ui: adding PopupMenu view as alternate to make_popup_menu and allow changing option text, adding/removing options, and adding checkmarks for togglable options; index.mako: use PopupMenu for history-options-button; history panel: use alternate_history.mako to add 'collapse all', 'Include hidden datasets'(toggle), 'Include deleted datasets'(toggle) to history-options-button; alternate_history.mako: include better system for debugging js when changing source directly is problematic (main/test); pack_scripts;

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -98,7 +98,6 @@ class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ):
         return trans.fill_template_mako( "/my_data.mako" )
 
     @web.expose
-    #def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ):
     def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ):
         """
         Display the current history, creating a new history if necessary.

static/scripts/mvc/base-mvc.js

@@ -288,7 +288,7 @@ var PersistantStorage = function( storageKey, storageDefaults ){
         },
         /** String representation.
          */
-        toString : function(){ return 'PersistantStorage(' + data + ')'; }
+        toString : function(){ return 'PersistantStorage(' + storageKey + ')'; }
     });
     
     return returnedStorage;

static/scripts/mvc/dataset/hda-base.js

@@ -28,6 +28,7 @@ var HDABaseView = BaseView.extend( LoggableMixin ).extend(
      *  @see Backbone.View#initialize
      */
     initialize  : function( attributes ){
+        if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
         this.log( this + '.initialize:', attributes );
 
         /** list of rendering functions for the default, primary icon-buttons. */
@@ -334,6 +335,8 @@ var HDABaseView = BaseView.extend( LoggableMixin ).extend(
 
         //TODO: not a fan of this dispatch
         switch( this.model.get( 'state' ) ){
+            case HistoryDatasetAssociation.STATES.NEW :
+                break;
             case HistoryDatasetAssociation.STATES.NOT_VIEWABLE :
                 this._render_body_not_viewable( body );
                 break;

static/scripts/mvc/dataset/hda-model.js

@@ -130,8 +130,7 @@ var HistoryDatasetAssociation = BaseModel.extend( LoggableMixin ).extend(
         //TODO: to list inclusion test
         //TODO: class level readyStates list
         return (
-            ( state === HistoryDatasetAssociation.STATES.NEW )
-        ||  ( state === HistoryDatasetAssociation.STATES.OK )
+            ( state === HistoryDatasetAssociation.STATES.OK )
         ||  ( state === HistoryDatasetAssociation.STATES.EMPTY )
         ||  ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA )
         ||  ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE )

static/scripts/mvc/history/history-panel.js

@@ -140,6 +140,8 @@ var HistoryPanel = BaseView.extend( LoggableMixin ).extend(
      *  @see Backbone.View#initialize
      */
     initialize : function( attributes ){
+        // set the logger if requested
+        if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
         this.log( this + '.initialize:', attributes );
 
         // set up url templates
@@ -203,7 +205,7 @@ var HistoryPanel = BaseView.extend( LoggableMixin ).extend(
             show_deleted : false,
             show_hidden  : false
         });
-        this.log( 'this.storage:', this.storage.get() );
+        this.log( this + ' (prev) storage:', JSON.stringify( this.storage.get(), null, 2 ) );
 
         // expanded Hdas is a map of hda.ids -> a boolean rep'ing whether this hda's body is expanded
         // store any pre-expanded ids passed in
@@ -226,7 +228,7 @@ var HistoryPanel = BaseView.extend( LoggableMixin ).extend(
         this.show_deleted = this.storage.get( 'show_deleted' );
         this.show_hidden  = this.storage.get( 'show_hidden' );
         //this.log( 'this.show_deleted:', this.show_deleted, 'show_hidden', this.show_hidden );
-        this.log( '(init\'d) this.storage:', this.storage.get() );
+        this.log( this + ' (init\'d) storage:', this.storage.get() );
     },
 
     /** Add an hda to this history's collection
@@ -351,7 +353,8 @@ var HistoryPanel = BaseView.extend( LoggableMixin ).extend(
             historyView.hdaViews[ hdaId ] = new historyView.HDAView({
                     model           : hda,
                     expanded        : expanded,
-                    urlTemplates    : historyView.hdaUrlTemplates
+                    urlTemplates    : historyView.hdaUrlTemplates,
+                    logger          : historyView.logger
                 });
             historyView._setUpHdaListeners( historyView.hdaViews[ hdaId ] );
 
@@ -432,19 +435,23 @@ var HistoryPanel = BaseView.extend( LoggableMixin ).extend(
     /** Handle the user toggling the deleted visibility by:
      *      (1) storing the new value in the persistant storage
      *      (2) re-rendering the history
+     * @returns {Boolean} new show_deleted setting
      */
     toggleShowDeleted : function(){
         this.storage.set( 'show_deleted', !this.storage.get( 'show_deleted' ) );
         this.render();
+        return this.storage.get( 'show_deleted' );
     },
 
