\n });\n },\n\n /**\n * Returns deferred that resolves to true when dataset is ready (or false if dataset\n * cannot be used).\n */\n data_is_ready: function() {\n var dataset = this.get('dataset'),\n ready_deferred = $.Deferred(),\n // If requesting raw data, query dataset state; if requesting (converted) data,\n // need to query converted datasets state.\n query_type = (this.get('data_type') === 'raw_data' ? 'state' :\n this.get('data_type') === 'data' ? 'converted_datasets_state' : \"error\" ),\n ss_deferred = new util_mod.ServerStateDeferred({\n ajax_settings: {\n url: this.get('dataset').url(),\n data: {\n hda_ldda: dataset.get('hda_ldda'),\n data_type: query_type\n },\n dataType: \"json\"\n },\n interval: 5000,\n success_fn: function(response) { return response !== \"pending\"; }\n });\n\n $.when(ss_deferred.go()).then(function(response) {\n ready_deferred.resolve(response === \"ok\" || response === \"data\" );\n });\n return ready_deferred;\n },\n\n /**\n * Perform a feature search from server; returns Deferred object that resolves when data is available.\n */\n search_features: function(query) {\n var dataset = this.get('dataset'),\n params = {\n query: query,\n hda_ldda: dataset.get('hda_ldda'),\n data_type: 'features'\n };\n return $.getJSON(dataset.url(), params);\n },\n\n /**\n * Load data from server and manages data entries. Adds a Deferred to manager\n * for region; when data becomes available, replaces Deferred with data.\n * Returns the Deferred that resolves when data is available.\n */\n load_data: function(region, mode, resolution, extra_params) {\n // Setup data request params.\n var dataset = this.get('dataset'),\n params = {\n \"data_type\": this.get('data_type'),\n \"chrom\": region.get('chrom'),\n \"low\": region.get('start'),\n \"high\": region.get('end'),\n \"mode\": mode,\n \"resolution\": resolution,\n \"hda_ldda\": dataset.get('hda_ldda')\n };\n\n $.extend(params, extra_params);\n\n // Add track filters to params.\n var filters_manager = this.get('filters_manager');\n if (filters_manager) {\n var filter_names = [];\n var filters = filters_manager.filters;\n for (var i = 0; i < filters.length; i++) {\n filter_names.push(filters[i].name);\n }\n params.filter_cols = JSON.stringify(filter_names);\n }\n\n // Do request.\n var manager = this,\n entry = $.getJSON(dataset.url(), params, function (result) {\n // Add region to the result.\n result.region = region;\n manager.set_data(region, result);\n });\n\n this.set_data(region, entry);\n return entry;\n },\n\n /**\n * Get data from dataset.\n */\n get_data: function(region, mode, resolution, extra_params) {\n // Look for entry and return if it's a deferred or if data available is compatible with mode.\n var entry = this.get_elt(region);\n if ( entry &&\n ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) {\n return entry;\n }\n\n //\n // Look in cache for data that can be used.\n // TODO: this logic could be improved if the visualization knew whether\n // the data was \"index\" or \"data.\"\n //\n var key_ary = this.get('key_ary'),\n obj_cache = this.get('obj_cache'),\n entry_region, is_subregion;\n for (var i = 0; i < key_ary.length; i++) {\n entry_region = key_ary[i];\n\n if (entry_region.contains(region)) {\n is_subregion = true;\n\n // This entry has data in the requested range. Return if data\n // is compatible and can be subsetted.\n entry = obj_cache[entry_region.toString()];\n if ( util_mod.is_deferred(entry) ||\n ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) {\n this.move_key_to_end(entry_region, i);\n\n // If there's data, subset it.