Merge branch 'collections' into dev

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

@@ -29,6 +29,17 @@ var DCListItemView = FoldoutListItemView.extend(
         FoldoutListItemView.prototype.initialize.call( this, attributes );
     },
 
+    /** event listeners */
+    _setUpListeners : function(){
+        FoldoutListItemView.prototype._setUpListeners.call( this );
+        // re-rendering on deletion
+        this.model.on( 'change', function( model, options ){
+            if( _.isEqual( _.keys( model.changed ), [ 'deleted' ] ) ){
+                this.render();
+            }
+        }, this );
+    },
+
     // ......................................................................... rendering
     //TODO:?? possibly move to listItem
     /** render a subtitle to show the user what sort of collection this is */
@@ -74,6 +85,32 @@ var DCListItemView = FoldoutListItemView.extend(
 /** underscore templates */
 DCListItemView.prototype.templates = (function(){
 
+    var warnings = _.extend( {}, FoldoutListItemView.prototype.templates.warnings, {
+        error : BASE_MVC.wrapTemplate([
+            // error during index fetch - show error on dataset
+            '<% if( model.error ){ %>',
+                '<div class="errormessagesmall">',
+                    _l( 'There was an error getting the data for this collection' ), ': <%- model.error %>',
+                '</div>',
+            '<% } %>'
+        ]),
+        purged : BASE_MVC.wrapTemplate([
+            '<% if( model.purged ){ %>',
+                '<div class="purged-msg warningmessagesmall">',
+                    _l( 'This collection has been deleted and removed from disk' ),
+                '</div>',
+            '<% } %>'
+        ]),
+        deleted : BASE_MVC.wrapTemplate([
+            // deleted not purged
+            '<% if( model.deleted && !model.purged ){ %>',
+                '<div class="deleted-msg warningmessagesmall">',
+                    _l( 'This collection has been deleted' ),
+                '</div>',
+            '<% } %>'
+        ])
+    });
+
     // use element identifier
     var titleBarTemplate = BASE_MVC.wrapTemplate([
         '<div class="title-bar clear" tabindex="0">',
@@ -85,6 +122,7 @@ DCListItemView.prototype.templates = (function(){
     ], 'collection' );
 
     return _.extend( {}, FoldoutListItemView.prototype.templates, {
+        warnings : warnings,
         titleBar : titleBarTemplate
     });
 }());

client/galaxy/scripts/mvc/collection/list-collection-creator.js

@@ -0,0 +1,52 @@
+define([
+    "mvc/dataset/states",
+    "mvc/ui/error-modal",
+    "utils/localization"
+], function( STATES, errorModal, _l ){
+/*==============================================================================
+
+==============================================================================*/
+function validElements( collection ){
+    var elements = collection.toJSON().filter( function( content ){
+        return content.history_content_type === 'dataset'
+            && content.state === STATES.OK;
+    });
+    return elements;
+}
+
+var noValidElementsMessage = 'No valid datasets were selected';
+
+function noValidElementsErrorModal(){
+    errorModal(
+        'Use the checkboxes at the left of the dataset names to select them. ' +
+        'Selected datasets should be error-free and should have completed running.',
+        noValidElementsMessage
+    );
+}
+
+function createListHDCA( collection ){
+    var name = 'New Dataset List',
+        elementIdentifiers = validElements( collection ).map( function( element ){
+            // TODO: Handle duplicate names.
+            return {
+                id      : element.id,
+                name    : element.name,
+                //TODO: this allows for list:list even if the filter above does not - reconcile
+                src     : ( element.history_content_type === 'dataset'? 'hda' : 'hdca' )
+            }
+        });
+    if( !elementIdentifiers.length ){
+        noValidElementsErrorModal();
+        return jQuery.Deferred().reject( noValidElementsMessage );
+    }
+    return collection.createHDCA( elementIdentifiers, 'list', name );
+}
+
+//==============================================================================
+    return {
+        validElements               : validElements,
+        noValidElementsMessage      : noValidElementsMessage,
+        noValidElementsErrorModal   : noValidElementsErrorModal,
+        createListHDCA              : createListHDCA
+    };
+});

client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

@@ -1,9 +1,10 @@
 define([
     "utils/levenshtein",
     "utils/natural-sort",
+    "mvc/collection/list-collection-creator",
     "mvc/base-mvc",
     "utils/localization"
-], function( levenshteinDistance, naturalSort, baseMVC, _l ){
+], function( levenshteinDistance, naturalSort, LIST_COLLECTION_CREATOR, baseMVC, _l ){
 /* ============================================================================
 TODO:
 
