Merge branch 'backport_2613' into release_16.04

(and rebuild client)

client/galaxy/scripts/mvc/collection/collection-li.js

@@ -33,30 +33,23 @@ var DCListItemView = FoldoutListItemView.extend(
     /** event listeners */
     _setUpListeners : function(){
         FoldoutListItemView.prototype._setUpListeners.call( this );
-        // re-rendering on deletion
         this.listenTo( this.model, 'change', function( model, options ){
-            if( _.isEqual( _.keys( model.changed ), [ 'deleted' ] ) ){
+            // if the model has changed deletion status render it entirely
+            if( _.has( model.changed, 'deleted' ) ){
                 this.render();
+
+            // if the model has been decorated after the fact with the element count,
+            // render the subtitle where the count is displayed
+            } else if( _.has( model.changed, 'element_count' ) ){
+                this.$( '> .title-bar .subtitle' ).replaceWith( this._renderSubtitle() );
             }
         });
     },
 
     // ......................................................................... rendering
-    //TODO:?? possibly move to listItem
     /** render a subtitle to show the user what sort of collection this is */
     _renderSubtitle : function(){
-        var $subtitle = $( '<div class="subtitle"></div>' );
-        //TODO: would be good to get this in the subtitle
-        //var len = this.model.elements.length;
-        switch( this.model.get( 'collection_type' ) ){
-            case 'list':
-                return $subtitle.text( _l( 'a list of datasets' ) );
-            case 'paired':
-                return $subtitle.text( _l( 'a pair of datasets' ) );
-            case 'list:paired':
-                return $subtitle.text( _l( 'a list of paired datasets' ) );
-        }
-        return $subtitle;
+        return $( this.templates.subtitle( this.model.toJSON(), this ) );
     },
 
     // ......................................................................... foldout
@@ -122,9 +115,26 @@ DCListItemView.prototype.templates = (function(){
         '</div>'
     ], 'collection' );
 
+    // use element identifier
+    var subtitleTemplate = BASE_MVC.wrapTemplate([
+        '<div class="subtitle">',
+            '<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>',
+            '<%        if( collection.collection_type === "list" ){ %>',
+                _l( 'a list of <%- countText %>datasets' ),
+            '<% } else if( collection.collection_type === "paired" ){ %>',
+                _l( 'a pair of datasets' ),
+            '<% } else if( collection.collection_type === "list:paired" ){ %>',
+                _l( 'a list of <%- countText %>dataset pairs' ),
+            '<% } else if( collection.collection_type === "list:list" ){ %>',
+                _l( 'a list of <%- countText %>dataset lists' ),
+            '<% } %>',
+        '</div>'
+    ], 'collection' );
+
     return _.extend( {}, FoldoutListItemView.prototype.templates, {
-        warnings : warnings,
-        titleBar : titleBarTemplate
+        warnings    : warnings,
+        titleBar    : titleBarTemplate,
+        subtitle    : subtitleTemplate
     });
 }());
 

client/galaxy/scripts/mvc/collection/collection-model.js

@@ -504,10 +504,58 @@ var ListPairedDatasetCollection = DatasetCollection.extend(
 });
 
 
+//==============================================================================
+/** @class Backbone model for a list dataset collection within a list:list dataset collection. */
+var NestedListDCDCE = ListDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,
+/** @lends NestedListDCDCE.prototype */{
+
+    /** This is both a collection and a collection element - call the constructor */
+    constructor : function( attributes, options ){
+        this.debug( '\t NestedListDCDCE.constructor:', attributes, options );
+        DatasetCollectionElementMixin.constructor.call( this, attributes, options );
+    },
+
+    /** String representation. */
+    toString : function(){
+        var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );
+        return ([ 'NestedListDCDCE(', objStr, ')' ].join( '' ));
+    }
+}));
+
+
+//==============================================================================
+/** @class Backbone collection containing list dataset collections. */
+var NestedListDCDCECollection = NestedDCDCECollection.extend({
+
+    /** We know this collection is composed of only nested pair collections */
+    model: NestedListDCDCE,
+
+    /** String representation. */
+    toString : function(){
+        return ([ 'NestedListDCDCECollection(', this.length, ')' ].join( '' ));
+    }
+});
+
+
+//==============================================================================
+/** @class Backbone Model for a DatasetCollection (list) that contains other lists. */
+var ListOfListsDatasetCollection = DatasetCollection.extend({
+
+    /** list:paired is the only collection that itself contains collections */
+    collectionClass : NestedListDCDCECollection,
+
+    /** String representation. */
+    toString : function(){
+        return ([ 'ListOfListsDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));
+    }
+});
+
+
 //==============================================================================
     return {
-        ListDatasetCollection               : ListDatasetCollection,
-        PairDatasetCollection               : PairDatasetCollection,
-        ListPairedDatasetCollection         : ListPairedDatasetCollection
+        ListDatasetCollection       : ListDatasetCollection,
+        PairDatasetCollection       : PairDatasetCollection,
+        ListPairedDatasetCollection : ListPairedDatasetCollection,
+        ListOfListsDatasetCollection: ListOfListsDatasetCollection
     };
 });