\n if ( !util_mod.is_deferred(entry) ) {\n var subset_entry = this.subset_entry(entry, region);\n this.set_data(region, subset_entry);\n entry = subset_entry;\n }\n\n return entry;\n }\n }\n }\n\n // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be\n // subsetted. For these cases, do not increase length because region will never be found (and\n // an infinite loop will occur.)\n // If needed, extend region to make it minimum size.\n if (!is_subregion && region.length() < this.attributes.min_region_size) {\n // IDEA: alternative heuristic is to find adjacent cache entry to region and use that to extend.\n // This would prevent bad extensions when zooming in/out while still preserving the behavior\n // below.\n\n // Use copy of region to avoid changing actual region.\n region = region.copy();\n\n // Use heuristic to extend region: extend relative to last data request.\n var last_request = this.most_recently_added();\n if (!last_request || (region.get('start') > last_request.get('start'))) {\n // This request is after the last request, so extend right.\n region.set('end', region.get('start') + this.attributes.min_region_size);\n }\n else {\n // This request is after the last request, so extend left.\n region.set('start', region.get('end') - this.attributes.min_region_size);\n }\n\n // Trim region to avoid invalid coordinates.\n region.set('genome', this.attributes.genome);\n region.trim();\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Alias for set_elt for readbility.\n */\n set_data: function(region, entry) {\n this.set_elt(region, entry);\n },\n\n /** \"Deep\" data request; used as a parameter for DataManager.get_more_data() */\n DEEP_DATA_REQ: \"deep\",\n\n /** \"Broad\" data request; used as a parameter for DataManager.get_more_data() */\n BROAD_DATA_REQ: \"breadth\",\n\n /**\n * Gets more data for a region using either a depth-first or a breadth-first approach.\n */\n get_more_data: function(region, mode, resolution, extra_params, req_type) {\n var cur_data = this._mark_stale(region);\n if (!(cur_data && this.get('data_mode_compatible')(cur_data, mode))) {\n console.log('ERROR: problem with getting more data: current data is not compatible');\n return;\n }\n\n //\n // Set parameters based on request type.\n //\n var query_low = region.get('start');\n if (req_type === this.DEEP_DATA_REQ) {\n // Use same interval but set start_val to skip data that's already in cur_data.\n $.extend(extra_params, {start_val: cur_data.data.length + 1});\n }\n else if (req_type === this.BROAD_DATA_REQ) {\n // To get past an area of extreme feature depth, set query low to be after either\n // (a) the maximum high or HACK/FIXME (b) the end of the last feature returned.\n query_low = (cur_data.max_high ? cur_data.max_high : cur_data.data[cur_data.data.length - 1][2]) + 1;\n }\n var query_region = region.copy().set('start', query_low);\n\n //\n // Get additional data, append to current data, and set new data. Use a custom deferred object\n // to signal when new data is available.\n //\n var data_manager = this,\n new_data_request = this.load_data(query_region, mode, resolution, extra_params),\n new_data_available = $.Deferred();\n // load_data sets cache to new_data_request, but use custom deferred object so that signal and data\n // is all data, not just new data.\n this.set_data(region, new_data_available);\n $.when(new_data_request).then(function(result) {\n // Update data and message.\n if (result.data) {\n result.data = cur_data.data.concat(result.data);\n if (result.max_low) {\n result.max_low = cur_data.max_low;\n }\n if (result.message) {\n // HACK: replace number in message with current data length. Works but is ugly.\n result.message = result.message.replace(/[0-9]+/, result.data.length);\n }\n }\n data_manager.set_data(region, result);\n new_data_available.resolve(result);\n });\n return new_data_available;\n },\n\n /**\n * Returns true if more detailed data can be obtained for entry.