@@ -247,6 +248,9 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
         /** DOM elements currently being dragged */
         this.$dragging = null;
 
+        /** Used for blocking UI events during ajax/operations (don't post twice) */
+        this.blocking = false;
+
         this._setUpBehaviors();
         this._dataSetUp();
     },
@@ -576,12 +580,16 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
 
         };
         //this.debug( JSON.stringify( ajaxData ) );
+        creator.blocking = true;
         return jQuery.ajax( url, {
             type        : 'POST',
             contentType : 'application/json',
             dataType    : 'json',
             data        : JSON.stringify( ajaxData )
         })
+        .always( function(){
+            creator.blocking = false;
+        })
         .fail( function( xhr, status, message ){
             creator._ajaxErrHandler( xhr, status, message );
         })
@@ -855,7 +863,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
             what.addClass( VALIDATION_CLASS );
         }
     },
-    
+
     // ------------------------------------------------------------------------ events
     /** set up event handlers on self */
     _setUpBehaviors : function(){
@@ -1406,7 +1414,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
 
     /** check for enter key press when in the collection name and submit */
     _nameCheckForEnter : function( ev ){
-        if( ev.keyCode === 13 ){
+        if( ev.keyCode === 13 && !this.blocking ){
             this._clickCreate();
         }
     },
@@ -1421,7 +1429,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
         var name = this._getName();
         if( !name ){
             this._validationWarning( 'name' );
-        } else {
+        } else if( !this.blocking ){
             this.createList();
         }
     },
@@ -1683,12 +1691,18 @@ PairedCollectionCreator.templates = PairedCollectionCreator.templates || {
 /** a modal version of the paired collection creator */
 var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){
 
+    var deferred = jQuery.Deferred(),
+        creator;
+
     options = _.defaults( options || {}, {
         datasets    : datasets,
-        oncancel    : function(){ Galaxy.modal.hide(); },
-        oncreate    : function(){
+        oncancel    : function(){
             Galaxy.modal.hide();
-            Galaxy.currHistoryPanel.refreshContents();
+            deferred.reject( 'cancelled' );
+        },
+        oncreate    : function( creator, response ){
+            Galaxy.modal.hide();
+            deferred.resolve( response );
         }
     });
 
@@ -1696,7 +1710,7 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datas
         throw new Error( 'Galaxy or Galaxy.modal not found' );
     }
 
-    var creator = new PairedCollectionCreator( options );
+    creator = new PairedCollectionCreator( options );
     Galaxy.modal.show({
         title   : 'Create a collection of paired datasets',
         body    : creator.$el,
@@ -1705,15 +1719,31 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datas
         closing_events: true
     });
     creator.render();
+    window.creator = creator;
+
     //TODO: remove modal header
-    window.PCC = creator;
-    return creator;
+    return deferred;
 };
 
 
+//=============================================================================
+function createListOfPairsCollection( collection ){
+    var elements = LIST_COLLECTION_CREATOR.validElements( collection );
+    if( !elements.length ){
+        LIST_COLLECTION_CREATOR.noValidElementsErrorModal();
+        return jQuery.Deferred().reject( LIST_COLLECTION_CREATOR.noValidElementsMessage );
+    }
+
+    return pairedCollectionCreatorModal( elements, {
+        historyId : collection.historyId
+    });
+}
+
+
 //=============================================================================
     return {
         PairedCollectionCreator : PairedCollectionCreator,
-        pairedCollectionCreatorModal : pairedCollectionCreatorModal
+        pairedCollectionCreatorModal : pairedCollectionCreatorModal,
+        createListOfPairsCollection : createListOfPairsCollection
     };
 });