     /** Handle the user toggling the deleted visibility by:
      *      (1) storing the new value in the persistant storage
      *      (2) re-rendering the history
+     * @returns {Boolean} new show_hidden setting
      */
     toggleShowHidden : function(){
         this.storage.set( 'show_hidden', !this.storage.get( 'show_hidden' ) );
         this.render();
+        return this.storage.get( 'show_hidden' );
     },
 
     /** Collapse all hda bodies and clear expandedHdas in the storage

static/scripts/mvc/ui.js

@@ -76,11 +76,11 @@ IconButtonView.templates = {
     iconButton : Handlebars.partials.iconButton
 };
 
-
 var IconButtonCollection = Backbone.Collection.extend({
     model: IconButton
 });
 
+
 //------------------------------------------------------------------------------
 /**
  * Menu with multiple icon buttons. Views are not needed nor used for individual buttons.
@@ -166,15 +166,319 @@ var GalaxyPaths = Backbone.Model.extend({
 });
 
 
+// =============================================================================
+/** @class View for a popup menu
+ *  @name PopupMenu
+ *
+ *  @constructs
+ */
+var PopupMenu = Backbone.View.extend(
+/** @lends PopupMenu.prototype */{
 
+    /* TODO:
+        add submenus
+        add hrefs
+        test various html keys
+        add make_popupmenus style
+        get template inside this file somehow
+    */
+    /** Cache the desired button element and options, set up the button click handler
+     *  NOTE: attaches this view as HTML/jQ data on the button for later use.
+     */
+    //TODO: include docs on special option keys (divider, checked, etc.)
+    initialize : function( $button, options ){
+        // default settings
+        this.$button = $button || $( '<div/>' );
+        this.options = options || [];
+        //console.debug( this + '.initialize, button:', $button, ', options:', options );
 
+        // set up button click -> open menu behavior
+        var menu = this;
+        this.$button.click( function( event ){
+            menu._renderAndShow( event );
+            //event.stopPropagation();
+            return false;
+        });
 
+        // attach this view as a data object on the button - for later access
+        //TODO:?? memleak?
+        this.$button.data( 'PopupMenu', this );
 
+        // template loading is problematic - ui is loaded in base.mako
+        //  and the template (prev.) needed to be loaded before ui
+        if( !this.templates.wrapper ){
+            this.templates.wrapper = Handlebars.templates[ 'template-popupmenu-wrapper' ];
+        }
+    },
 
+    /** Render the menu. NOTE: doesn't attach itself to the DOM.
+     *  @see PopupMenu#_renderAndShow
+     */
+    render : function(){
+        var menu = this;
 
+        // render the menu body
+        this.$el.addClass( 'popmenu-wrapper' )
+            .css({
+                position:   'absolute',
+                display:    'none'
+            });
 
+        //BUG: anchors within a.popupmenu-option render OUTSIDE the a.popupmenu-option!?
+        this.$el.html( PopupMenu.templates.menu({
+            options     : this.options,
+            // sets menu div id to '{{ id }}-menu'
+            id          : this.$button.attr( 'id' )
+        }));
+        //console.debug( this.$el, ':', this.$el.html() );
 
+        // set up behavior on each link/anchor elem
+        if( this.options.length ){
+            this.$el.find( 'li' ).each( function( i, li ){
+                var $li = $( li ),
+                    $anchor = $li.children( 'a.popupmenu-option' ),
+                    menuFunc = menu.options[ i ].func;
 
+                //console.debug( 'setting up behavior:', i, menu.options[ i ], $li, $anchor );
+                if( $anchor.length && menuFunc ){
+                    $anchor.click( function( event ){
+                        menuFunc( event, menu.options[ i ] );
+                    });
+                }
 
+                // cache the anchor as a jq obj within the options obj
+                menu.options[ i ].$li = $li;
+            });
+        }
+        return this;
+    },
 