\n */\n can_get_more_detailed_data: function(region) {\n var cur_data = this.get_elt(region);\n\n // Can only get more detailed data for bigwig data that has less than 8000 data points.\n // Summary tree returns *way* too much data, and 8000 data points ~ 500KB.\n return (cur_data.dataset_type === 'bigwig' && cur_data.data.length < 8000);\n },\n\n /**\n * Returns more detailed data for an entry.\n */\n get_more_detailed_data: function(region, mode, resolution, detail_multiplier, extra_params) {\n // Mark current entry as stale.\n var cur_data = this._mark_stale(region);\n if (!cur_data) {\n console.log(\"ERROR getting more detailed data: no current data\");\n return;\n }\n\n if (!extra_params) { extra_params = {}; }\n\n // Use additional parameters to get more detailed data.\n if (cur_data.dataset_type === 'bigwig') {\n // FIXME: constant should go somewhere.\n extra_params.num_samples = 1000 * detail_multiplier;\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Marks cache data as stale.\n */\n _mark_stale: function(region) {\n var entry = this.get_elt(region);\n if (!entry) {\n console.log(\"ERROR: no data to mark as stale: \", this.get('dataset'), region.toString());\n }\n entry.stale = true;\n return entry;\n },\n\n /**\n * Returns an array of data with each entry representing one chromosome/contig\n * of data or, if data is not available, returns a Deferred that resolves to the\n * data when it becomes available.\n */\n get_genome_wide_data: function(genome) {\n // -- Get all data. --\n\n var self = this,\n all_data_available = true,\n\n // Map chromosome info into genome data.\n gw_data = _.map(genome.get('chroms_info').chrom_info, function(chrom_info) {\n var chrom_data = self.get_elt(\n new GenomeRegion({\n chrom: chrom_info.chrom,\n start: 0,\n end: chrom_info.len\n })\n );\n\n // Set flag if data is not available.\n if (!chrom_data) { all_data_available = false; }\n\n return chrom_data;\n });\n\n // -- If all data is available, return it. --\n if (all_data_available) {\n return gw_data;\n }\n\n // -- All data is not available, so load from server. --\n\n var deferred = $.Deferred();\n $.getJSON(this.get('dataset').url(), { data_type: 'genome_data' }, function(genome_wide_data) {\n self.add_data(genome_wide_data.data);\n deferred.resolve(genome_wide_data.data);\n });\n\n return deferred;\n },\n\n /**\n * Returns entry with only data in the subregion.\n */\n subset_entry: function(entry, subregion) {\n // Dictionary from entry type to function for subsetting data.\n var subset_fns = {\n bigwig: function(data, subregion) {\n return _.filter(data, function(data_point) {\n return data_point[0] >= subregion.get('start') &&\n data_point[0] <= subregion.get('end');\n });\n },\n refseq: function(data, subregion) {\n var seq_start = subregion.get('start') - entry.region.get('start');\n return entry.data.slice(seq_start, seq_start + subregion.length());\n }\n };\n\n // Subset entry if there is a function for subsetting and regions are not the same.\n var subregion_data = entry.data;\n if (!entry.region.same(subregion) && entry.dataset_type in subset_fns) {\n subregion_data = subset_fns[entry.dataset_type](entry.data, subregion);\n }\n\n // Return entry with subregion's data.\n return {\n region: subregion,\n data: subregion_data,\n dataset_type: entry.dataset_type\n };\n }\n});\n\nvar GenomeReferenceDataManager = GenomeDataManager.extend({\n initialize: function(options) {\n // Use generic object in place of dataset and set urlRoot to fetch data.\n var dataset_placeholder = new Backbone.Model();\n dataset_placeholder.urlRoot = options.data_url;\n this.set('dataset', dataset_placeholder);\n },\n\n load_data: function(region, mode, resolution, extra_params) {\n // Fetch data if region is not too large.