client/galaxy/scripts/mvc/collection/pair-collection-creator.js

@@ -0,0 +1,33 @@
+define([
+    "mvc/collection/list-collection-creator",
+    "mvc/ui/error-modal",
+    "utils/localization"
+], function( LIST_COLLECTION_CREATOR, errorModal, _l ){
+
+    function createPairHDCA( collection ){
+        // currently: datasets in the ok state
+        var elementsJSON = LIST_COLLECTION_CREATOR.validElements( collection );
+        if( !elementsJSON.length ){
+            LIST_COLLECTION_CREATOR.noValidElementsErrorModal();
+            return jQuery.Deferred().reject( LIST_COLLECTION_CREATOR.noValidElementsMessage );
+        }
+        if( elementsJSON.length !== 2 ){
+            errorModal(
+                'When pairing datasets, select only two datasets: one forward and one reverse.',
+                'Not a valid pair'
+            );
+            return jQuery.Deferred().reject( LIST_COLLECTION_CREATOR.noValidElementsMessage );
+        }
+
+        var name = 'New Dataset Pair',
+            elementIdentifiers = [
+                { name: "forward", src: "hda", id: elementsJSON[0].id },
+                { name: "reverse", src: "hda", id: elementsJSON[1].id }
+            ];
+        return collection.createHDCA( elementIdentifiers, 'paired', name );
+    }
+
+    return {
+        createPairHDCA : createPairHDCA
+    };
+});

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

@@ -18,6 +18,17 @@ var HDCAListItemView = _super.extend(
 
     className   : _super.prototype.className + " history-content",
 
+    /** event listeners */
+    _setUpListeners : function(){
+        _super.prototype._setUpListeners.call( this );
+        // re-rendering on deletion
+        this.model.on( 'change', function( model, options ){
+            if( _.isEqual( _.keys( model.changed ), [ 'visible' ] ) ){
+                this.render();
+            }
+        }, this );
+    },
+
     /** Override to provide the proper collections panels as the foldout */
     _getFoldoutPanelClass : function(){
         switch( this.model.get( 'collection_type' ) ){
@@ -53,6 +64,17 @@ var HDCAListItemView = _super.extend(
 /** underscore templates */
 HDCAListItemView.prototype.templates = (function(){
 
+    var warnings = _.extend( {}, _super.prototype.templates.warnings, {
+        hidden : BASE_MVC.wrapTemplate([
+            // add a warning when hidden
+            '<% if( !collection.visible ){ %>',
+                '<div class="hidden-msg warningmessagesmall">',
+                    _l( 'This collection has been hidden' ),
+                '</div>',
+            '<% } %>'
+        ], 'collection' )
+    });
+
 // could steal this from hda-base (or use mixed content)
     var titleBarTemplate = BASE_MVC.wrapTemplate([
         // adding the hid display to the title
@@ -68,6 +90,7 @@ HDCAListItemView.prototype.templates = (function(){
     ], 'collection' );
 
     return _.extend( {}, _super.prototype.templates, {
+        warnings : warnings,
         titleBar : titleBarTemplate
     });
 }());

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

@@ -220,12 +220,12 @@ var HistoryContents = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).exten
                 source  : contentType,
                 type    : type
             })
-            .done( function( json ){
-                collection.add([ json ]);
+            .done( function( response ){
+                collection.add([ response ]);
             })
             .fail( function( error, status, message ){
                 collection.trigger( 'error', collection, xhr, {},
-                                    'Error copying contents', { type: type, id: id, source: contentType });
+                    'Error copying contents', { type: type, id: id, source: contentType });
             });
         return xhr;
     },

client/galaxy/scripts/mvc/history/history-panel-edit.js

@@ -7,6 +7,9 @@ define([
     "mvc/history/hdca-li-edit",
     "mvc/tags",
     "mvc/annotations",
+    "mvc/collection/list-collection-creator",
+    "mvc/collection/pair-collection-creator",
+    "mvc/collection/list-of-pairs-collection-creator",
     "ui/fa-icon-button",
     "mvc/ui/popup-menu",
     "utils/localization"
@@ -19,6 +22,9 @@ define([
     HDCA_LI_EDIT,
     TAGS,
     ANNOTATIONS,
+    LIST_COLLECTION_CREATOR,
+    PAIR_COLLECTION_CREATOR,
+    LIST_OF_PAIRS_COLLECTION_CREATOR,
     faIconButton,
     PopupMenu,
     _l
@@ -27,63 +33,6 @@ define([
 TODO:
 