+    /** Get the absolute position/offset for the menu
+     */
+    _getShownPosition : function( clickEvent ){
+        var menuWidth = this.$el.width(),
+            // display menu horiz. centered on click...
+            x = clickEvent.pageX - menuWidth / 2 ;
+
+        // ...but adjust that to handle horiz. scroll and window dimensions (draw entirely on visible screen area)
+        x = Math.min( x, $( document ).scrollLeft() + $( window ).width() - menuWidth - 5 );
+        x = Math.max( x, $( document ).scrollLeft() + 5 );
+
+        return {
+            top: clickEvent.pageY,
+            left: x
+        };
+    },
+
+    /** Render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show
+     */
+    _renderAndShow : function( clickEvent ){
+        this.render();
+        this.$el.appendTo( 'body' );
+        this.$el.css( this._getShownPosition( clickEvent ) );
+        this._setUpCloseBehavior();
+        this.$el.show();
+    },
+
+    /** Bind an event handler to all available frames so that when anything is clicked
+     *      * the menu is removed from the DOM
+     *      * The event handler unbinds itself
+     */
+    _setUpCloseBehavior : function(){
+        var menu = this,
+            // function to close popup and unbind itself
+            closePopupWhenClicked = function( $elClicked ){
+                $elClicked.bind( "click.close_popup", function(){
+                    menu.remove();
+                    $elClicked.unbind( "click.close_popup" );
+                });
+            };
+
+        // bind to current, parent, and sibling frames
+        //TODO: (Assuming for now that this is the best way to do this...)
+        closePopupWhenClicked( $( window.document ) );
+        closePopupWhenClicked( $( window.top.document ) );
+        _.each( window.top.frames, function( siblingFrame ){
+            closePopupWhenClicked( $( siblingFrame.document ) );
+        });
+    },
+
+    /** Add a menu option/item at the given index
+     */
+    addItem : function( item, index ){
+        // append to end if no index
+        index = ( index >= 0 )?( index ):( this.options.length );
+        this.options.splice( index, 0, item );
+        return this;
+    },
+
+    /** Remove a menu option/item at the given index
+     */
+    removeItem : function( index ){
+        if( index >=0 ){
+            this.options.splice( index, 1 );
+        }
+        return this;
+    },
+
+    /** Search for a menu option by it's html
+     */
+    findIndexByHtml : function( html ){
+        for( var i=0; i<this.options.length; i++ ){
+            if( ( _.has( this.options[i], 'html' ) )
+            &&  ( this.options[i].html === html ) ){
+                return i;
+            }
+        }
+        return null;
+    },
+
+    /** Search for a menu option by it's html
+     */
+    findItemByHtml : function( html ){
+        return this.options[( this.findIndexByHtml( html ) )];
+    },
+
+    /** String representation. */
+    toString : function(){
+        return 'PopupMenu';
+    }
+});
+PopupMenu.templates = {
+    menu    : Handlebars.templates[ 'template-popupmenu-menu' ]
+};
+
+// -----------------------------------------------------------------------------
+// the following class functions are bridges from the original make_popupmenu and make_popup_menus
+//  to the newer backbone.js PopupMenu
+
+/** Create a PopupMenu from simple map initial_options activated by clicking button_element.
+ *      Converts initial_options to object array used by PopupMenu.
+ *  @param {jQuery|DOMElement} button_element element which, when clicked, activates menu
+ *  @param {Object} initial_options map of key -> values, where
+ *      key is option text, value is fn to call when option is clicked
+ *  @returns {PopupMenu} the PopupMenu created
+ */
+PopupMenu.make_popupmenu = function( button_element, initial_options ){
+    var convertedOptions = [];
+    _.each( initial_options, function( optionVal, optionKey ){
+        var newOption = { html: optionKey };
+
+        // keys with null values indicate: header
+        if( optionVal === null ){ // !optionVal? (null only?)
+            newOption.header = true;
+
+        // keys with function values indicate: a menu option
+        } else if( jQuery.type( optionVal ) === 'function' ){
+            newOption.func = optionVal;
+        }
+        //TODO:?? any other special optionVals?
+        // there was no divider option originally
+        convertedOptions.push( newOption );
+    });
+    return new PopupMenu( $( button_element ), convertedOptions );
+};
+
+/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.
+ *  @param {jQuery} $parent the element that contains the links to convert to options
+ *  @param {String} selector jq selector string to find links
+ *  @returns {Object[]} the options array to initialize a PopupMenu
+ */
+//TODO: lose parent and selector, pass in array of links, use map to return options
+PopupMenu.convertLinksToOptions = function( $parent, selector ){
+    $parent = $( $parent );
+    selector = selector || 'a';
+    var options = [];
+    $parent.find( selector ).each( function( elem, i ){
+        var option = {},
+            $link = $( elem );
+
+        // convert link text to the option text (html) and the href into the option func
+        option.html = $link.text();
+        if( linkHref ){
+            var linkHref    = $link.attr( 'href' ),
+                linkTarget  = $link.attr( 'target' ),
+                confirmText = $link.attr( 'confirm' );
+
+            option.func = function(){
+                // if there's a "confirm" attribute, throw up a confirmation dialog, and
+                //  if the user cancels - do nothing
+                if( ( confirmText ) && ( !confirm( confirmText ) ) ){ return; }
+
+                // if there's no confirm attribute, or the user accepted the confirm dialog:
+                var f;
+                switch( linkTarget ){
+                    // relocate the center panel
+                    case '_parent':
+                        window.parent.location = linkHref;
+                        break;
+
+                    // relocate the entire window
+                    case '_top':
+                        window.top.location = linkHref;
+                        break;
+
+                    // Http request target is a window named demolocal on the local box
+                    //TODO: I still don't understand this option (where the hell does f get set? confirm?)
+                    case 'demo':
+                        if( f === undefined || f.closed ){
+                            f = window.open( linkHref, linkTarget );
+                            f.creator = self;
+                        }
+                        break;
+
+                    // relocate this panel
+                    default:
+                        window.location = linkHref;
+                }
+            };
+        }
+        options.push( option );
+    });
+    return options;
+};
+
+/** Create a single popupmenu from existing DOM button and anchor elements
+ *  @param {jQuery} $buttonElement the element that when clicked will open the menu
+ *  @param {jQuery} $menuElement the element that contains the anchors to convert into a menu
+ *  @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options
+ *  @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu
+ */
+PopupMenu.fromExistingDom = function( $buttonElement, $menuElement, menuElementLinkSelector ){
+    $buttonElement = $( $buttonElement );
+    $menuElement = $( $menuElement );
+    var options = PopupMenu.convertLinksToOptions( $menuElement, menuElementLinkSelector );
+    // we're done with the menu (having converted it to an options map)
+    $menuElement.remove();
+    return new PopupMenu( $buttonElement, options );
+};
+
+/** Create all popupmenus within a document or a more specific element
+ *  @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)
+ *  @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to "div[popupmenu]")
+ *  @param {Function} buttonSelectorBuildFn the function to build the jq button selector.
+ *      Will be passed $menuElement, parent.
+ *      (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )
+ *  @returns {PopupMenu[]} array of popupmenus created
+ */
+PopupMenu.make_popup_menus = function( parent, menuSelector, buttonSelectorBuildFn ){
+    parent = parent || document;
+    // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'
+    //  which contains the id of the button that activates the menu
+    menuSelector = menuSelector || 'div[popupmenu]';
+    // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button
+    buttonSelectorBuildFn = buttonSelectorBuildFn || function( $menuElement, parent ){
+        return '#' + $menuElement.attr( 'popupmenu' );
+    };
+
+    // aggregate and return all PopupMenus
+    var popupMenusCreated = [];
+    $( parent ).find( menuSelector ).each( function(){
+        var $menuElement    = $( this ),
+            $buttonElement  = $( parent ).find( buttonSelectorBuildFn( $menuElement, parent ) );
+        popupMenusCreated.push( PopupMenu.fromDom( $buttonElement, $menuElement ) );
+        $buttonElement.addClass( 'popup' );
+    });
+    return popupMenusCreated;
+}
 