\n return ( region.length() <= 100000 ?\n GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params) :\n { data: null, region: region } );\n }\n});\n\n/**\n * A genome build.\n */\nvar Genome = Backbone.Model.extend({\n defaults: {\n name: null,\n key: null,\n chroms_info: null\n },\n\n initialize: function(options) {\n this.id = options.dbkey;\n },\n\n /**\n * Shorthand for getting to chromosome information.\n */\n get_chroms_info: function() {\n return this.attributes.chroms_info.chrom_info;\n },\n\n /**\n * Returns a GenomeRegion object denoting a complete chromosome.\n */\n get_chrom_region: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) {\n return chrom_info.chrom === chr_name;\n });\n return new GenomeRegion({\n chrom: chrom_info.chrom,\n end: chrom_info.len\n });\n },\n\n /** Returns the length of a chromosome. */\n get_chrom_len: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n return _.find(this.get_chroms_info(), function(chrom_info) {\n return chrom_info.chrom === chr_name;\n }).len;\n }\n});\n\n/**\n * A genomic region.\n */\nvar GenomeRegion = Backbone.Model.extend({\n defaults: {\n chrom: null,\n start: 0,\n end: 0,\n str_val: null,\n genome: null\n },\n\n /**\n * Returns true if this region is the same as a given region.\n * It does not test the genome right now.\n */\n same: function(region) {\n return this.attributes.chrom === region.get('chrom') &&\n this.attributes.start === region.get('start') &&\n this.attributes.end === region.get('end');\n },\n\n /**\n * If from_str specified, use it to initialize attributes.\n */\n initialize: function(options) {\n if (options.from_str) {\n var pieces = options.from_str.split(':'),\n chrom = pieces[0],\n start_end = pieces[1].split('-');\n this.set({\n chrom: chrom,\n start: parseInt(start_end[0], 10),\n end: parseInt(start_end[1], 10)\n });\n }\n\n // Keep a copy of region's string value for fast lookup.\n this.attributes.str_val = this.get('chrom') + \":\" + this.get('start') + \"-\" + this.get('end');\n\n // Set str_val on attribute change.\n this.on('change', function() {\n this.attributes.str_val = this.get('chrom') + \":\" + this.get('start') + \"-\" + this.get('end');\n }, this);\n },\n\n copy: function() {\n return new GenomeRegion({\n chrom: this.get('chrom'),\n start: this.get('start'),\n end: this.get('end')\n });\n },\n\n length: function() {\n return this.get('end') - this.get('start');\n },\n\n /** Returns region in canonical form chrom:start-end */\n toString: function() {\n return this.attributes.str_val;\n },\n\n toJSON: function() {\n return {\n chrom: this.get('chrom'),\n start: this.get('start'),\n end: this.get('end')\n };\n },\n\n /**\n * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region;\n * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.\n */\n compute_overlap: function(a_region) {\n var first_chrom = this.get('chrom'), second_chrom = a_region.get('chrom'),\n first_start = this.get('start'), second_start = a_region.get('start'),\n first_end = this.get('end'), second_end = a_region.get('end'),\n overlap;\n\n // Compare chroms.\n if (first_chrom && second_chrom && first_chrom !== second_chrom) {\n return GenomeRegion.overlap_results.DIF_CHROMS;\n }\n\n // Compare regions.\n if (first_start < second_start) {\n if (first_end < second_start) {\n overlap = GenomeRegion.overlap_results.BEFORE;\n }\n else if (first_end < second_end) {\n overlap = GenomeRegion.overlap_results.OVERLAP_START;\n }\n else { // first_end >= second_end\n overlap = GenomeRegion.overlap_results.CONTAINS;\n }\n }\n else if (first_start > second_start) {\n if (first_start > second_end) {\n overlap = GenomeRegion.overlap_results.AFTER;\n }\n else if (first_end <= second_end) {\n overlap = GenomeRegion.overlap_results.CONTAINED_BY;\n }\n else {\n overlap = GenomeRegion.overlap_results.OVERLAP_END;\n }\n }\n else { // first_start === second_start\n overlap = (first_end >= second_end ?