From 7a6794e104fc978b279c61d15812791302d6fef2 Mon Sep 17 00:00:00 2001 From: carlfeberhard Date: Mon, 2 May 2016 15:47:25 -0400 Subject: [PATCH] UI, history: move show deleted/hidden into content - Move d/h (deleted/hidden) control into history contents - normalize names (show_deleted, showDeleted --> includeDeleted) - add History.contentsShown that checks d/h flags to return num. shown - move HistoryPreferences into HistoryContents.storage Misc. fixes: - fix collection.off to stopListening - provide interface to HistoryPreferences so that consumers don't need the model keys (easier to change them later on) - (some) cleanup --- .../mvc/history/history-content-model.js | 20 +- .../scripts/mvc/history/history-contents.js | 94 +- .../scripts/mvc/history/history-model.js | 23 +- .../mvc/history/history-preferences.js | 36 +- .../mvc/history/history-view-edit-current.js | 4 +- .../scripts/mvc/history/history-view-edit.js | 18 +- .../scripts/mvc/history/history-view.js | 155 +- .../galaxy/scripts/mvc/history/multi-panel.js | 17 +- client/galaxy/scripts/mvc/list/list-view.js | 6 +- .../mvc/history/history-content-model.js.map | 2 +- .../maps/mvc/history/history-contents.js.map | 2 +- static/maps/mvc/history/history-model.js.map | 2 +- .../mvc/history/history-preferences.js.map | 2 +- .../history/history-view-edit-current.js.map | 2 +- .../maps/mvc/history/history-view-edit.js.map | 2 +- static/maps/mvc/history/history-view.js.map | 2 +- static/maps/mvc/history/multi-panel.js.map | 2 +- static/maps/mvc/list/list-view.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 25602 +------------- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 29493 +--------------- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/bundled/login.bundled.js | 57 +- static/scripts/bundled/login.bundled.js.map | 2 +- .../scripts/mvc/history/history-contents.js | 2 +- static/scripts/mvc/history/history-model.js | 2 +- .../mvc/history/history-preferences.js | 2 +- .../mvc/history/history-view-edit-current.js | 2 +- .../scripts/mvc/history/history-view-edit.js | 2 +- static/scripts/mvc/history/history-view.js | 2 +- static/scripts/mvc/history/multi-panel.js | 2 +- static/scripts/mvc/list/list-view.js | 2 +- 32 files changed, 237 insertions(+), 55328 deletions(-) diff --git a/client/galaxy/scripts/mvc/history/history-content-model.js b/client/galaxy/scripts/mvc/history/history-content-model.js index a0953ee7a50..1c85909ea5d 100644 --- a/client/galaxy/scripts/mvc/history/history-content-model.js +++ b/client/galaxy/scripts/mvc/history/history-content-model.js @@ -28,31 +28,25 @@ var HistoryContentMixin = { // Instead, use type_id which prefixes the history_content_type so the bbone collection can differentiate idAttribute : 'type_id', - /** override because backbone tests boolean( idAttribute ), but it's not an empty string even for new models - * due to our use of type_id. - */ - // isNew : function(){ - // return !this.get( 'id' ); - // }, - // ........................................................................ common queries /** the more common alias of visible */ hidden : function(){ return !this.get( 'visible' ); }, - /** based on show_deleted, show_hidden (gen. from the container control), +//TODO: remove + /** based on includeDeleted, includeHidden (gen. from the container control), * would this ds show in the list of ds's? - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? + * @param {Boolean} includeDeleted are we showing deleted hdas? + * @param {Boolean} includeHidden are we showing hidden hdas? */ - isVisible : function( show_deleted, show_hidden ){ + isVisible : function( includeDeleted, includeHidden ){ var isVisible = true; - if( ( !show_deleted ) + if( ( !includeDeleted ) && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ isVisible = false; } - if( ( !show_hidden ) + if( ( !includeHidden ) && ( !this.get( 'visible' ) ) ){ isVisible = false; } diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js index b2479adcd8c..2983ef4429e 100644 --- a/client/galaxy/scripts/mvc/history/history-contents.js +++ b/client/galaxy/scripts/mvc/history/history-contents.js @@ -23,6 +23,7 @@ var _super = CONTROLLED_FETCH_COLLECTION.ControlledFetchCollection; var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ _logNamespace : 'history', + // ........................................................................ composite collection /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { if( attrs.history_content_type === "dataset" ) { @@ -46,6 +47,7 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ return { validationError : 'Unknown history_content_type: ' + attrs.history_content_type }; }, + // ........................................................................ set up /** @type {Number} limit used for the first fetch (or a reset) */ limitOnFirstFetch : 500, /** @type {Number} limit used for each subsequent fetch */ @@ -54,31 +56,6 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ /** @type {String} order used here and when fetching from server */ order : 'hid', - /** Set up */ - initialize : function( models, options ){ - options = options || {}; - _super.prototype.initialize.call( this, models, options ); - - this.history = options.history || null; - this.historyId = options.historyId || null; - - // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection - // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute - // manually here - if we don't, contents will not merge but be replaced/swapped. - this.model.prototype.idAttribute = 'type_id'; - - /** @type {Boolean} does this collection contain and fetch deleted elements */ - this.includeDeleted = options.includeDeleted || false; - /** @type {Boolean} does this collection contain and fetch non-visible elements */ - this.includeHidden = options.includeHidden || false; - - this.on( 'all', function(){ - var args = _.toArray( arguments ); - if( /^change:*/.test( args[0] ) ){ return; } - console.log.apply( console, [ this + '' ].concat( args ) ); - }); - }, - /** root api url */ urlRoot : Galaxy.root + 'api/histories', @@ -87,6 +64,58 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ return this.urlRoot + '/' + this.historyId + '/contents'; }, + /** Set up */ + initialize : function( models, options ){ + options = options || {}; + _super.prototype.initialize.call( this, models, options ); + + this.history = options.history || null; + this.setHistoryId( options.historyId || null ); + /** @type {Boolean} does this collection contain and fetch deleted elements */ + this.includeDeleted = options.includeDeleted || this.includeDeleted; + /** @type {Boolean} does this collection contain and fetch non-visible elements */ + this.includeHidden = options.includeHidden || this.includeHidden; + + // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection + // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute + // manually here - if we don't, contents will not merge but be replaced/swapped. + this.model.prototype.idAttribute = 'type_id'; + + // this.on( 'all', function(){ + // var args = _.toArray( arguments ); + // if( /^change:*/.test( args[0] ) ){ return; } + // console.log.apply( console, [ this + '' ].concat( args ) ); + // }); + }, + + setHistoryId : function( newId ){ + this.historyId = newId; + this._setUpWebStorage(); + }, + + /** Set up client side storage. Currently PersistanStorage keyed under 'history:' */ + _setUpWebStorage : function( initialSettings ){ +// TODO: use initialSettings + if( !this.historyId ){ return; } + this.storage = new HISTORY_PREFS.HistoryPrefs({ + id: HISTORY_PREFS.HistoryPrefs.historyStorageKey( this.historyId ) + }); + this.trigger( 'new-storage', this.storage, this ); + + this.on({ + 'change:include-deleted' : function( newVal ){ + this.storage.includeDeleted( newVal ); + }, + 'change:include-hidden' : function( newVal ){ + this.storage.includeHidden( newVal ); + } + }); + + this.includeDeleted = this.storage.includeDeleted() || false; + this.includeHidden = this.storage.includeHidden() || false; + return this; + }, + // ........................................................................ common queries /** @type {Object} map of collection available sorting orders containing comparator fns */ comparators : _.extend( _.clone( _super.prototype.comparators ), { @@ -145,17 +174,22 @@ var HistoryContents = _super.extend( BASE_MVC.LoggableMixin ).extend({ }, /** create a setter in order to publish the change */ - setIncludeDeleted : function( setting ){ + setIncludeDeleted : function( setting, options ){ if( _.isBoolean( setting ) && setting !== this.includeDeleted ){ this.includeDeleted = setting; + if( _.result( options, 'silent' ) ){ return; } +// TODO: change from change: this.trigger( 'change:include-deleted', setting, this ); } }, /** create a setter in order to publish the change */ - setIncludeHidden : function( setting ){ + setIncludeHidden : function( setting, options ){ if( _.isBoolean( setting ) && setting !== this.includeHidden ){ this.includeHidden = setting; + options = options || {}; + if( _.result( options, 'silent' ) ){ return; } +// TODO: change from change: this.trigger( 'change:include-hidden', setting, this ); } }, @@ -531,9 +565,9 @@ var HidSectionedHistoryContents = HistoryContents.extend({ var hid = content.get( 'hid' ); if( descending ){ - if( hid < range.first ){ console.log( '< first' ); break; } + if( hid < range.first ){ break; } } else { - if( hid > range.last ){ console.log( '> last' ); break; } + if( hid > range.last ){ break; } } subcollection.push( content ); } @@ -600,7 +634,7 @@ var HidSectionedHistoryContents = HistoryContents.extend({ fetchFirst : function( options ){ _.extend( options || {}, { silent: true }); - // console.log( 'fetchFirst?' ); + // console.log( 'fetchFirst?', options ); this.currentSection = 0; if( this.order === 'hid' && this._countSections() > 1 ){ this.currentSection = this._lastFullSection(); diff --git a/client/galaxy/scripts/mvc/history/history-model.js b/client/galaxy/scripts/mvc/history/history-model.js index 85ec26db3e8..cdc64079212 100644 --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -40,16 +40,15 @@ var History = Backbone.Model // ........................................................................ set up/tear down /** Set up the model * @param {Object} historyJSON model data for this History - * @param {Object[]} contentsJSON array of model data for this History's contents (hdas or collections) * @param {Object} options any extra settings including logger */ - initialize : function( historyJSON, contentsJSON, options ){ + initialize : function( historyJSON, options ){ options = options || {}; this.logger = options.logger || null; - this.log( this + ".initialize:", historyJSON, contentsJSON, options ); + this.log( this + ".initialize:", historyJSON, options ); /** HistoryContents collection of the HDAs contained in this history. */ - this.contents = new HISTORY_CONTENTS.HistoryContents( contentsJSON || [], { + this.contents = new HISTORY_CONTENTS.HistoryContents( [], { history : this, historyId : this.get( 'id' ), order : options.order, @@ -91,6 +90,15 @@ var History = Backbone.Model }, // ........................................................................ derived attributes + /** */ + contentsShown : function(){ + var contentsActive = this.get( 'contents_active' ); + var shown = contentsActive.active || 0; + shown += this.contents.includeDeleted? contentsActive.deleted : 0; + shown += this.contents.includeHidden? contentsActive.hidden : 0; + return shown; + }, + /** convert size in bytes to a more human readable version */ nice_size : function(){ return UTILS.bytesToString( this.get( 'size' ), true, 2 ); @@ -246,7 +254,7 @@ var History = Backbone.Model // fetch history then use history data to fetch (paginated) contents return this.fetch( options ).pipe( function getContents( history ){ self.contents.history = self; - self.contents.historyId = history.id; + self.contents.setHistoryId( history.id ); return self.fetchContents( contentsOptions ); }); }, @@ -255,11 +263,6 @@ var History = Backbone.Model fetchContents : function( options ){ options = options || {}; var self = this; - // now that we have a history id, we can read the prefs - // and make the contents fetch based on those - var prefs = HISTORY_PREFS.HistoryPrefs.get( self.id ).toJSON(); - self.contents.includeDeleted = prefs.show_deleted; - self.contents.includeHidden = prefs.show_hidden; // we're updating, reset the update time self.lastUpdateTime = new Date(); diff --git a/client/galaxy/scripts/mvc/history/history-preferences.js b/client/galaxy/scripts/mvc/history/history-preferences.js index dc0c522053a..31fba2d249b 100644 --- a/client/galaxy/scripts/mvc/history/history-preferences.js +++ b/client/galaxy/scripts/mvc/history/history-preferences.js @@ -20,14 +20,42 @@ var HistoryPrefs = BASE_MVC.SessionStorageModel.extend( /** add an hda id to the hash of expanded hdas */ addExpanded : function( model ){ - var key = 'expandedIds'; - this.save( key, _.extend( this.get( key ), _.object([ model.id ], [ model.get( 'id' ) ]) ) ); +//TODO: use type_id and not model + var current = this.get( 'expandedIds' ); + current[ model.id ] = model.get( 'id' ); + this.save( 'expandedIds', current ); }, /** remove an hda id from the hash of expanded hdas */ removeExpanded : function( model ){ - var key = 'expandedIds'; - this.save( key, _.omit( this.get( key ), model.id ) ); + var current = this.get( 'expandedIds' ); + delete current[ model.id ]; + this.save( 'expandedIds', current ); + }, + + isExpanded : function( contentId ){ + return _.result( this.get( 'expandedIds' ), contentId, false ); + }, + + allExpanded : function(){ + return _.values( this.get( 'expandedIds' ) ); + }, + + clearExpanded : function(){ + this.set( 'expandedIds', {} ); + }, + + includeDeleted : function( val ){ + // moving the invocation here so other components don't need to know the key + // TODO: change this key later + if( !_.isUndefined( val ) ){ this.set( 'show_deleted', val ); } + return this.get( 'show_deleted' ); + }, + + includeHidden : function( val ){ + // TODO: change this key later + if( !_.isUndefined( val ) ){ this.set( 'show_hidden', val ); } + return this.get( 'show_hidden' ); }, toString : function(){ diff --git a/client/galaxy/scripts/mvc/history/history-view-edit-current.js b/client/galaxy/scripts/mvc/history/history-view-edit-current.js index 24f9081165c..88eade4fcc1 100644 --- a/client/galaxy/scripts/mvc/history/history-view-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-view-edit-current.js @@ -141,12 +141,12 @@ var CurrentHistoryView = _super.extend(/** @lends CurrentHistoryView.prototype * /** listening for collection events */ _setUpCollectionListeners : function(){ _super.prototype._setUpCollectionListeners.call( this ); - //TODO:?? may not be needed? see history-view-edit, 369 +//TODO:?? may not be needed? see history-view-edit, _handleItemVisibleChange // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state, // then: remove it from the collection if the panel is set to NOT show hidden datasets this.listenTo( this.collection, 'state:ready', function( model, newState, oldState ){ if( ( !model.get( 'visible' ) ) - && ( !this.storage.get( 'show_hidden' ) ) ){ + && ( !this.collection.storage.includeHidden() ) ){ this.removeItemView( model ); } }); diff --git a/client/galaxy/scripts/mvc/history/history-view-edit.js b/client/galaxy/scripts/mvc/history/history-view-edit.js index b0df941adb2..f5c537db25b 100644 --- a/client/galaxy/scripts/mvc/history/history-view-edit.js +++ b/client/galaxy/scripts/mvc/history/history-view-edit.js @@ -316,17 +316,18 @@ var HistoryViewEdit = _super.extend( * @param {Model} the item model to check */ _handleItemDeletionChange : function( itemModel ){ - // console.log( '_handleItemDeletionChange:', contentsShown, itemModel.get( 'deleted' ), this.showDeleted ); + var contents = this.model.contents; var contentsShown = this.model.get( 'contents_active' ); + // console.log( '_handleItemDeletionChange:', contentsShown, itemModel.get( 'deleted' ), contents.includeDeleted ); if( itemModel.get( 'deleted' ) ){ contentsShown.deleted += 1; - if( !this.showDeleted ){ + if( !contents.includeDeleted ){ this.removeItemView( itemModel ); } contentsShown.active -= 1; } else { contentsShown.deleted -= 1; - if( !this.showDeleted ){ + if( !contents.includeDeleted ){ contentsShown.active -= 1; } } @@ -339,17 +340,18 @@ var HistoryViewEdit = _super.extend( * @param {Model} the item model to check */ _handleItemVisibleChange : function( itemModel ){ + var contents = this.model.contents; var contentsShown = this.model.get( 'contents_active' ); - // console.log( '_handleHdaVisibleChange:', contentsShown, itemModel.hidden(), this.showHidden ); + // console.log( '_handleItemDeletionChange:', contentsShown, itemModel.get( 'deleted' ), contents.includeHidden ); if( itemModel.hidden() ){ contentsShown.hidden += 1; - if( !this.showHidden ){ + if( !contents.includeHidden ){ this.removeItemView( itemModel ); } contentsShown.active -= 1; } else { contentsShown.hidden -= 1; - if( !this.showHidden ){ + if( !contents.includeHidden ){ contentsShown.active -= 1; } } @@ -519,7 +521,7 @@ HistoryViewEdit.prototype.templates = (function(){ '<% if( history.contents_active.deleted ){ %>', '', - '<% if( view.showDeleted ){ %>', + '<% if( view.model.contents.includeDeleted ){ %>', '', _l( 'hide deleted' ), '', @@ -534,7 +536,7 @@ HistoryViewEdit.prototype.templates = (function(){ '<% if( history.contents_active.hidden ){ %>', '', - '<% if( view.showHidden ){ %>', + '<% if( view.model.contents.includeHidden ){ %>', '', _l( 'hide hidden' ), '', diff --git a/client/galaxy/scripts/mvc/history/history-view.js b/client/galaxy/scripts/mvc/history/history-view.js index adcd9ae654a..7457394cc25 100644 --- a/client/galaxy/scripts/mvc/history/history-view.js +++ b/client/galaxy/scripts/mvc/history/history-view.js @@ -138,24 +138,6 @@ var HistoryView = _super.extend( return $.when(); }, - /** release/free/shutdown old models and set up panel for new models - * @fires new-model with the panel as parameter - */ - setModel : function( model, attributes ){ - _super.prototype.setModel.call( this, model, attributes ); - if( this.model ){ - this._setUpWebStorage(); - } - }, - - /** Override to reset web storage when the id changes (since it needs the id) */ - _setUpModelListeners : function(){ - _super.prototype._setUpModelListeners.call( this ); - return this.listenTo( this.model, { - 'change:id' : this._setUpWebStorage, - }); - }, - /** Override to reset web storage when the id changes (since it needs the id) */ _setUpCollectionListeners : function(){ _super.prototype._setUpCollectionListeners.call( this ); @@ -166,38 +148,6 @@ var HistoryView = _super.extend( }); }, - // ------------------------------------------------------------------------ browser stored prefs - /** Set up client side storage. Currently PersistanStorage keyed under 'history:' - * @see PersistentStorage - */ - _setUpWebStorage : function(){ - if( !this.model || !this.model.id ){ return this; } - //this.log( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); - if( this.storage ){ - this.stopListening( this.storage ); - } - - this.storage = new HISTORY_PREFS.HistoryPrefs({ - id: HISTORY_PREFS.HistoryPrefs.historyStorageKey( this.model.get( 'id' ) ) - }); - this.trigger( 'new-storage', this.storage, this ); - this.log( this + ' (init\'d) storage:', this.storage.get() ); - -// TODO: reverse this - have storage reflect what's used in the view and not visversa - this.listenTo( this.storage, { - 'change:show_deleted' : function( view, newVal ){ - this.showDeleted = newVal; - }, - 'change:show_hidden' : function( view, newVal ){ - this.showHidden = newVal; - } - }, this ); - this.showDeleted = this.storage.get( 'show_deleted' ) || false; - this.showHidden = this.storage.get( 'show_hidden' ) || false; - - return this; - }, - // ------------------------------------------------------------------------ panel rendering /** In this override, add a btn to toggle the selectors */ _buildNewRender : function(){ @@ -250,7 +200,7 @@ var HistoryView = _super.extend( // ------------------------------------------------------------------------ client-side pagination /** */ renderItems : function( $whereTo ){ - console.log( 'renderItems -----------------------------------------------------------' ); + // console.log( 'renderItems -----------------------------------------------------------' ); $whereTo = $whereTo || this.$el; var self = this; var contents = self.model.contents; @@ -258,9 +208,9 @@ var HistoryView = _super.extend( self.freeViews(); // render sections - console.log( 'renderItems:', self.$list( $whereTo ) ); + // console.log( 'renderItems:', self.$list( $whereTo ) ); self.$list( $whereTo ).html( contents._mapSectionRanges( function( section ){ - console.log( 'renderItems:', section ); + // console.log( 'renderItems:', section ); return self.templates.listItemsSection( section, self ); }).join( '\n' )); // render content views into (only) the current section @@ -268,12 +218,12 @@ var HistoryView = _super.extend( self._renderEmptyMessage( $whereTo ).toggle( !self.views.length ); self.trigger( 'views:ready', self.views ); - console.log( '----------------------------------------------------------- renderItems' ); + // console.log( '----------------------------------------------------------- renderItems' ); return self.views; }, _renderSection : function( section, $whereTo ){ - console.debug( this + '._renderSection', section, $whereTo ); + // console.debug( this + '._renderSection', section, $whereTo ); var self = this; // render views from collection for the current section, replacing that section marker with them // note: shows only one section's worth of views at a time @@ -298,12 +248,13 @@ var HistoryView = _super.extend( }, // ------------------------------------------------------------------------ sub-views - /** in this override, check if the contents would also display based on show_deleted/hidden */ + /** in this override, check if the contents would also display based on includeDeleted/hidden */ _filterItem : function( model ){ - var panel = this; - return ( _super.prototype._filterItem.call( panel, model ) - && ( !model.hidden() || panel.showHidden ) - && ( !model.isDeletedOrPurged() || panel.showDeleted ) ); + var self = this; + var contents = self.model.contents; + return ( contents.includeHidden || !model.hidden() ) + && ( contents.includeDeleted || !model.isDeletedOrPurged() ) + && ( _super.prototype._filterItem.call( self, model ) ); }, /** In this override, since history contents are mixed, @@ -325,7 +276,7 @@ var HistoryView = _super.extend( var options = _super.prototype._getItemViewOptions.call( this, model ); return _.extend( options, { linkTarget : this.linkTarget, - expanded : !!this.storage.get( 'expandedIds' )[ model.id ], + expanded : this.model.contents.storage.isExpanded( model.id ), hasUser : this.model.ownedByCurrUser() }); }, @@ -334,21 +285,21 @@ var HistoryView = _super.extend( _setUpItemViewListeners : function( view ){ var panel = this; _super.prototype._setUpItemViewListeners.call( panel, view ); - //TODO:?? could use 'view:expanded' here? +//TODO: send from content view: this.model.collection.storage.addExpanded // maintain a list of items whose bodies are expanded return panel.listenTo( view, { 'expanded': function( v ){ - panel.storage.addExpanded( v.model ); + panel.model.contents.storage.addExpanded( v.model ); }, 'collapsed': function( v ){ - panel.storage.removeExpanded( v.model ); + panel.model.contents.storage.removeExpanded( v.model ); } }); }, /** override to remove expandedIds from webstorage */ collapseAll : function(){ - this.storage.set( 'expandedIds', {} ); + this.model.contents.storage.clearExpanded(); _super.prototype.collapseAll.call( this ); }, @@ -376,35 +327,35 @@ var HistoryView = _super.extend( } self.scrollTo( 0 ); - console.log( 'contains?', contents.contains( model ) ); - console.log( 'get:', contents.get( model.id ) + '' ); - console.log( contents.length ); + // console.log( 'contains?', contents.contains( model ) ); + // console.log( 'get:', contents.get( model.id ) + '' ); + // console.log( contents.length ); // contents.on( 'all', console.info, console ); - console.log( '^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^' ); + // console.log( '^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^' ); var hid = model.get( 'hid' ); var insertionIndex = contents._indexOfHidInSection( hid, contents.currentSection ); - console.log( hid, insertionIndex, contents.at( insertionIndex ) + '' ); - console.log( contents.at( insertionIndex - 1 ) + '', contents.at( insertionIndex + 1 ) + '' ); + // console.log( hid, insertionIndex, contents.at( insertionIndex ) + '' ); + // console.log( contents.at( insertionIndex - 1 ) + '', contents.at( insertionIndex + 1 ) + '' ); if( insertionIndex === null ){ return null; } //TODO: this should happen elsewhere // have to manually update the hid_counter self.model.set( 'hid_counter', self.model.get( 'hid_counter' ) + 1 ); - console.log( 'hid_counter:', self.model.get( 'hid_counter' ) ); + // console.log( 'hid_counter:', self.model.get( 'hid_counter' ) ); - console.log( 'at index', insertionIndex, 'adding: ' + model ); + // console.log( 'at index', insertionIndex, 'adding: ' + model ); var view = self._createItemView( model ); self.$emptyMessage().fadeOut( self.fxSpeed ); self._attachView( view, insertionIndex ); - console.log( '^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^' ); + // console.log( '^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^' ); return view; }, /** */ _attachView : function( view, modelIndex, useFx ){ - console.log( '_attachView:', view, modelIndex, useFx ); + // console.log( '_attachView:', view, modelIndex, useFx ); useFx = _.isUndefined( useFx )? true : useFx; var self = this; var $el = self._renderItemView$el( view ).hide(); @@ -412,19 +363,18 @@ var HistoryView = _super.extend( // Im not sure any of this shit is needed - (it prob. isn't *when adding to the last section*) var viewIndex = 0; var prevModel = self.model.contents.at( modelIndex - 1 ); - window.prevModel = prevModel; - console.log( 'prevModel: ' + prevModel, prevModel ); + // console.log( 'prevModel: ' + prevModel, prevModel ); if( prevModel ){ var found = _.findIndex( self.views, function( v ){ - console.log( ' ', v + '', v.model + '' ); - console.log( ' ', v.model === prevModel ); + // console.log( ' ', v + '', v.model + '' ); + // console.log( ' ', v.model === prevModel ); return v.model === prevModel; }); - console.log( 'found:', found ); + // console.log( 'found:', found ); if( found !== -1 ){ viewIndex = found + 1; } } // var viewIndex = Math.max( 0, _.findIndex( self.views, function( v ){ return v.model === prevModel; }) ); - console.log( 'viewIndex:', viewIndex ); + // console.log( 'viewIndex:', viewIndex ); self.views.splice( viewIndex, 0, view ); if( viewIndex === 0 ){ @@ -432,12 +382,12 @@ var HistoryView = _super.extend( } else { var prevView = self.views[ viewIndex ]; - console.log( 'prevView:', prevView + '', prevView.$el.get(0) ); - console.log( prevView.$el.parent().get(0) ); + // console.log( 'prevView:', prevView + '', prevView.$el.get(0) ); + // console.log( prevView.$el.parent().get(0) ); // $el.insertAfter( prevView.$el ); self.$currentSection().children( '.history-content' ).eq( viewIndex - 1 ).after( $el ); } - console.log( 'self.views[ viewIndex ]:', self.views[ viewIndex ] ); + // console.log( 'self.views[ viewIndex ]:', self.views[ viewIndex ] ); self.trigger( 'view:attached', view ); if( useFx ){ @@ -515,42 +465,33 @@ var HistoryView = _super.extend( }, /** Toggle and store the deleted visibility and re-render items - * @returns {Boolean} new show_deleted setting + * @returns {Boolean} new setting */ - toggleShowDeleted : function( show, store ){ - show = ( show !== undefined )?( show ):( !this.showDeleted ); - store = ( store !== undefined )?( store ):( true ); - + toggleShowDeleted : function( show, options ){ + show = ( show !== undefined )?( show ):( !this.model.contents.includeDeleted ); var self = this; - self.showDeleted = show; - //TODO: at this point deleted/hidden makes more sense (simpler) in the collection - self.model.contents.includeDeleted = show; + var contents = self.model.contents; + contents.setIncludeDeleted( show, options ); self.trigger( 'show-deleted', show ); - if( store ){ self.storage.set( 'show_deleted', show ); } - var fetch = show? fetchDeletedInSection( self.model.contents.currentSection ) : jQuery.when(); + var fetch = show? contents.fetchDeletedInSection( contents.currentSection ) : jQuery.when(); fetch.done( function(){ self.renderItems(); }); - return self.showDeleted; + return contents.includeDeleted; }, /** Toggle and store whether to render explicity hidden contents - * @returns {Boolean} new show_hidden setting + * @returns {Boolean} new setting */ - toggleShowHidden : function( show, store ){ - show = ( show !== undefined )?( show ):( !this.showHidden ); - store = ( store !== undefined )?( store ):( true ); - + toggleShowHidden : function( show, store, options ){ + show = ( show !== undefined )?( show ):( !this.model.contents.includeHidden ); var self = this; - self.showHidden = show; - self.model.contents.includeHidden = show; + var contents = self.model.contents; + contents.setIncludeHidden( show, options ); self.trigger( 'show-hidden', show ); - if( store ){ - self.storage.set( 'show_hidden', show ); - } - var fetch = show? fetchHiddenInSection( self.model.contents.currentSection ) : jQuery.when(); + var fetch = show? contents.fetchHiddenInSection( contents.currentSection ) : jQuery.when(); fetch.done( function(){ self.renderItems(); }); - return self.showDeleted; + return contents.includeHidden; }, /** On the first search, if there are no details - load them, then search */ diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js index ee9423fb901..936f509871f 100644 --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -682,18 +682,20 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ * queueing the ajax call and using a named queue to prevent the call being sent twice */ queueHdaFetch : function queueHdaFetch( column ){ + // console.log( column.model + '.contentsShown:', column.model.contentsShown() ); + var contents = column.model.contents; // console.log( 'queueHdaFetch:', column, column.model.get( 'contents_active' ) ); // if the history model says it has hdas but none are present, queue an ajax req for them - if( column.model.contents.length === 0 && column.model.get( 'contents_active' ).active ){ - // console.log( 'fetch needed: ' + column ); + if( contents.length === 0 && column.model.contentsShown() ){ + console.log( 'fetch needed: ' + column ); var fetchOptions = { silent: true }; - var ids = _.values( column.panel.storage.get( 'expandedIds' ) ).join(); + var ids = _.values( contents.storage.allExpanded() ).join(); if( ids ){ fetchOptions.details = ids; } // this uses a 'named' queue so that duplicate requests are ignored this.hdaQueue.add({ name : column.model.id, fn : function(){ - return column.model.contents.fetchFirst( fetchOptions ) + return contents.fetchFirst( fetchOptions ) .done( function(){ column.panel.renderItems(); }); } }); @@ -704,13 +706,14 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ /** Get the *detailed* json for *all* of a column's history's contents - req'd for searching */ queueHdaFetchDetails : function( column ){ - if( ( column.model.contents.length === 0 && column.model.get( 'contents_active' ).active ) - || ( !column.model.contents.haveDetails() ) ){ + var contents = column.model.contents; + var needsContentsLoaded = contents.length === 0 && column.model.contentsShown(); + if( needsContentsLoaded || !contents.haveDetails() ){ // this uses a 'named' queue so that duplicate requests are ignored this.hdaQueue.add({ name : column.model.id, fn : function(){ - return column.model.contents.progressivelyFetchDetails() + return contents.progressivelyFetchDetails() .done( function(){ column.panel._renderEmptyMessage(); }); } }); diff --git a/client/galaxy/scripts/mvc/list/list-view.js b/client/galaxy/scripts/mvc/list/list-view.js index 0db511b88c5..c234af47157 100644 --- a/client/galaxy/scripts/mvc/list/list-view.js +++ b/client/galaxy/scripts/mvc/list/list-view.js @@ -157,14 +157,14 @@ var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(/** @lends /** create and return a collection for when none is initially passed */ _createDefaultCollection : function(){ // override - console.log( '(_createDefaultCollection)' ); +// console.log( '(_createDefaultCollection)' ); return new this.collectionClass([]); }, /** listening for collection events */ _setUpCollectionListeners : function(){ this.log( this + '._setUpCollectionListeners', this.collection ); - this.collection.off(); + this.stopListening( this.collection ); // bubble up error events this.listenTo( this.collection, { @@ -960,8 +960,8 @@ var ModelListPanel = ListPanel.extend({ //TODO: relation btwn model, collection becoming tangled here // free the collection, and assign the new collection to either // the model[ modelCollectionKey ], attributes.collection, or an empty vanilla collection - this.collection.off(); // console.log( this + '(ModelListPanel) creating collection:', this.modelCollectionKey, this.model[ this.modelCollectionKey ] ); + this.stopListening( this.collection ); this.collection = this.model[ this.modelCollectionKey ] || 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\ No newline at end of file diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js index 49adcbb1b4c..6dda0b81641 100644 --- a/static/scripts/bundled/analysis.bundled.js +++ b/static/scripts/bundled/analysis.bundled.js @@ -1,25592 +1,12 @@ -webpackJsonp([0,1],[ -/* 0 */ -/*!*****************************************!*\ - !*** ./galaxy/scripts/apps/analysis.js ***! - \*****************************************/ -/***/ function(module, exports, __webpack_require__) { - - /* WEBPACK VAR INJECTION */(function(_, Backbone) { - var jQuery = __webpack_require__( /*! jquery */ 3 ), - $ = jQuery, - GalaxyApp = __webpack_require__( /*! galaxy */ 4 ).GalaxyApp, - QUERY_STRING = __webpack_require__( /*! utils/query-string-parsing */ 11 ), - PANEL = __webpack_require__( /*! layout/panel */ 12 ), - ToolPanel = __webpack_require__( /*! ./tool-panel */ 13 ), - HistoryPanel = __webpack_require__( /*! ./history-panel */ 60 ), - PAGE = __webpack_require__( /*! layout/page */ 103 ), - ToolForm = __webpack_require__( /*! mvc/tool/tool-form */ 20 ), - Tours = __webpack_require__( /*! mvc/tours */ 106 ); - - /** define the 'Analyze Data'/analysis/main/home page for Galaxy - * * has a masthead - * * a left tool menu to allow the user to load tools in the center panel - * * a right history menu that shows the user's current data - * * a center panel - * Both panels (generally) persist while the center panel shows any - * UI needed for the current step of an analysis, like: - * * tool forms to set tool parameters, - * * tables showing the contents of datasets - * * etc. - */ - window.app = function app( options, bootstrapped ){ - window.Galaxy = new GalaxyApp( options, bootstrapped ); - Galaxy.debug( 'analysis app' ); - // TODO: use router as App base (combining with Galaxy) - - // .................................................... panels and page - var config = options.config, - toolPanel = new ToolPanel({ - el : '#left', - userIsAnonymous : Galaxy.user.isAnonymous(), - search_url : config.search_url, - toolbox : config.toolbox, - toolbox_in_panel : config.toolbox_in_panel, - stored_workflow_menu_entries : config.stored_workflow_menu_entries, - nginx_upload_path : config.nginx_upload_path, - ftp_upload_site : config.ftp_upload_site, - default_genome : config.default_genome, - default_extension : config.default_extension, - }), - centerPanel = new PANEL.CenterPanel({ - el : '#center' - }), - historyPanel = new HistoryPanel({ - el : '#right', - galaxyRoot : Galaxy.root, - userIsAnonymous : Galaxy.user.isAnonymous(), - allow_user_dataset_purge: config.allow_user_dataset_purge, - }), - analysisPage = new PAGE.PageLayoutView( _.extend( options, { - el : 'body', - left : toolPanel, - center : centerPanel, - right : historyPanel, - })); - - // .................................................... decorate the galaxy object - // TODO: most of this is becoming unnecessary as we move to apps - Galaxy.page = analysisPage; - Galaxy.params = Galaxy.config.params; - - // add tool panel to Galaxy object - Galaxy.toolPanel = toolPanel.tool_panel; - Galaxy.upload = toolPanel.uploadButton; - - Galaxy.currHistoryPanel = historyPanel.historyView; - Galaxy.currHistoryPanel.listenToGalaxy( Galaxy ); - - //HACK: move there - Galaxy.app = { - display : function( view, target ){ - // TODO: Remove this line after select2 update - $( '.select2-hidden-accessible' ).remove(); - centerPanel.display( view ); - }, - }; - - // .................................................... routes - /** */ - var router = new ( Backbone.Router.extend({ - // TODO: not many client routes at this point - fill and remove from server. - // since we're at root here, this may be the last to be routed entirely on the client. - initialize : function( options ){ - this.options = options; - }, - - /** override to parse query string into obj and send to each route */ - execute: function( callback, args, name ){ - Galaxy.debug( 'router execute:', callback, args, name ); - var queryObj = QUERY_STRING.parse( args.pop() ); - args.push( queryObj ); - if( callback ){ - callback.apply( this, args ); - } - }, - - routes : { - '(/)' : 'home', - // TODO: remove annoying 'root' from root urls - '(/)root*' : 'home', - '(/)tours(/)(:tour_id)' : 'show_tours', - }, - - show_tours : function( tour_id ){ - if (tour_id){ - Tours.giveTour(tour_id); - } - else{ - centerPanel.display( new Tours.ToursView() ); - } - }, - - /** */ - home : function( params ){ - // TODO: to router, remove Globals - // load a tool by id (tool_id) or rerun a previous tool execution (job_id) - if( params.tool_id || params.job_id ) { - if ( params.tool_id === 'upload1' ) { - Galaxy.upload.show(); - this._loadCenterIframe( 'welcome' ); - } else { - this._loadToolForm( params ); - } - } else { - // show the workflow run form - if( params.workflow_id ){ - this._loadCenterIframe( 'workflow/run?id=' + params.workflow_id ); - // load the center iframe with controller.action: galaxy.org/?m_c=history&m_a=list -> history/list - } else if( params.m_c ){ - this._loadCenterIframe( params.m_c + '/' + params.m_a ); - // show the workflow run form - } else { - this._loadCenterIframe( 'welcome' ); - } - } - }, - - /** load the center panel with a tool form described by the given params obj */ - _loadToolForm : function( params ){ - //TODO: load tool form code async - params.id = params.tool_id; - centerPanel.display( new ToolForm.View( params ) ); - }, - - /** load the center panel iframe using the given url */ - _loadCenterIframe : function( url, root ){ - root = root || Galaxy.root; - url = root + url; - centerPanel.