static/scripts/packed/mvc/base-mvc.js

@@ -1 +1 @@
-var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+data+")"}});return f};
+var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+g+")"}});return f};

static/scripts/packed/mvc/dataset/hda-model.js

@@ -1 +1 @@
-var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}});
+var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}});

static/scripts/packed/templates/compiled/template-popupmenu-menu.js

@@ -0,0 +1 @@
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-popupmenu-menu"]=b(function(f,s,q,l,x){q=q||f.helpers;var r="",i,h,d="function",c=this.escapeExpression,p=this;function o(B,A){var y="",z;y+="\n    ";z=B.options;z=q.each.call(B,z,{hash:{},inverse:p.noop,fn:p.program(2,n,A)});if(z||z===0){y+=z}y+="\n";return y}function n(B,A){var y="",z;y+="\n        ";z=B.divider;z=q["if"].call(B,z,{hash:{},inverse:p.program(5,k,A),fn:p.program(3,m,A)});if(z||z===0){y+=z}y+="\n    ";return y}function m(z,y){return'\n            <li class="divider"></li>\n        '}function k(B,A){var y="",z;y+="\n            ";z=B.header;z=q["if"].call(B,z,{hash:{},inverse:p.program(8,g,A),fn:p.program(6,j,A)});if(z||z===0){y+=z}y+="\n        ";return y}function j(C,B){var z="",A,y;z+='\n                <li class="head"><a href=""javascript:void(0);">';y=q.html;if(y){A=y.call(C,{hash:{}})}else{A=C.html;A=typeof A===d?A():A}if(A||A===0){z+=A}z+="</a></li>\n            ";return z}function g(C,B){var z="",A,y;z+="\n                ";z+='\n                <li><a href="';A=C.href;A=q["if"].call(C,A,{hash:{},inverse:p.program(11,w,B),fn:p.program(9,e,B)});if(A||A===0){z+=A}z+='"\n                    ';A=C.href;A=q["if"].call(C,A,{hash:{},inverse:p.noop,fn:p.program(13,v,B)});if(A||A===0){z+=A}z+=' class="popupmenu-option">\n                        ';A=C.checked;A=q["if"].call(C,A,{hash:{},inverse:p.noop,fn:p.program(15,u,B)});if(A||A===0){z+=A}z+="\n                        ";y=q.html;if(y){A=y.call(C,{hash:{}})}else{A=C.html;A=typeof A===d?A():A}if(A||A===0){z+=A}z+="\n                </a></li>\n            ";return z}function e(B,A){var z,y;y=q.href;if(y){z=y.call(B,{hash:{}})}else{z=B.href;z=typeof z===d?z():z}return c(z)}function w(z,y){return"javascript:void(0);"}function v(C,B){var z="",A,y;z+='target="';y=q.target;if(y){A=y.call(C,{hash:{}})}else{A=C.target;A=typeof A===d?A():A}z+=c(A)+'"';return z}function u(z,y){return'<span class="ficon ok"></span>'}function t(z,y){return"\n    <li>No Options.</li>\n"}r+='<ul id="';h=q.id;if(h){i=h.call(s,{hash:{}})}else{i=s.id;i=typeof i===d?i():i}r+=c(i)+'-menu" class="dropdown-menu">\n';i=s.options;i=i==null||i===false?i:i.length;i=q["if"].call(s,i,{hash:{},inverse:p.program(17,t,x),fn:p.program(1,o,x)});if(i||i===0){r+=i}r+="\n</ul>";return r})})();