 ============================================================================= */
-function createListCollection( history, collection ){
-    //TODO: filter out non-datasets, non-ready
-    //TODO: fail if no valid elements remain
-    //return jQuery.Deferred().reject( _l( 'No valid datasets to add' ) );
-    var name = 'New Dataset List',
-        elementIdentifiers = collection.toJSON().map( function( element ){
-            // TODO: Handle duplicate names.
-            return {
-                id      : element.id,
-                name    : element.name,
-                src     : ( element.history_content_type === 'dataset'? 'hda' : 'hdca' )
-            }
-        });
-    return collection.createHDCA( elementIdentifiers, 'list', name );
-}
-
-function createPairCollection( history, collection ){
-    //TODO: filter out non-datasets, non-ready
-    //TODO: fail if no valid elements remain
-    //return jQuery.Deferred().reject( _l( 'No valid datasets to add' ) );
-    var elementsJSON = collection.toJSON(),
-        name = 'New Dataset Pair',
-        elementIdentifiers = [
-            { name: "forward", src: "hda", id: elementsJSON[0].id },
-            { name: "reverse", src: "hda", id: elementsJSON[1].id }
-        ];
-    return collection.createHDCA( elementIdentifiers, 'paired', name );
-}
-
-function createListOfPairsCollection( history, collection ){
-    var datasets = collection.toJSON().filter( function( content ){
-            return content.history_content_type === 'dataset'
-                && content.state === STATES.OK;
-        });
-
-    if( datasets.length ){
-        require([ 'mvc/collection/paired-collection-creator' ], function( creator ){
-            window.creator = creator.pairedCollectionCreatorModal( datasets, {
-                historyId : history.id
-            });
-        });
-
-    } else {
-        Galaxy.modal.show({
-            title   : _l( 'No valid datasets were selected' ),
-            body    : _l([
-                          'Use the checkboxes at the left of the dataset names to select them.',
-                          'Selected datasets should be error-free and should have completed running.'
-                      ].join(' ')),
-            buttons : { 'Ok': function(){ Galaxy.modal.hide(); } },
-            closing_events: true
-        });
-    }
-}
-
-
-// =============================================================================
 var _super = HPANEL.HistoryPanel;
 // base class for current-history-panel and used as-is in history/view.mako
 /** @class Editable View/Controller for the history model.
@@ -329,23 +278,31 @@ var HistoryPanelEdit = _super.extend(
                 }
             });
         }
-        return actions.concat([
+        actions = actions.concat( panel._collectionActions() );
+        return actions;
+    },
+
+    /**   */
+    _collectionActions : function(){
+        var panel = this;
+        return [
             {   html: _l( 'Build Dataset List' ), func: function() {
-                    createListCollection( panel.model, panel.getSelectedModels() )
+                    LIST_COLLECTION_CREATOR.createListHDCA( panel.getSelectedModels() )
                         .done( function(){ panel.model.refresh() });
                 }
             },
             // TODO: Only show quick pair if two things selected.
             {   html: _l( 'Build Dataset Pair' ), func: function() {
-                    createPairCollection( panel.model, panel.getSelectedModels() )
+                    PAIR_COLLECTION_CREATOR.createPairHDCA( panel.getSelectedModels() )
                         .done( function(){ panel.model.refresh() });
                 }
             },
             {   html: _l( 'Build List of Dataset Pairs' ), func: function() {
-                    createListOfPairsCollection( panel.model, panel.getSelectedModels() );
+                    LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection( panel.getSelectedModels() )
+                        .done( function(){ panel.model.refresh() });
                 }
             },
-        ]);
+        ];
     },
 