\n GenomeRegion.overlap_results.CONTAINS :\n GenomeRegion.overlap_results.CONTAINED_BY);\n }\n\n return overlap;\n },\n\n /**\n * Trim a region to match genome's constraints.\n */\n trim: function(genome) {\n // Assume that all chromosome/contigs start at 0.\n if (this.attributes.start < 0) {\n this.attributes.start = 0;\n }\n\n // Only try to trim the end if genome is set.\n if (this.attributes.genome) {\n var chrom_len = this.attributes.genome.get_chrom_len(this.attributes.chrom);\n if (this.attributes.end > chrom_len) {\n this.attributes.end = chrom_len - 1;\n }\n }\n\n return this;\n },\n\n /**\n * Returns true if this region contains a given region.\n */\n contains: function(a_region) {\n return this.compute_overlap(a_region) === GenomeRegion.overlap_results.CONTAINS;\n },\n\n /**\n * Returns true if regions overlap.\n */\n overlaps: function(a_region) {\n return _.intersection( [this.compute_overlap(a_region)],\n [GenomeRegion.overlap_results.DIF_CHROMS, GenomeRegion.overlap_results.BEFORE, GenomeRegion.overlap_results.AFTER] ).length === 0;\n }\n},\n{\n overlap_results: {\n DIF_CHROMS: 1000,\n BEFORE: 1001,\n CONTAINS: 1002,\n OVERLAP_START: 1003,\n OVERLAP_END: 1004,\n CONTAINED_BY: 1005,\n AFTER: 1006\n }\n});\n\nvar GenomeRegionCollection = Backbone.Collection.extend({\n model: GenomeRegion\n});\n\n/**\n * A genome browser bookmark.\n */\nvar BrowserBookmark = Backbone.Model.extend({\n defaults: {\n region: null,\n note: ''\n },\n\n initialize: function(options) {\n this.set('region', new GenomeRegion(options.region));\n }\n});\n\n/**\n * Bookmarks collection.\n */\nvar BrowserBookmarkCollection = Backbone.Collection.extend({\n model: 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dataset: this.get('dataset'),\n init_data: preloaded_data\n }));\n }\n},\n{\n // This definition matches that produced by to_dict() methods in tracks.js\n to_json_keys: [\n 'track_type',\n 'dataset',\n 'prefs',\n 'mode',\n 'filters',\n 'tool_state'\n ],\n to_json_mappers: {\n prefs: function(p, self) {\n if (_.size(p) === 0) {\n p = {\n name: self.get('config').get('name').get('value'),\n color: self.get('config').get('color').get('value')\n };\n }\n return p;\n },\n dataset: function(d) {\n return {\n id: d.id,\n hda_ldda: d.get('hda_ldda')\n };\n }\n }\n});\n\nvar BackboneTrackCollection = Backbone.Collection.extend({\n model: BackboneTrack\n});\n\n/**\n * A visualization.\n */\nvar Visualization = Backbone.Model.extend({\n defaults: {\n title: '',\n type: ''\n },\n\n urlRoot: Galaxy.root + \"api/visualizations\",\n\n /**\n * POSTs visualization's JSON to its URL using the parameter 'vis_json'\n * Note: This is necessary because (a) Galaxy requires keyword args and\n * (b) Galaxy does not handle PUT now.\n */\n save: function() {\n return $.ajax({\n url: this.url(),\n type: \"POST\",\n dataType: \"json\",\n data: {\n vis_json: JSON.stringify(this)\n }\n });\n }\n});\n\n/**\n * A visualization of genome data.\n */\nvar GenomeVisualization = Visualization.extend(CustomToJSON).extend({\n defaults: _.extend({}, Visualization.prototype.defaults, {\n dbkey: '',\n drawables: null,\n bookmarks: null,\n viewport: null\n }),\n\n initialize: function(options) {\n // Replace drawables with tracks.\n this.set('drawables', new BackboneTrackCollection(options.tracks));\n\n var models = [];\n this.set('config', config_mod.ConfigSettingCollection.from_models_and_saved_values(models, options.prefs));\n\n // Clear track and data definitions to avoid storing large objects.