static/scripts/templates/compiled/template-popupmenu-menu.js

@@ -0,0 +1,117 @@
+(function() {
+  var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
+templates['template-popupmenu-menu'] = template(function (Handlebars,depth0,helpers,partials,data) {
+  helpers = helpers || Handlebars.helpers;
+  var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this;
+
+function program1(depth0,data) {
+  
+  var buffer = "", stack1;
+  buffer += "\n    ";
+  stack1 = depth0.options;
+  stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n";
+  return buffer;}
+function program2(depth0,data) {
+  
+  var buffer = "", stack1;
+  buffer += "\n        ";
+  stack1 = depth0.divider;
+  stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(5, program5, data),fn:self.program(3, program3, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n    ";
+  return buffer;}
+function program3(depth0,data) {
+  
+  
+  return "\n            <li class=\"divider\"></li>\n        ";}
+
+function program5(depth0,data) {
+  
+  var buffer = "", stack1;
+  buffer += "\n            ";
+  stack1 = depth0.header;
+  stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(8, program8, data),fn:self.program(6, program6, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n        ";
+  return buffer;}
+function program6(depth0,data) {
+  
+  var buffer = "", stack1, foundHelper;
+  buffer += "\n                <li class=\"head\"><a href=\"\"javascript:void(0);\">";
+  foundHelper = helpers.html;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.html; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "</a></li>\n            ";
+  return buffer;}
+
+function program8(depth0,data) {
+  
+  var buffer = "", stack1, foundHelper;
+  buffer += "\n                ";
+  buffer += "\n                <li><a href=\"";
+  stack1 = depth0.href;
+  stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(11, program11, data),fn:self.program(9, program9, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\"\n                    ";
+  stack1 = depth0.href;
+  stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += " class=\"popupmenu-option\">\n                        ";
+  stack1 = depth0.checked;
+  stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n                        ";
+  foundHelper = helpers.html;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.html; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n                </a></li>\n            ";
+  return buffer;}
+function program9(depth0,data) {
+  
+  var stack1, foundHelper;
+  foundHelper = helpers.href;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  return escapeExpression(stack1);}
+
+function program11(depth0,data) {
+  
+  
+  return "javascript:void(0);";}
+
+function program13(depth0,data) {
+  
+  var buffer = "", stack1, foundHelper;
+  buffer += "target=\"";
+  foundHelper = helpers.target;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  buffer += escapeExpression(stack1) + "\"";
+  return buffer;}
+
+function program15(depth0,data) {
+  
+  
+  return "<span class=\"ficon ok\"></span>";}
+
+function program17(depth0,data) {
+  
+  
+  return "\n    <li>No Options.</li>\n";}
+
+  buffer += "<ul id=\"";
+  foundHelper = helpers.id;
+  if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); }
+  else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; }
+  buffer += escapeExpression(stack1) + "-menu\" class=\"dropdown-menu\">\n";
+  stack1 = depth0.options;
+  stack1 = stack1 == null || stack1 === false ? stack1 : stack1.length;
+  stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(17, program17, data),fn:self.program(1, program1, data)});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n</ul>";
+  return buffer;});
+})();

static/scripts/templates/ui-templates.html

@@ -1,4 +1,4 @@
-<script type="text/template" class="template-history" id="template-user-quotaMeter-quota">
+<script type="text/template" class="template-user" id="template-user-quotaMeter-quota">
 <div id="quota-meter" class="quota-meter progress">
     <div id="quota-meter-bar"  class="quota-meter-bar bar" style="width: {{quota_percent}}%"></div>
     {{! TODO: remove the hardcoded style }}
@@ -8,7 +8,7 @@
 </div>
 </script>
 