client/galaxy/scripts/mvc/collection/collection-view-edit.js

@@ -128,7 +128,7 @@ var NestedPairCollectionViewEdit = PairCollectionViewEdit.extend(
 
 
 // =============================================================================
-/** @class non-editable, read-only View/Controller for a dataset collection. */
+/** @class editable, View/Controller for a list of pairs dataset collection. */
 var ListOfPairsCollectionViewEdit = CollectionViewEdit.extend(
 /** @lends ListOfPairsCollectionView.prototype */{
 
@@ -146,11 +146,31 @@ var ListOfPairsCollectionViewEdit = CollectionViewEdit.extend(
 });
 
 
+// =============================================================================
+/** @class View/Controller for a list of lists dataset collection. */
+var ListOfListsCollectionViewEdit = CollectionViewEdit.extend(
+/** @lends ListOfListsCollectionView.prototype */{
+
+    //TODO: not strictly needed - due to switch in CollectionView._getContentClass
+    /** sub view class used for nested collections */
+    NestedDCDCEViewClass : DC_EDIT.NestedDCDCEListItemEdit.extend({
+        foldoutPanelClass : NestedPairCollectionViewEdit
+    }),
+
+    // ........................................................................ misc
+    /** string rep */
+    toString    : function(){
+        return 'ListOfListsCollectionViewEdit(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';
+    }
+});
+
+
 //==============================================================================
     return {
         CollectionViewEdit              : CollectionViewEdit,
         ListCollectionViewEdit          : ListCollectionViewEdit,
         PairCollectionViewEdit          : PairCollectionViewEdit,
-        ListOfPairsCollectionViewEdit   : ListOfPairsCollectionViewEdit
+        ListOfPairsCollectionViewEdit   : ListOfPairsCollectionViewEdit,
+        ListOfListsCollectionViewEdit   : ListOfListsCollectionViewEdit
     };
 });

client/galaxy/scripts/mvc/collection/collection-view.js

@@ -153,6 +153,8 @@ CollectionView.prototype.templates = (function(){
                         _l( 'a pair of datasets' ),
                     '<% } else if( collection.collection_type === "list:paired" ){ %>',
                         _l( 'a list of paired datasets' ),
+                    '<% } else if( collection.collection_type === "list:list" ){ %>',
+                        _l( 'a list of dataset lists' ),
                     '<% } %>',
                 '</div>',
             '</div>',
@@ -215,11 +217,28 @@ var ListOfPairsCollectionView = CollectionView.extend(
 });
 
 
+// =============================================================================
+/** @class non-editable, read-only View/Controller for a list of lists dataset collection. */
+var ListOfListsCollectionView = CollectionView.extend({
+
+    /** sub view class used for nested collections */
+    NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView.extend({
+        foldoutPanelClass : PairCollectionView
+    }),
+
+    /** string rep */
+    toString    : function(){
+        return 'ListOfListsCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';
+    }
+});
+
+
 //==============================================================================
     return {
         CollectionView              : CollectionView,
         ListCollectionView          : ListCollectionView,
         PairCollectionView          : PairCollectionView,
-        ListOfPairsCollectionView   : ListOfPairsCollectionView
+        ListOfPairsCollectionView   : ListOfPairsCollectionView,
+        ListOfListsCollectionView   : ListOfListsCollectionView
     };
 });

client/galaxy/scripts/mvc/history/hdca-li-edit.js

@@ -26,6 +26,8 @@ var HDCAListItemEdit = _super.extend(
                 return DC_VIEW_EDIT.PairCollectionViewEdit;
             case 'list:paired':
                 return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;
+            case 'list:list':
+                return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;
         }
         throw new TypeError( 'Uknown collection_type: ' + this.model.get( 'collection_type' ) );
     },