     // ------------------------------------------------------------------------ sub-views

client/galaxy/scripts/mvc/ui/error-modal.js

@@ -0,0 +1,29 @@
+define([
+    "utils/localization"
+], function( _l ){
+
+    function _errorModal( message, title ){
+        Galaxy.modal.show({
+            title   : _l( title ),
+            body    : _l( message ),
+            buttons : { 'Ok': function(){ Galaxy.modal.hide(); } },
+            closing_events: true
+        });
+    }
+
+    function _errorAlert( message, title ){
+        alert( title + '\n\n' + message );
+    }
+
+    function errorModal( message, title ){
+        if( !message ){ return; }
+        title = title || 'Error';
+        if( window.Galaxy && Galaxy.modal ){
+            return _errorModal( message, title );
+        }
+        return _errorAlert( message, title );
+    }
+
+
+return errorModal;
+});

lib/galaxy/managers/histories.py

@@ -283,23 +283,24 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
         deletable.PurgableSerializerMixin.add_serializers( self )
 
         self.serializers.update({
-            'model_class': lambda *a: 'History',
-            'id': self.serialize_id,
-            'create_time': self.serialize_date,
-            'update_time': self.serialize_date,
-            'size': lambda t, i, k: int( i.get_disk_size() ),
-            'nice_size': lambda t, i, k: i.get_disk_size( nice_size=True ),
-            'state': lambda t, i, k: self.history_manager.get_history_state( t, i ),
+            'model_class'   : lambda *a: 'History',
+            'id'            : self.serialize_id,
+            'create_time'   : self.serialize_date,
+            'update_time'   : self.serialize_date,
+            'size'          : lambda t, i, k: int( i.get_disk_size() ),
+            'nice_size'     : lambda t, i, k: i.get_disk_size( nice_size=True ),
+            'state'         : lambda t, i, k: self.history_manager.get_history_state( t, i ),
 
-            'url': lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
-            'contents_url': lambda t, i, k: self.url_for( 'history_contents', history_id=t.security.encode_id( i.id ) ),
+            'url'           : lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
+            'contents_url'  : lambda t, i, k: self.url_for( 'history_contents',
+                history_id=t.security.encode_id( i.id ) ),
 
-            'empty': lambda t, i, k: len( i.datasets ) <= 0,
-            'count': lambda trans, item, key: len( item.datasets ),
-            'hdas': lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
-            'state_details': lambda t, i, k: self.history_manager.get_state_counts( t, i ),
-            'state_ids': lambda t, i, k: self.history_manager.get_state_ids( t, i ),
-            'contents': self.serialize_contents
+            'empty'         : lambda t, i, k: ( len( i.datasets ) + len( i.dataset_collections ) ) <= 0,
+            'count'         : lambda trans, item, key: len( item.datasets ),
+            'hdas'          : lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
+            'state_details' : lambda t, i, k: self.history_manager.get_state_counts( t, i ),
+            'state_ids'     : lambda t, i, k: self.history_manager.get_state_ids( t, i ),
+            'contents'      : self.serialize_contents
         })
 
     def serialize_contents( self, trans, history, *args ):

static/maps/mvc/collection/collection-li.js.map

@@ -1 +1 @@
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static/maps/mvc/collection/list-collection-creator.js.map

@@ -0,0 +1 @@
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static/maps/mvc/collection/pair-collection-creator.js.map

@@ -0,0 +1 @@
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static/maps/mvc/history/hdca-li.js.map

@@ -1 +1 @@
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static/maps/mvc/ui/error-modal.js.map

@@ -0,0 +1 @@
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static/scripts/mvc/collection/collection-li.js