-<script type="text/template" class="template-history" id="template-user-quotaMeter-usage">
+<script type="text/template" class="template-user" id="template-user-quotaMeter-usage">
 {{! TODO: remove the hardcoded styles }}
 <div id="quota-meter" class="quota-meter" style="background-color: transparent">
     <div id="quota-meter-text" class="quota-meter-text" style="top: 6px; color: white">
@@ -16,3 +16,28 @@
     </div>
 </div>
 </script>
+
+<script type="text/template" class="template-ui" id="template-popupmenu-menu">
+<ul id="{{ id }}-menu" class="dropdown-menu">
+{{#if options.length }}
+    {{#each options }}
+        {{#if divider }}
+            <li class="divider"></li>
+        {{else}}
+            {{#if header }}
+                <li class="head"><a href=""javascript:void(0);">{{{ html }}}</a></li>
+            {{else}}
+                {{!NOTE: changed from # to void fn }}
+                <li><a href="{{#if href }}{{ href }}{{else}}javascript:void(0);{{/if}}"
+                    {{#if href }}target="{{ target }}"{{/if}} class="popupmenu-option">
+                        {{#if checked }}<span class="ficon ok"></span>{{/if}}
+                        {{{ html }}}
+                </a></li>
+            {{/if}}
+        {{/if}}
+    {{/each}}
+{{else}}
+    <li>No Options.</li>
+{{/if}}
+</ul>
+</script>

templates/base.mako

@@ -31,11 +31,18 @@
         "libs/jquery/jquery",
         "libs/json2",
         "libs/bootstrap",
-        "galaxy.base",
         "libs/underscore",
         "libs/backbone/backbone",
         "libs/backbone/backbone-relational",
         "libs/handlebars.runtime",
+        "galaxy.base"
+    )}
+
+    ${h.templates(
+        "template-popupmenu-menu"
+    )}
+
+    ${h.js(
         "mvc/ui"
     )}
     

templates/base/base_panels.mako

@@ -56,9 +56,17 @@
         'libs/backbone/backbone',
         'libs/backbone/backbone-relational',
         'libs/handlebars.runtime',
-        'mvc/ui',
         'galaxy.base'
     )}
+
+    ${h.templates(
+        "template-popupmenu-menu"
+    )}
+
+    ${h.js(
+        "mvc/ui"
+    )}
+
     <script type="text/javascript">
         // console protection
         window.console = window.console || {

templates/root/alternate_history.mako

@@ -223,10 +223,12 @@ ${parent.javascripts()}
 ${h.js(
     "libs/jquery/jstorage",
     "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging",
-    "libs/json2",
+    ##"libs/json2",
     ##"libs/bootstrap",
-    "libs/backbone/backbone-relational",
-    "mvc/base-mvc", "mvc/ui"
+    ## I think we can remove some of these
+    ##"libs/backbone/backbone-relational",
+    "mvc/base-mvc",
+    ##"mvc/ui"
 )}
 
 ${h.templates(
@@ -302,13 +304,9 @@ $(function(){
     galaxyPageSetUp();
     Galaxy.historyFrame = window;
 
-    // ostensibly, this is the App
-    //if( window.console && console.debug ){
-    //    //if( console.clear ){ console.clear(); }
-    //    console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); }
-    //    top.storage = jQuery.jStorage
-    //}
+    var debugging = ( new PersistantStorage( '__history_panel' ).get( 'debugging' ) || false );
 
+    // ostensibly, this is the App
     // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it...
     //  ...use mako to 'bootstrap' the models
     var user    = ${ get_current_user() },
@@ -325,7 +323,7 @@ $(function(){
     var historyPanel = new HistoryPanel({
         model           : new History( history, hdas ),
         urlTemplates    : galaxy_paths.attributes,
-        //logger          : console,
+        logger          : ( debugging )?( console ):( null ),
         // is page sending in show settings? if so override history's
         show_deleted    : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) },
         show_hidden     : ${ 'true' if show_hidden  == True else ( 'null' if show_hidden  == None else 'false' ) }
@@ -336,13 +334,17 @@ $(function(){
     //historyPanel = new HistoryPanel({
     //    model: new History(),
     //    urlTemplates    : galaxy_paths.attributes,
-    //    logger          : console,
+    //    logger          : ( debugging )?( console ):( null ),
     //    // is page sending in show settings? if so override history's
     //    show_deleted    : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) },
     //    show_hidden     : ${ 'true' if show_hidden  == True else ( 'null' if show_hidden  == None else 'false' ) }
     //});
     //historyPanel.model.loadFromApi( history.id );
 