\n this.unset('tracks');\n this.get('drawables').each(function(d) {\n d.unset('preloaded_data');\n });\n },\n\n /**\n * Add a track or array of tracks to the visualization.\n */\n add_tracks: function(tracks) {\n this.get('drawables').add(tracks);\n }\n},\n{\n // This definition matches that produced by to_dict() methods in tracks.js\n to_json_keys: [\n 'view',\n 'viewport',\n 'bookmarks'\n ],\n\n to_json_mappers: {\n 'view': function(dummy, self) {\n return {\n obj_type: 'View',\n prefs: {\n name: self.get('title'),\n content_visible: true\n },\n drawables: self.get('drawables')\n };\n }\n }\n}\n);\n\n/**\n * -- Routers --\n */\n\n/**\n * Router for track browser.\n */\nvar TrackBrowserRouter = Backbone.Router.extend({\n initialize: function(options) {\n this.view = options.view;\n\n // Can't put regular expression in routes dictionary.\n // NOTE: parentheses are used to denote parameters returned to callback.\n this.route(/([\\w]+)$/, 'change_location');\n this.route(/([\\w\\+]+\\:[\\d,]+-[\\d,]+)$/, 'change_location');\n\n // Handle navigate events from view.\n var self = this;\n self.view.on(\"navigate\", function(new_loc) {\n self.navigate(new_loc);\n });\n },\n\n change_location: 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Masthead Collection **/\ndefine(['layout/generic-nav-view', 'mvc/webhooks', 'utils/localization', 'utils/utils'], function( GenericNav, Webhooks, _l, Utils ) {\nvar Collection = Backbone.Collection.extend({\n model: Backbone.Model.extend({\n defaults: {\n visible : true,\n target : '_parent'\n }\n }),\n fetch: function( options ){\n var self = this;\n options = options || {};\n this.reset();\n\n //\n // Chat server tab\n //\n var extendedNavItem = new GenericNav.GenericNavView();\n this.add(extendedNavItem.render());\n\n //\n // Analyze data tab.\n //\n this.add({\n id : 'analysis',\n title : _l('Analyze Data'),\n url : '',\n tooltip : _l('Analysis home view')\n });\n\n //\n // Workflow tab.\n //\n this.add({\n id : 'workflow',\n title : _l('Workflow'),\n tooltip : _l('Chain tools into workflows'),\n disabled : !Galaxy.user.id,\n url : 'workflow'\n });\n\n //\n // 'Shared Items' or Libraries tab.\n //\n this.add({\n id : 'shared',\n title : _l('Shared Data'),\n url : 'library/index',\n tooltip : _l('Access published resources'),\n menu : [{\n title : _l('Data Libraries'),\n url : 'library/list'\n },{\n title : _l('Histories'),\n url : 'histories/list_published'\n },{\n title : _l('Workflows'),\n url : 'workflows/list_published'\n },{\n title : _l('Visualizations'),\n url : 'visualizations/list_published'\n },{\n title : _l('Pages'),\n url : 'pages/list_published'\n }]\n });\n\n //\n // Lab menu.\n //\n options.user_requests && this.add({\n id : 'lab',\n title : 'Lab',\n menu : [{\n title : 'Sequencing Requests',\n url : 'requests/index'\n },{\n title : 'Find Samples',\n url : 'requests/find_samples_index'\n },{\n title : 'Help',\n url : options.lims_doc_url\n }]\n });\n\n //\n // Visualization tab.\n //\n this.add({\n id : 'visualization',\n title : _l('Visualization'),\n url : 'visualizations/list',\n tooltip : _l('Visualize datasets'),\n disabled : !Galaxy.user.id,\n menu : [{\n title : _l('New Track Browser'),\n url : 'visualization/trackster',\n target : '_frame'\n },{\n title : _l('Saved Visualizations'),\n url : 'visualizations/list',\n target : '_frame'\n },{\n title : _l('Interactive Environments'),\n url : 'visualization/gie_list',\n target : 'galaxy_main'\n }\n ]\n });\n\n //\n // Webhooks\n //\n Webhooks.add({\n url: 'api/webhooks/masthead/all',\n callback: function(webhooks) {\n $(document).ready(function() {\n $.each(webhooks.models, function(index, model) {\n var webhook = model.toJSON();\n if (webhook.activate) {\n var obj = {\n id : webhook.name,\n icon : webhook.config.icon,\n url : webhook.config.url,\n tooltip : webhook.config.tooltip,\n onclick : webhook.config.function && new Function(webhook.config.function),\n };\n\n // Galaxy.page is undefined for data libraries, workflows pages\n if( Galaxy.page ) {\n Galaxy.page.masthead.collection.add(obj);\n }\n else if( Galaxy.masthead ) {\n Galaxy.masthead.collection.add(obj);\n }\n \n // Append masthead script and styles to Galaxy main\n Utils.appendScriptStyle( webhook );\n }\n });\n });\n }\n });\n\n //\n // Admin.