$( '#galaxy_main' ).prop( 'src', url ); - }, - - }))( options ); - - // .................................................... when the page is ready - // render and start the router - $(function(){ - analysisPage - .render() - .right.historyView.loadCurrentHistory(); - - // use galaxy to listen to history size changes and then re-fetch the user's total size (to update the quota meter) - // TODO: we have to do this here (and after every page.render()) because the masthead is re-created on each - // page render. It's re-created each time because there is no render function and can't be re-rendered without - // re-creating it. - Galaxy.listenTo( analysisPage.right.historyView, 'history-size-change', function(){ - // fetch to update the quota meter adding 'current' for any anon-user's id - Galaxy.user.fetch({ url: Galaxy.user.urlRoot() + '/' + ( Galaxy.user.id || 'current' ) }); - }); - analysisPage.right.historyView.connectToQuotaMeter( analysisPage.masthead.quotaMeter ); - - // start the router - which will call any of the routes above - Backbone.history.start({ - root : Galaxy.root, - pushState : true, - }); - - window.HDA = __webpack_require__( /*! mvc/history/hda-model */ 69 ).HistoryDatasetAssociation; - window.h = analysisPage.right.historyView; - window.c = h.model.contents; - window.sect = function(s){ return c.fetchSection( s ).done( function(){ console.log( c._sectionCollection( s ).map( function( m ){ return m.get( 'hid' ); }).join( ' ' ) ); }) } - window.hid = function(i){ return c.at(i).get( 'hid' ); }; - }); - }; - - /* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(/*! underscore */ 1), __webpack_require__(/*! libs/backbone */ 2))) - -/***/ }, -/* 1 */, -/* 2 */, -/* 3 */, -/* 4 */, -/* 5 */, -/* 6 */, -/* 7 */, -/* 8 */, -/* 9 */, -/* 10 */, -/* 11 */, -/* 12 */, -/* 13 */ -/*!*******************************************!*\ - !*** ./galaxy/scripts/apps/tool-panel.js ***! - \*******************************************/ -/***/ function(module, exports, __webpack_require__) { - - /* WEBPACK VAR INJECTION */(function($, _) {var LeftPanel = __webpack_require__( /*! layout/panel */ 12 ).LeftPanel, - Tools = __webpack_require__( /*! mvc/tool/tools */ 14 ), - Upload = __webpack_require__( /*! mvc/upload/upload-view */ 47 ), - _l = __webpack_require__( /*! utils/localization */ 7 ); - - /* Builds the tool menu panel on the left of the analysis page */ - var ToolPanel = LeftPanel.extend({ - - title : _l( 'Tools' ), - - initialize: function( options ){ - LeftPanel.prototype.initialize.call( this, options ); - this.log( this + '.initialize:', options ); - - /** @type {Object[]} descriptions of user's workflows to be shown in the tool menu */ - this.stored_workflow_menu_entries = options.stored_workflow_menu_entries || []; - - // create tool search, tool panel, and tool panel view. - var tool_search = new Tools.ToolSearch({ - search_url : options.search_url, - hidden : false - }); - var tools = new Tools.ToolCollection( options.toolbox ); - this.tool_panel = new Tools.ToolPanel({ - tool_search : tool_search, - tools : tools, - layout : options.toolbox_in_panel - }); - this.tool_panel_view = new Tools.ToolPanelView({ model: this.tool_panel }); - - // add upload modal - this.uploadButton = new Upload({ - nginx_upload_path : options.nginx_upload_path, - ftp_upload_site : options.ftp_upload_site, - default_genome : options.default_genome, - default_extension : options.default_extension, - }); - }, - - render : function(){ - var self = this; - LeftPanel.prototype.render.call( self ); - self.$( '.panel-header-buttons' ).append( self.uploadButton.$el ); - - // if there are tools, render panel and display everything - if (self.tool_panel.get( 'layout' ).size() > 0) { - self.tool_panel_view.render(); - //TODO: why the hide/show? - self.$( '.toolMenu' ).show(); - } - self.$( '.toolMenuContainer' ).prepend( self.tool_panel_view.$el ); - - self._renderWorkflowMenu(); - - // if a tool link has the minsizehint attribute, handle it here (gen. by hiding the tool panel) - self.$( 'a[minsizehint]' ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( $( self ).attr( 'minsizehint' ) ); - } - }); - }, - - /** build the dom for the workflow portion of the tool menu */ - _renderWorkflowMenu : function(){ - var self = this; - // add internal workflow list - self.$( '#internal-workflows' ).append( self._templateTool({ - title : _l( 'All workflows' ), - href : 'workflow/list_for_run' - })); - _.each( self.stored_workflow_menu_entries, function( menu_entry ){ - self.$( '#internal-workflows' ).append( self._templateTool({ - title : menu_entry.stored_workflow.name, - href : 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id - })); - }); - }, - - /** build a link to one tool */ - _templateTool: function( tool ) { - return [ - '
', - // global - '', tool.title, '', - '
' - ].join(''); - }, - - /** override to include inital menu dom and workflow section */ - _templateBody : function(){ - return [ - '
', - '
', - '', - '
', - '
', - '
', - '', _l( 'Workflows' ), '', - '
', - '
', - '
', - '
', - '
', - '
' - ].join(''); - }, - - toString : function(){ return 'ToolPanel'; } - }); - - module.exports = ToolPanel; - /* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(/*! jquery */ 3), __webpack_require__(/*! underscore */ 1))) - -/***/ }, -/* 14 */ -/*!******************************************!*\ - !*** ./galaxy/scripts/mvc/tool/tools.js ***! - \******************************************/ -/***/ function(module, exports, __webpack_require__) { - - var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** - * Model, view, and controller objects for Galaxy tools and tool panel. - */ - - !(__WEBPACK_AMD_DEFINE_ARRAY__ = [ - __webpack_require__(/*! libs/underscore */ 1), - __webpack_require__(/*! viz/trackster/util */ 15), - __webpack_require__(/*! mvc/dataset/data */ 16), - __webpack_require__(/*! mvc/tool/tool-form */ 20) - - ], __WEBPACK_AMD_DEFINE_RESULT__ = function(_, util, data, ToolForm) { - 'use strict'; - - /** - * Mixin for tracking model visibility. - */ - var VisibilityMixin = { - hidden: false, - - show: function() { - this.set("hidden", false); - }, - - hide: function() { - this.set("hidden", true); - }, - - toggle: function() { - this.set("hidden", !this.get("hidden")); - }, - - is_visible: function() { - return !this.attributes.hidden; - } - - }; - - /** - * A tool parameter. - */ - var ToolParameter = Backbone.Model.extend({ - defaults: { - name: null, - label: null, - type: null, - value: null, - html: null, - num_samples: 5 - }, - - initialize: function(options) { - this.attributes.html = unescape(this.attributes.html); - }, - - copy: function() { - return new ToolParameter(this.toJSON()); - }, - - set_value: function(value) { - this.set('value', value || ''); - } - }); - - var ToolParameterCollection = Backbone.Collection.extend({ - model: ToolParameter - }); - - /** - * A data tool parameter. - */ - var DataToolParameter = ToolParameter.extend({}); - - /** - * An integer tool parameter. - */ - var IntegerToolParameter = ToolParameter.extend({ - set_value: function(value) { - this.set('value', parseInt(value, 10)); - }, - - /** - * Returns samples from a tool input. - */ - get_samples: function() { - return d3.scale.linear() - .domain([this.get('min'), this.get('max')]) - .ticks(this.get('num_samples')); - } - }); - - var FloatToolParameter = IntegerToolParameter.extend({ - set_value: function(value) { - this.set('value', parseFloat(value)); - } - }); - - /** - * A select tool parameter. - */ - var SelectToolParameter = ToolParameter.extend({ - /** - * Returns tool options. - */ - get_samples: function() { - return _.map(this.get('options'), function(option) { - return option[0]; - }); - } - }); - - // Set up dictionary of parameter types. - ToolParameter.subModelTypes = { - 'integer': IntegerToolParameter, - 'float': FloatToolParameter, - 'data': DataToolParameter, - 'select': SelectToolParameter - }; - - /** - * A Galaxy tool. - */ - var Tool = Backbone.Model.extend({ - // Default attributes. - defaults: { - id: null, - name: null, - description: null, - target: null, - inputs: [], - outputs: [] - }, - - urlRoot: Galaxy.root + 'api/tools', - - initialize: function(options) { - - // Set parameters. - this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function(p) { - var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter; - return new p_class(p); - }))); - }, - - /** - * - */ - toJSON: function() { - var rval = Backbone.Model.prototype.toJSON.call(this); - - // Convert inputs to JSON manually. - rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); }); - return rval; - }, - - /** - * Removes inputs of a particular type; this is useful because not all inputs can be handled by - * client and server yet. - */ - remove_inputs: function(types) { - var tool = this, - incompatible_inputs = tool.get('inputs').filter( function(input) { - return ( types.indexOf( input.get('type') ) !