+    // set it up to be accessible across iframes
+    //TODO:?? mem leak
+    top.Galaxy.currHistoryPanel = historyPanel;
+
 
     // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history)
     //  create it and join them here for now (via events)
@@ -352,6 +354,7 @@ $(function(){
     //window.currUser.logger = console;
     var quotaMeter = new UserQuotaMeter({
         model   : currUser,
+        //logger  : ( debugging )?( console ):( null ),
         el      : $( top.document ).find( '.quota-meter-container' )
     });
     //quotaMeter.logger = console; window.quotaMeter = quotaMeter
@@ -373,9 +376,81 @@ $(function(){
         quotaMeter.update()
     }, quotaMeter );
 
-    // set it up to be accessible across iframes
-    //TODO:?? mem leak
-    top.Galaxy.currHistoryPanel = historyPanel;
+
+    //ANOTHER cross-frame element is the history-options-button...
+    // in this case, we need to change the popupmenu options listed to include some functions for this history
+    // these include: current (1 & 2) 'show/hide' delete and hidden functions, and (3) the collapse all option
+    (function(){
+        // don't try this if the history panel is in it's own window
+        if( top.document === window.document ){
+            return;
+        }
+
+        // lots of wtf here...due to infernalframes
+        var $historyButtonWindow = $( top.document ),
+            HISTORY_MENU_BUTTON_ID = 'history-options-button',
+            $historyMenuButton = $historyButtonWindow.find( '#' + HISTORY_MENU_BUTTON_ID ),
+            // jq data in another frame can only be accessed by the jQuery in that frame,
+            //  get the jQuery from the top frame (that contains the history-options-button)
+            START_INSERTING_AT_INDEX = 11,
+            COLLAPSE_OPTION_TEXT = _l("Collapse Expanded Datasets"),
+            DELETED_OPTION_TEXT  = _l("Include Deleted Datasets"),
+            HIDDEN_OPTION_TEXT   = _l("Include Hidden Datasets");
+            windowJQ = $( top )[0].jQuery,
+            popupMenu = ( windowJQ && $historyMenuButton[0] )?( windowJQ.data( $historyMenuButton[0], 'PopupMenu' ) )
+                                                             :( null );
+
+        //console.debug(
+        //    '$historyButtonWindow:', $historyButtonWindow,
+        //    '$historyMenuButton:', $historyMenuButton,
+        //    'windowJQ:', windowJQ,
+        //    'popupmenu:', popupMenu
+        //);
+        if( !popupMenu ){ return; }
+
+        // since the history frame reloads so often (compared to the main window),
+        //  we need to check whether these options are there already before we add them again
+        //NOTE: we use the global here because these remain bound in the main window even if panel refreshes
+        //TODO: too much boilerplate
+        if( popupMenu.findIndexByHtml( COLLAPSE_OPTION_TEXT ) === null ){
+            popupMenu.addItem({
+                html    : COLLAPSE_OPTION_TEXT,
+                func    : function() {
+                    Galaxy.currHistoryPanel.collapseAllHdaBodies();
+                }
+            }, START_INSERTING_AT_INDEX )
+        }
+
+        var deletedOptionIndex = popupMenu.findIndexByHtml( DELETED_OPTION_TEXT );
+        if( deletedOptionIndex === null ){
+            popupMenu.addItem({
+                html    : DELETED_OPTION_TEXT,
+                func    : function( clickEvent, thisMenuOption ){
+                    var show_deleted = Galaxy.currHistoryPanel.toggleShowDeleted();
+                    thisMenuOption.checked = show_deleted;
+                }
+            }, START_INSERTING_AT_INDEX + 1 )
+            deletedOptionIndex = START_INSERTING_AT_INDEX + 1;
+        }
+        // whether was there or added, update the checked option to reflect the panel's settings on the panel render
+        popupMenu.options[ deletedOptionIndex ].checked = Galaxy.currHistoryPanel.storage.get( 'show_deleted' );
+
+        var hiddenOptionIndex = popupMenu.findIndexByHtml( HIDDEN_OPTION_TEXT );
+        if( hiddenOptionIndex === null ){
+            popupMenu.addItem({
+                html    : HIDDEN_OPTION_TEXT,
+                func    : function( clickEvent, thisMenuOption ){
+                    var show_hidden = Galaxy.currHistoryPanel.toggleShowHidden();
+                    thisMenuOption.checked = show_hidden;
+                }
+            }, START_INSERTING_AT_INDEX + 2 )
+            hiddenOptionIndex = START_INSERTING_AT_INDEX + 2;
+        }
+        // whether was there or added, update the checked option to reflect the panel's settings on the panel render
+        popupMenu.options[ hiddenOptionIndex ].checked = Galaxy.currHistoryPanel.storage.get( 'show_hidden' );
+    })();
+
+    //TODO: both the quota meter and the options-menu stuff need to be moved out when iframes are removed
 