\n //\n Galaxy.user.get( 'is_admin' ) && this.add({\n id : 'admin',\n title : _l('Admin'),\n url : 'admin',\n tooltip : _l('Administer this Galaxy'),\n cls : 'admin-only'\n });\n\n //\n // Help tab.\n //\n var helpTab = {\n id : 'help',\n title : _l('Help'),\n tooltip : _l('Support, contact, and community'),\n menu : [{\n title : _l('Support'),\n url : options.support_url,\n target : '_blank'\n },{\n title : _l('Search'),\n url : options.search_url,\n target : '_blank'\n },{\n title : _l('Mailing Lists'),\n url : options.mailing_lists,\n target : '_blank'\n },{\n title : _l('Videos'),\n url : options.screencasts_url,\n target : '_blank'\n },{\n title : _l('Wiki'),\n url : options.wiki_url,\n target : '_blank'\n },{\n title : _l('How to Cite Galaxy'),\n url : options.citation_url,\n target : '_blank'\n },{\n title : _l('Interactive Tours'),\n url : 'tours'\n }]\n };\n options.terms_url && helpTab.menu.push({\n title : _l('Terms and Conditions'),\n url : options.terms_url,\n target : '_blank'\n });\n options.biostar_url && helpTab.menu.unshift({\n title : _l('Ask a question'),\n url : 'biostar/biostar_question_redirect',\n target : '_blank'\n });\n options.biostar_url && helpTab.menu.unshift({\n title : _l('Galaxy Biostar'),\n url : options.biostar_url_redirect,\n target : '_blank'\n });\n this.add( helpTab );\n\n //\n // User tab.\n //\n var userTab = {};\n if ( !Galaxy.user.id ){\n if ( options.allow_user_creation ) {\n userTab = {\n id : 'user',\n title : _l('Login or Register'),\n cls : 'loggedout-only',\n tooltip : _l('Account registration or login'),\n menu : [{\n title : _l('Login'),\n url : 'user/login',\n target : 'galaxy_main',\n noscratchbook : true\n }, {\n title: _l('Register'),\n url: 'user/create',\n target: 'galaxy_main',\n noscratchbook: true\n }\n ]\n };\n } else {\n userTab = {\n id: 'user',\n title: _l('Login'),\n cls: 'loggedout-only',\n tooltip: _l('Login'),\n url: 'user/login',\n target: 'galaxy_main',\n noscratchbook: true\n };\n }\n } else {\n userTab = {\n id : 'user',\n title : _l('User'),\n cls : 'loggedin-only',\n tooltip : _l('Account and saved data'),\n menu : [{\n title : _l('Logged in as') + ' ' + Galaxy.user.get( 'email' )\n },{\n title : _l('Preferences'),\n url : 'user'\n },{\n title : _l('Custom Builds'),\n url : 'custom_builds'\n },{\n title : _l('Logout'),\n url : 'user/logout?session_csrf_token=' + Galaxy.session_csrf_token,\n target : '_top',\n divider : true\n },{\n title : _l('Saved Histories'),\n url : 'histories/list',\n target : '_top'\n },{\n title : _l('Saved Datasets'),\n url : 'datasets/list',\n target : '_top'\n },{\n title : _l('Saved Pages'),\n url : 'pages/list',\n target : '_top'\n }]\n };\n }\n this.add( userTab );\n var activeView = this.get( options.active_view );\n activeView && activeView.set( 'active', true );\n return new jQuery.Deferred().resolve().promise();\n }\n});\n\n/** Masthead tab **/\nvar Tab = Backbone.View.extend({\n initialize: function ( options ) {\n this.model = options.model;\n this.setElement( this._template() );\n this.$dropdown = this.$( '.dropdown' );\n this.$toggle = this.$( '.dropdown-toggle' );\n this.$menu = this.$( '.dropdown-menu' );\n this.$note = this.$( '.dropdown-note' );\n this.listenTo( this.model, 'change', this.render, this );\n },\n\n events: {\n 'click .dropdown-toggle' : '_toggleClick'\n },\n\n render: function() {\n var self = this;\n $( '.tooltip' ).remove();\n this.