== -1); - }); - tool.get('inputs').remove(incompatible_inputs); - }, - - /** - * Returns object copy, optionally including only inputs that can be sampled. - */ - copy: function(only_samplable_inputs) { - var copy = new Tool(this.toJSON()); - - // Return only samplable inputs if flag is set. - if (only_samplable_inputs) { - var valid_inputs = new Backbone.Collection(); - copy.get('inputs').each(function(input) { - if (input.get_samples()) { - valid_inputs.push(input); - } - }); - copy.set('inputs', valid_inputs); - } - - return copy; - }, - - apply_search_results: function(results) { - ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); - return this.is_visible(); - }, - - /** - * Set a tool input's value. - */ - set_input_value: function(name, value) { - this.get('inputs').find(function(input) { - return input.get('name') === name; - }).set('value', value); - }, - - /** - * Set many input values at once. - */ - set_input_values: function(inputs_dict) { - var self = this; - _.each(_.keys(inputs_dict), function(input_name) { - self.set_input_value(input_name, inputs_dict[input_name]); - }); - }, - - /** - * Run tool; returns a Deferred that resolves to the tool's output(s). - */ - run: function() { - return this._run(); - }, - - /** - * Rerun tool using regions and a target dataset. - */ - rerun: function(target_dataset, regions) { - return this._run({ - action: 'rerun', - target_dataset_id: target_dataset.id, - regions: regions - }); - }, - - /** - * Returns input dict for tool's inputs. - */ - get_inputs_dict: function() { - var input_dict = {}; - this.get('inputs').each(function(input) { - input_dict[input.get('name')] = input.get('value'); - }); - return input_dict; - }, - - /** - * Run tool; returns a Deferred that resolves to the tool's output(s). - * NOTE: this method is a helper method and should not be called directly. - */ - _run: function(additional_params) { - // Create payload. - var payload = _.extend({ - tool_id: this.id, - inputs: this.get_inputs_dict() - }, additional_params); - - // Because job may require indexing datasets, use server-side - // deferred to ensure that job is run. Also use deferred that - // resolves to outputs from tool. - var run_deferred = $.Deferred(), - ss_deferred = new util.ServerStateDeferred({ - ajax_settings: { - url: this.urlRoot, - data: JSON.stringify(payload), - dataType: "json", - contentType: 'application/json', - type: "POST" - }, - interval: 2000, - success_fn: function(response) { - return response !== "pending"; - } - }); - - // Run job and resolve run_deferred to tool outputs. - $.when(ss_deferred.go()).then(function(result) { - run_deferred.resolve(new data.DatasetCollection(result)); - }); - return run_deferred; - } - }); - _.extend(Tool.prototype, VisibilityMixin); - - /** - * Tool view. - */ - var ToolView = Backbone.View.extend({ - - }); - - /** - * Wrap collection of tools for fast access/manipulation. - */ - var ToolCollection = Backbone.Collection.extend({ - model: Tool - }); - - /** - * Label or section header in tool panel. - */ - var ToolSectionLabel = Backbone.Model.extend(VisibilityMixin); - - /** - * Section of tool panel with elements (labels and tools). - */ - var ToolSection = Backbone.Model.extend({ - defaults: { - elems: [], - open: false - }, - - clear_search_results: function() { - _.each(this.attributes.elems, function(elt) { - elt.show(); - }); - - this.show(); - this.set("open", false); - }, - - apply_search_results: function(results) { - var all_hidden = true, - cur_label; - _.each(this.attributes.elems, function(elt) { - if (elt instanceof ToolSectionLabel) { - cur_label = elt; - cur_label.hide(); - } - else if (elt instanceof Tool) { - if (elt.apply_search_results(results)) { - all_hidden = false; - if (cur_label) { - cur_label.show(); - } - } - } - }); - - if (all_hidden) { - this.hide(); - } - else { - this.show(); - this.set("open", true); - } - } - }); - _.extend(ToolSection.prototype, VisibilityMixin); - - /** - * Tool search that updates results when query is changed. Result value of null - * indicates that query was not run; if not null, results are from search using - * query. - */ - var ToolSearch = Backbone.Model.extend({ - defaults: { - search_hint_string: "search tools", - min_chars_for_search: 3, - clear_btn_url: "", - search_url: "", - visible: true, - query: "", - results: null, - // ESC (27) will clear the input field and tool search filters - clear_key: 27 - }, - - urlRoot: Galaxy.root + 'api/tools', - - initialize: function() { - this.on("change:query", this.do_search); - }, - - /** - * Do the search and update the results. - */ - do_search: function() { - var query = this.attributes.query; - - // If query is too short, do not search. - if (query.length < this.attributes.min_chars_for_search) { - this.set("results", null); - return; - } - - // Do search via AJAX. - var q = query; - // Stop previous ajax-request - if (this.timer) { - clearTimeout(this.timer); - } - // Start a new ajax-request in X ms - $("#search-clear-btn").hide(); - $("#search-spinner").show(); - var self = this; - this.timer = setTimeout(function () { - // log the search to analytics if present - if ( typeof ga !== 'undefined' ) { - ga( 'send', 'pageview', Galaxy.root + '?q=' + q ); - } - $.get( self.urlRoot, { q: q }, function (data) { - self.set("results", data); - $("#search-spinner").hide(); - $("#search-clear-btn").show(); - }, "json" ); - }, 400 ); - }, - - clear_search: function() { - this.set("query", ""); - this.set("results", null); - } - - }); - _.extend(ToolSearch.prototype, VisibilityMixin); - - /** - * Tool Panel. - */ - var ToolPanel = Backbone.Model.extend({ - - initialize: function(options) { - this.attributes.tool_search = options.tool_search; - this.attributes.tool_search.on("change:results", this.apply_search_results, this); - this.attributes.tools = options.tools; - this.attributes.layout = new Backbone.Collection( this.parse(options.layout) ); - }, - - /** - * Parse tool panel dictionary and return collection of tool panel elements. - */ - parse: function(response) { - // Recursive function to parse tool panel elements. - var self = this, - // Helper to recursively parse tool panel. - parse_elt = function(elt_dict) { - var type = elt_dict.model_class; - // There are many types of tools; for now, anything that ends in 'Tool' - // is treated as a generic tool. - if ( type.indexOf('Tool') === type.length - 4 ) { - return self.attributes.tools.get(elt_dict.id); - } - else if (type === 'ToolSection') { - // Parse elements. - var elems = _.map(elt_dict.elems, parse_elt); - elt_dict.elems = elems; - return new ToolSection(elt_dict); - } - else if (type === 'ToolSectionLabel') { - return new ToolSectionLabel(elt_dict); - } - }; - - return _.map(response, parse_elt); - }, - - clear_search_results: function() { - this.get('layout').each(function(panel_elt) { - if (panel_elt instanceof ToolSection) { - panel_elt.clear_search_results(); - } - else { - // Label or tool, so just show. - panel_elt.show(); - } - }); - }, - - apply_search_results: function() { - var results = this.get('tool_search').get('results'); - if (results === null) { - this.clear_search_results(); - return; - } - - var cur_label = null; - this.get('layout').each(function(panel_elt) { - if (panel_elt instanceof ToolSectionLabel) { - cur_label = panel_elt; - cur_label.hide(); - } - else if (panel_elt instanceof Tool) { - if (panel_elt.apply_search_results(results)) { - if (cur_label) { - cur_label.show(); - } - } - } - else { - // Starting new section, so clear current label. - cur_label = null; - panel_elt.apply_search_results(results); - } - }); - } - }); - - /** - * View classes for Galaxy tools and tool panel. - * - * Views use the templates defined below for rendering. Views update as needed - * based on (a) model/collection events and (b) user interactions; in this sense, - * they are controllers are well and the HTML is the real view in the MVC architecture. - */ - - /** - * Base view that handles visibility based on model's hidden attribute. - */ - var BaseView = Backbone.View.extend({ - initialize: function() { - this.model.on("change:hidden", this.update_visible, this); - this.update_visible(); - }, - update_visible: function() { - ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); - } - }); - - /** - * Link to a tool. - */ - var ToolLinkView = BaseView.extend({ - tagName: 'div', - - render: function() { - // create element - var $link = $('
'); - $link.append(templates.tool_link(this.model.toJSON())); - - // open upload dialog for upload tool - if (this.model.id === 'upload1') { - $link.find('a').on('click', function(e) { - e.preventDefault(); - Galaxy.upload.show(); - }); - } - else if ( this.model.get( 'model_class' ) === 'Tool' ) { // regular tools - var self = this; - $link.find('a').on('click', function(e) { - e.preventDefault(); - var form = new ToolForm.View( { id : self.model.id, version : self.model.get('version') } ); - form.deferred.execute(function() { - Galaxy.app.display( form ); - }); - }); - } - - // add element - this.$el.append($link); - return this; - } - }); - - /** - * Panel label/section header. - */ - var ToolSectionLabelView = BaseView.extend({ - tagName: 'div', - className: 'toolPanelLabel', - - render: function() { - this.$el.append( $("").text(this.model.attributes.text) ); - return this; - } - }); - - /** - * Panel section. - */ - var ToolSectionView = BaseView.extend({ - tagName: 'div', - className: 'toolSectionWrapper', - - initialize: function() { - BaseView.prototype.initialize.call(this); - this.model.on("change:open", this.update_open, this); - }, - - render: function() { - // Build using template. - this.$el.append( templates.panel_section(this.model.toJSON()) ); - - // Add tools to section. - var section_body = this.$el.find(".toolSectionBody"); - _.each(this.model.attributes.elems, function(elt) { - if (elt instanceof Tool) { - var tool_view = new ToolLinkView({model: elt, className: "toolTitle"}); - tool_view.render(); - section_body.append(tool_view.$el); - } - else if (elt instanceof ToolSectionLabel) { - var label_view = new ToolSectionLabelView({model: elt}); - label_view.render(); - section_body.append(label_view.$el); - } - else { - // TODO: handle nested section bodies? - } - }); - return this; - }, - - events: { - 'click .toolSectionTitle > a': 'toggle' - }, - - /** - * Toggle visibility of tool section. - */ - toggle: function() { - this.model.set("open", !this.model.attributes.open); - }, - - /** - * Update whether section is open or close. - */ - update_open: function() { - (this.model.attributes.open ? - this.$el.children(".toolSectionBody").slideDown("fast") : - this.$el.children(".toolSectionBody").slideUp("fast") - ); - } - }); - - var ToolSearchView = Backbone.View.extend({ - tagName: 'div', - id: 'tool-search', - className: 'bar', - - events: { - 'click': 'focus_and_select', - 'keyup :input': 'query_changed', - 'click #search-clear-btn': 'clear' - }, - - render: function() { - this.$el.append( templates.tool_search(this.model.toJSON()) ); - if (!this.model.is_visible()) { - this.$el.hide(); - } - this.$el.find('[title]').tooltip(); - return this; - }, - - focus_and_select: function() { - this.$el.find(":input").focus().select(); - }, - - clear: function() { - this.model.clear_search(); - this.$el.find(":input").val(''); - this.focus_and_select(); - return false; - }, - - query_changed: function( evData ) { - // check for the 'clear key' (ESC) first - if( ( this.model.attributes.clear_key ) && - ( this.model.attributes.clear_key === evData.which ) ){ - this.clear(); - return false; - } - this.model.set("query", this.$el.find(":input").val()); - } - }); - - /** - * Tool panel view. Events triggered include: - * tool_link_click(click event, tool_model) - */ - var ToolPanelView = Backbone.View.extend({ - tagName: 'div', - className: 'toolMenu', - - /** - * Set up view. - */ - initialize: function() { - this.model.get('tool_search').on("change:results", this.handle_search_results, this); - }, - - render: function() { - var self = this; - - // Render search. - var search_view = new ToolSearchView( { model: this.model.get('tool_search') } ); - search_view.render(); - self.$el.append(search_view.$el); - - // Render panel. - this.model.get('layout').each(function(panel_elt) { - if (panel_elt instanceof ToolSection) { - var section_title_view = new ToolSectionView({model: panel_elt}); - section_title_view.render(); - self.$el.append(section_title_view.$el); - } - else if (panel_elt instanceof Tool) { - var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); - tool_view.render(); - self.$el.append(tool_view.$el); - } - else if (panel_elt instanceof ToolSectionLabel) { - var label_view = new ToolSectionLabelView({model: panel_elt}); - label_view.render(); - self.$el.append(label_view.$el); - } - }); - - // Setup tool link click eventing. - self.$el.find("a.tool-link").click(function(e) { - // Tool id is always the first class. - var - tool_id = $(this).attr('class').split(/\s+/)[0], - tool = self.model.get('tools').get(tool_id); - - self.trigger("tool_link_click", e, tool); - }); - - return this; - }, - - handle_search_results: function() { - var results = this.model.get('tool_search').get('results'); - if (results && results.length === 0) { - $("#search-no-results").show(); - } - else { - $("#search-no-results").hide(); - } - } - }); - - /** - * View for working with a tool: setting parameters and inputs and executing the tool. - */ - var ToolFormView = Backbone.View.extend({ - className: 'toolForm', - - render: function() { - this.$el.children().remove(); - this.$el.append( templates.tool_form(this.model.toJSON()) ); - } - }); - - /** - * Integrated tool menu + tool execution. - */ - var IntegratedToolMenuAndView = Backbone.View.extend({ - className: 'toolMenuAndView', - - initialize: function() { - this.tool_panel_view = new ToolPanelView({collection: this.collection}); - this.tool_form_view = new ToolFormView(); - }, - - render: function() { - // Render and append tool panel. - this.tool_panel_view.render(); - this.tool_panel_view.$el.css("float", "left"); - this.$el.append(this.tool_panel_view.$el); - - // Append tool form view. - this.tool_form_view.$el.hide(); - this.$el.append(this.tool_form_view.$el); - - // On tool link click, show tool. - var self = this; - this.tool_panel_view.on("tool_link_click", function(e, tool) { - // Prevents click from activating link: - e.preventDefault(); - // Show tool that was clicked on: - self.show_tool(tool); - }); - }, - - /** - * Fetch and display tool. - */ - show_tool: function(tool) { - var self = this; - tool.fetch().done( function() { - self.tool_form_view.model = tool; - self.tool_form_view.render(); - self.tool_form_view.$el.show(); - $('#left').width("650px"); - }); - } - }); - - // TODO: move into relevant views - var templates = { - // the search bar at the top of the tool panel - tool_search : _.template([ - '', - ' ', - //TODO: replace with icon - '', - ].join('')), - - // the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation') - panel_section : _.template([ - '
', - '<%- name %>', - '
', - '