@@ -1,2 +1,2 @@
-define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,e.prototype.initialize.call(this,a)},_renderSubtitle:function(){var a=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return a.text(d("a list of datasets"));case"paired":return a.text(d("a pair of datasets"));case"list:paired":return a.text(d("a list of paired datasets"))}return a},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCListItemView("+a+")"}});g.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{titleBar:a})}();var h=f.extend({className:f.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DCEListItemView.initialize:",a),f.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCEListItemView("+a+")"}});h.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},f.prototype.templates,{titleBar:a})}();var i=b.DatasetListItemView.extend({className:b.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DatasetDCEListItemView.initialize:",a),b.DatasetListItemView.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+a+")"}});i.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},b.DatasetListItemView.prototype.templates,{titleBar:a})}();var j=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(a){g.prototype._swapNewRender.call(this,a);var b=this.model.get("state")||"ok";return this.$el.addClass("state-"+b),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
+define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,e.prototype.initialize.call(this,a)},_setUpListeners:function(){e.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["deleted"])&&this.render()},this)},_renderSubtitle:function(){var a=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return a.text(d("a list of datasets"));case"paired":return a.text(d("a pair of datasets"));case"list:paired":return a.text(d("a list of paired datasets"))}return a},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCListItemView("+a+")"}});g.prototype.templates=function(){var a=_.extend({},e.prototype.templates.warnings,{error:c.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',d("There was an error getting the data for this collection"),": <%- model.error %>","</div>","<% } %>"]),purged:c.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',d("This collection has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:c.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',d("This collection has been deleted"),"</div>","<% } %>"])}),b=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{warnings:a,titleBar:b})}();var h=f.extend({className:f.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DCEListItemView.initialize:",a),f.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCEListItemView("+a+")"}});h.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},f.prototype.templates,{titleBar:a})}();var i=b.DatasetListItemView.extend({className:b.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DatasetDCEListItemView.initialize:",a),b.DatasetListItemView.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+a+")"}});i.prototype.templates=function(){var a=c.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},b.DatasetListItemView.prototype.templates,{titleBar:a})}();var j=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(a){g.prototype._swapNewRender.call(this,a);var b=this.model.get("state")||"ok";return this.$el.addClass("state-"+b),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
 //# sourceMappingURL=../../../maps/mvc/collection/collection-li.js.map

static/scripts/mvc/collection/list-collection-creator.js

@@ -0,0 +1,2 @@
+define(["mvc/dataset/states","mvc/ui/error-modal","utils/localization"],function(a,b){function c(b){var c=b.toJSON().filter(function(b){return"dataset"===b.history_content_type&&b.state===a.OK});return c}function d(){b("Use the checkboxes at the left of the dataset names to select them. Selected datasets should be error-free and should have completed running.",f)}function e(a){var b="New Dataset List",e=c(a).map(function(a){return{id:a.id,name:a.name,src:"dataset"===a.history_content_type?"hda":"hdca"}});return e.length?a.createHDCA(e,"list",b):(d(),jQuery.Deferred().reject(f))}var f="No valid datasets were selected";return{validElements:c,noValidElementsMessage:f,noValidElementsErrorModal:d,createListHDCA:e}});
+//# sourceMappingURL=../../../maps/mvc/collection/list-collection-creator.js.map

static/scripts/mvc/collection/pair-collection-creator.js

@@ -0,0 +1,2 @@
+define(["mvc/collection/list-collection-creator","mvc/ui/error-modal","utils/localization"],function(a,b){function c(c){var d=a.validElements(c);if(!d.length)return a.noValidElementsErrorModal(),jQuery.Deferred().reject(a.noValidElementsMessage);if(2!==d.length)return b("When pairing datasets, select only two datasets: one forward and one reverse.","Not a valid pair"),jQuery.Deferred().reject(a.noValidElementsMessage);var e="New Dataset Pair",f=[{name:"forward",src:"hda",id:d[0].id},{name:"reverse",src:"hda",id:d[1].id}];return c.createHDCA(f,"paired",e)}return{createPairHDCA:c}});
+//# sourceMappingURL=../../../maps/mvc/collection/pair-collection-creator.js.map

static/scripts/mvc/history/hdca-li.js

@@ -1,2 +1,2 @@
-define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=b.DCListItemView,f=e.extend({className:e.prototype.className+" history-content",_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){e.prototype._swapNewRender.call(this,b);var c=this.model.get("state")||a.OK;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return f.prototype.templates=function(){var a=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- collection.hid %></span> ','<span class="name"><%- collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{titleBar:a})}(),{HDCAListItemView:f}});
+define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("state")||a.OK;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',e("This collection has been hidden"),"</div>","<% } %>"],"collection")}),b=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- collection.hid %></span> ','<span class="name"><%- collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}});
 //# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map

static/scripts/mvc/ui/error-modal.js

@@ -0,0 +1,2 @@
+define(["utils/localization"],function(a){function b(b,c){Galaxy.modal.show({title:a(c),body:a(b),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:!0})}function c(a,b){alert(b+"\n\n"+a)}function d(a,d){return a?(d=d||"Error",window.Galaxy&&Galaxy.modal?b(a,d):c(a,d)):void 0}return d});
+//# sourceMappingURL=../../../maps/mvc/ui/error-modal.js.map