$el.attr( 'id', this.model.id )\n .css( { visibility : this.model.get( 'visible' ) && 'visible' || 'hidden' } );\n this.model.set( 'url', this._formatUrl( this.model.get( 'url' ) ) );\n this.$note.html( this.model.get( 'note' ) || '' )\n .removeClass().addClass( 'dropdown-note' )\n .addClass( this.model.get( 'note_cls' ) )\n .css( { 'display' : this.model.get( 'show_note' ) && 'block' || 'none' } );\n this.$toggle.html( this.model.get( 'title' ) || '' )\n .removeClass().addClass( 'dropdown-toggle' )\n .addClass( this.model.get( 'cls' ) )\n .addClass( this.model.get( 'icon' ) && 'dropdown-icon fa ' + this.model.get( 'icon' ) )\n .addClass( this.model.get( 'toggle' ) && 'toggle' )\n .attr( 'target', this.model.get( 'target' ) )\n .attr( 'href', this.model.get( 'url' ) )\n .attr( 'title', this.model.get( 'tooltip' ) )\n .tooltip( 'destroy' );\n this.model.get( 'tooltip' ) && this.$toggle.tooltip( { placement: 'bottom' } );\n this.$dropdown.removeClass().addClass( 'dropdown' )\n .addClass( this.model.get( 'disabled' ) && 'disabled' )\n .addClass( this.model.get( 'active' ) && 'active' );\n if ( this.model.get( 'menu' ) && this.model.get( 'show_menu' ) ) {\n this.$menu.show();\n $( '#dd-helper' ).show().off().on( 'click', function() {\n $( '#dd-helper' ).hide();\n self.model.set( 'show_menu', false );\n });\n } else {\n self.$menu.hide();\n $( '#dd-helper' ).hide();\n }\n this.$menu.empty().removeClass( 'dropdown-menu' );\n if ( this.model.get( 'menu' ) ) {\n _.each( this.model.get( 'menu' ), function( menuItem ) {\n self.$menu.append( self._buildMenuItem( menuItem ) );\n menuItem.divider && self.$menu.append( $( '' ).addClass( 'divider' ) );\n });\n self.$menu.addClass( 'dropdown-menu' );\n self.$toggle.append( $( '' ).addClass( 'caret' ) );\n }\n return this;\n },\n\n /** Add new menu item */\n _buildMenuItem: function ( options ) {\n var self = this;\n options = _.defaults( options || {}, {\n title : '',\n url : '',\n target : '_parent',\n noscratchbook : false\n });\n options.url = self._formatUrl( options.url );\n return $( '' ).append(\n $( '' ).attr( 'href', options.url )\n .attr( 'target', options.target )\n .html( options.title )\n .on( 'click', function( e ) {\n e.preventDefault();\n self.model.set( 'show_menu', false );\n if (options.onclick){\n options.onclick();\n } else {\n Galaxy.frame.add( options );\n }\n })\n );\n },\n\n /** Handle click event */\n _toggleClick: function( e ) {\n var self = this;\n var model = this.model;\n e.preventDefault();\n $( '.tooltip' ).hide();\n model.trigger( 'dispatch', function( m ) {\n model.id !== m.id && m.get( 'menu' ) && m.set( 'show_menu', false );\n });\n if ( !model.get( 'disabled' ) ) {\n if ( !model.get( 'menu' ) ) {\n model.get( 'onclick' ) ? model.get( 'onclick' )() : Galaxy.frame.add( model.attributes );\n } else {\n model.set( 'show_menu', true );\n }\n } else {\n function buildLink( label, url ) {\n return $( '' ).append( $( '' ).attr( 'href', Galaxy.root + url ).html( label ) ).html();\n }\n this.$toggle.popover && this.$toggle.popover( 'destroy' );\n this.$toggle.popover({\n html : true,\n placement : 'bottom',\n content : 'Please ' + buildLink( 'login', 'user/login?use_panels=True' ) + ' or ' +\n buildLink( 'register', 'user/create?use_panels=True' ) + ' to use this feature.'\n }).popover( 'show' );\n setTimeout( function() { self.$toggle.popover( 'destroy' ) }, 5000 );\n }\n },\n\n /** Url formatting */\n _formatUrl: function( url ) {\n return typeof url == 'string' && url.indexOf( '//' ) === -1 && url.charAt( 0 ) != '/' ? Galaxy.root + url : url;\n },\n\n /** body tempate */\n _template: function () {\n return '- ' +\n '
- ' +\n '' +\n '