client/galaxy/scripts/mvc/history/hdca-li.js

@@ -38,6 +38,8 @@ var HDCAListItemView = _super.extend(
                 return DC_VIEW.PairCollectionView;
             case 'list:paired':
                 return DC_VIEW.ListOfPairsCollectionView;
+            case 'list:list':
+                return DC_VIEW.ListOfListsCollectionView;
         }
         throw new TypeError( 'Uknown collection_type: ' + this.model.get( 'collection_type' ) );
     },

client/galaxy/scripts/mvc/history/hdca-model.js

@@ -18,7 +18,8 @@ TODO:
 var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,
     ListDC = DC_MODEL.ListDatasetCollection,
     PairDC = DC_MODEL.PairDatasetCollection,
-    ListPairedDC = DC_MODEL.ListPairedDatasetCollection;
+    ListPairedDC = DC_MODEL.ListPairedDatasetCollection,
+    ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;
 
 //==============================================================================
 /** Override to post to contents route w/o id. */
@@ -91,11 +92,8 @@ var HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend(
 
 
 //==============================================================================
-/** @class Backbone model for List of Pairs Dataset Collection within a History.
- *  @constructs
- */
-var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend(
-/** @lends HistoryListPairedDatasetCollection.prototype */{
+/** @class Backbone model for List of Pairs Dataset Collection within a History. */
+var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend({
 
     defaults : _.extend( _.clone( ListPairedDC.prototype.defaults ), {
         history_content_type: 'dataset_collection',
@@ -118,10 +116,36 @@ var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).ex
 });
 
 
+//==============================================================================
+/** @class Backbone model for List of Lists Dataset Collection within a History. */
+var HistoryListOfListsDatasetCollection = ListOfListsDC.extend( hcontentMixin ).extend({
+
+    defaults : _.extend( _.clone( ListOfListsDC.prototype.defaults ), {
+        history_content_type: 'dataset_collection',
+        collection_type     : 'list:list',
+        model_class         : 'HistoryDatasetCollectionAssociation'
+    }),
+
+    initialize : function( model, options ){
+        ListOfListsDC.prototype.initialize.call( this, model, options );
+        hcontentMixin.initialize.call( this, model, options );
+    },
+
+    /** Override to post to contents route w/o id. */
+    save : buildHDCASave( ListOfListsDC.prototype.save ),
+
+    /** String representation. */
+    toString : function(){
+         return ([ 'HistoryListOfListsDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));
+    }
+});
+
+
 //==============================================================================
     return {
         HistoryListDatasetCollection        : HistoryListDatasetCollection,
         HistoryPairDatasetCollection        : HistoryPairDatasetCollection,
-        HistoryListPairedDatasetCollection  : HistoryListPairedDatasetCollection
+        HistoryListPairedDatasetCollection  : HistoryListPairedDatasetCollection,
+        HistoryListOfListsDatasetCollection : HistoryListOfListsDatasetCollection
     };
 });

client/galaxy/scripts/mvc/history/history-contents.js

@@ -44,12 +44,16 @@ var HistoryContents = Backbone.Collection
                     return new HDCA_MODEL.HistoryPairDatasetCollection( attrs, options );
                 case 'list:paired':
                     return new HDCA_MODEL.HistoryListPairedDatasetCollection( attrs, options );
+                case 'list:list':
+                    return new HDCA_MODEL.HistoryListOfListsDatasetCollection( attrs, options );
             }
             // This is a hack inside a hack:
             // Raise a plain object with validationError to fake a model.validationError
             // (since we don't have a model to use validate with)
             // (the outer hack being the mixed content/model function in this collection)
-            return { validationError : 'Unknown collection_type: ' + attrs.history_content_type };
+            var msg = 'Unknown collection_type: ' + attrs.collection_type;
+            console.warn( msg, attrs );
+            return { validationError : msg };
         }
         return { validationError : 'Unknown history_content_type: ' + attrs.history_content_type };
     },
@@ -205,6 +209,19 @@ var HistoryContents = Backbone.Collection
         return this.fetch( options );
     },
 
+    /** specialty fetch method for retrieving the element_counts of all hdcas in the history */
+    fetchCollectionCounts : function( options ){
+        options = options || {};
+        options.data = _.defaults({
+            keys : [ 'type_id', 'element_count' ].join( ',' ),
+            q    : 'history_content_type',
+            qv   : 'dataset_collection',
+        }, options.data || {} );
+        options.merge = true;
+        options.remove = false;
+        return this.fetch( options );
+    },
+
     /** using a queue, perform ajaxFn on each of the models in this collection */
     ajaxQueue : function( ajaxFn, options ){
         var deferred = jQuery.Deferred(),