     return;
 });

templates/root/index.mako

@@ -10,7 +10,7 @@
     $(function(){
         // Init history options.
         $("#history-options-button").css( "position", "relative" );
-        make_popupmenu( $("#history-options-button"), {
+        var popupmenu = PopupMenu.make_popupmenu( $("#history-options-button"), {
             "${_("History Lists")}": null,
             "${_("Saved Histories")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='list')}";
@@ -40,18 +40,6 @@
             "${_("Resume Paused Jobs")}": function() {
                 galaxy_history.location = "${h.url_for( controller='history', action='resume_paused_jobs', current=True)}";
             },
-            "${_("Collapse Expanded Datasets")}": function() {
-                Galaxy.currHistoryPanel.collapseAllHdaBodies();
-                //galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}";
-            },
-            "${_("Show/Hide Deleted Datasets")}": function() {
-                Galaxy.currHistoryPanel.toggleShowDeleted();
-                //galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}";
-            },
-            "${_("Show/Hide Hidden Datasets")}": function() {
-                Galaxy.currHistoryPanel.toggleShowHidden();
-                //galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}";
-            },
             "${_("Unhide Hidden Datasets")}": function() {
                 if ( confirm( "Really unhide all hidden datasets?" ) ) {
                     galaxy_main.location = "${h.url_for( controller='history', action='unhide_datasets', current=True )}";
@@ -83,7 +71,6 @@
                 galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}";
             }
         });
-        
     });
     </script>
 </%def>

test/functional/test_history_functions.py

@@ -14,11 +14,12 @@ class TestHistory( TwillTestCase ):
         name = 'anonymous'
         self.new_history( name=name )
         global anonymous_history
-        anonymous_history = sa_session.query( galaxy.model.History ) \
-                                      .filter( and_( galaxy.model.History.table.c.deleted==False,
-                                                     galaxy.model.History.table.c.name==name ) ) \
-                                      .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
-                                      .first()
+        anonymous_history = (
+            sa_session.query( galaxy.model.History )
+                .filter( and_( galaxy.model.History.table.c.deleted==False, galaxy.model.History.table.c.name==name ) )
+                .order_by( desc( galaxy.model.History.table.c.create_time ) )
+                .first()
+        )
         assert anonymous_history is not None, "Problem retrieving anonymous_history from database"
         # Upload a dataset to anonymous_history so it will be set as the current history after login
         self.upload_file( '1.bed', dbkey='hg18' )
@@ -235,27 +236,35 @@ class TestHistory( TwillTestCase ):
         # Check list of histories to make sure shared history3 was cloned
         strings_displayed=[ "Clone of '%s' shared by '%s'" % ( history3.name, admin_user.email ) ]
         self.view_stored_active_histories( strings_displayed=strings_displayed )
+
     def test_035_clone_current_history( self ):
         """Testing cloning the current history"""
         # logged in as regular_user1
         self.logout()
         self.login( email=admin_user.email )
+
         # Current history should be history3, add more datasets to history3, then delete them so we can
         # test cloning activatable datasets as well as only the active datasets
         self.upload_file( '2.bed', dbkey='hg18' )
-        hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
-                              .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id,
-                                             galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \
-                              .first()
+        hda_2_bed = (
+            sa_session.query( galaxy.model.HistoryDatasetAssociation )
+                .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id,
+                               galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) )
+                .first()
+        )
         assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database"
         self.delete_history_item( str( hda_2_bed.id ) )
+
         self.upload_file( '3.bed', dbkey='hg18' )
-        hda_3_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
-                              .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id,
-                                             galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) \
-                              .first()
+        hda_3_bed = (
+            sa_session.query( galaxy.model.HistoryDatasetAssociation )
+                .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id,
+                               galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) )
+                .first()
+        )
         assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database"
         self.delete_history_item( str( hda_3_bed.id ) )
+
         # Test cloning activatable datasets
         self.clone_history( self.security.encode_id( history3.id ),
                             'activatable',
@@ -267,6 +276,7 @@ class TestHistory( TwillTestCase ):
                                     .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
                                     .first()
         assert history3_clone2 is not None, "Problem retrieving history3_clone2 from database"
+
         # Check list of histories to make sure shared history3 was cloned
         self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history3.name ] )
         # Switch to the cloned history to make sure activatable datasets were cloned
@@ -307,6 +317,7 @@ class TestHistory( TwillTestCase ):
             raise AssertionError, "Deleted datasets incorrectly included in cloned history history3_clone3"
         except:
             pass
+
     def test_040_sharing_mulitple_histories_with_multiple_users( self ):
         """Testing sharing multiple histories containing only public datasets with multiple users"""
         # Logged in as admin_user