Merge branch 'dev' into azure-blob-objectstore

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

@@ -125,6 +125,8 @@ DCListItemView.prototype.templates = (function(){
                 _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' );

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/dataset/data.js

@@ -64,7 +64,7 @@ var TabularDataset = Dataset.extend({
     defaults: _.extend({}, Dataset.prototype.defaults, {
         chunk_url: null,
         first_data_chunk: null,
-        chunk_index: -1,
+        offset: 0,
         at_eof: false
     }),
 
@@ -72,7 +72,9 @@ var TabularDataset = Dataset.extend({
         Dataset.prototype.initialize.call(this);
 
         // If first data chunk is available, next chunk is 1.
-        this.attributes.chunk_index = (this.attributes.first_data_chunk ? 1 : 0);
+        if (this.attributes.first_data_chunk){
+            this.attributes.offset = this.attributes.first_data_chunk.offset;
+        }
         this.attributes.chunk_url = Galaxy.root + 'dataset/display?dataset_id=' + this.id;
         this.attributes.url_viz = Galaxy.root + 'visualization';
     },
@@ -90,12 +92,13 @@ var TabularDataset = Dataset.extend({
         var self = this,
             next_chunk = $.Deferred();
         $.getJSON(this.attributes.chunk_url, {
-            chunk: self.attributes.chunk_index++
+            offset: self.attributes.offset
         }).success(function(chunk) {
             var rval;
             if (chunk.ck_data !== '') {
                 // Found chunk.
                 rval = chunk;
+                self.attributes.offset = chunk.offset;
             }
             else {
                 // At EOF.

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 };
     },
@@ -281,10 +285,14 @@ var HistoryContents = Backbone.Collection
             type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' );
         }
         var collection = this,
-            xhr = jQuery.post( this.url(), {
-                content : id,
-                source  : contentType,
-                type    : type
+            xhr = jQuery.ajax( this.url(), {
+                method: 'POST',
+                contentType: 'application/json',
+                data: JSON.stringify({
+                    content : id,
+                    source  : contentType,
+                    type    : type
+                })
             })
             .done( function( response ){
                 collection.add([ response ]);

config/plugins/visualizations/graphviz/config/graphviz.xml

@@ -4,7 +4,17 @@
     <data_sources>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
-            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Text</test>
+            <test test_attr="ext" result_type="datatype">json</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext" result_type="datatype">txt</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="has_dataprovider" test_attr="datatype">node-edge</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>

config/plugins/visualizations/graphviz/static/js/graphVis.js

@@ -1,38 +1,49 @@
- var showNodeLabel;
- var showEdgeLabel;
- var showOut;
- var showIn;
- var demoNodes = [];
- var demoEdges = [];
- var shape;
- var allcy;
- var cy;
+var showNodeLabel;
+var showEdgeLabel;
+var showOut;
+var showIn;
+var demoNodes = [];
+var demoEdges = [];
+var shape;
+var allcy;
+var cy;
+// The key to hold down when brush/box selecting: 16 === shift
+var BRUSH_KEY = 16;
 
+$(function() {
+    // remove horizontal scrollbar
+    $("body").css("overflow-x", "hidden");
 
-
- $(function() { // on dom ready
-
-
- 	$("body").css("overflow-x", "hidden"); //// remove horizontal scrollbar
-
-
- }); // END on dom ready
+    // set up a key that, when held down, allows box selection and turns panning off
+    $( document )
+        .on( 'keydown', function( ev ){
+            if( cy && ev.keyCode === BRUSH_KEY ){
+                cy.panningEnabled( false );
+                cy.boxSelectionEnabled( true );
+            }
+        })
+        .on( 'keyup', function( ev ){
+            if( cy && ev.keyCode === BRUSH_KEY ){
+                cy.panningEnabled( true );
+                cy.boxSelectionEnabled( false );
+            }
+        });
+});
 
 // shape of the graph
- $("select option:selected").each(function() {
- 	shape = $(this).val();
+$("select option:selected").each(function() {
+    shape = $(this).val();
+});
 
- });
- 
- ///////// create graph
- function createGraph(data) {
+///////// create graph
+function createGraph(data) {
+    window.graphData = data;
 
  	allcy = cytoscape({
  		headless: true,
  	});
 
  	cy = cytoscape({
-
  		container: document.getElementById('cy'),
 
  		layout: {
@@ -45,121 +56,131 @@
  		motionBlur: true,
  		textureOnViewport: true,
 
+        // initially have click and drag pan the viewport
+        panningEnabled: true,
+        boxSelectionEnabled: false,
+
  		ready: function() {
 
  			window.cy = this;
  			cy.nodes().on("click", function(e) {
-
  				showNodeInfo(e.cyTarget);
-
  			});
  		},
+
  		style: cytoscape.stylesheet()
  			.selector('node')
  			.css({
- 			'content': showNodeLabel,
- 			'text-valign': 'center',
- 			'background-color': '#888888',
- 			'opacity': 0.8
+     			'content': showNodeLabel,
+     			'text-valign': 'center',
+     			'background-color': '#888888',
+     			'opacity': 0.8
+            })
 
- 		})
  			.selector('edge')
  			.css({
- 			'curve-style': 'unbundled-bezier',
- 			'target-arrow-shape': 'triangle',
- 			'width': 4,
- 			'line-color': '#ddd',
- 			'target-arrow-color': '#ddd',
- 			'content': showEdgeLabel
+     			'curve-style': 'unbundled-bezier',
+     			'target-arrow-shape': 'triangle',
+     			'width': 2,
+     			'line-color': '#ddd',
+     			'target-arrow-color': '#ddd',
+     			'content': showEdgeLabel
+            })
 
-
- 		})
  			.selector(':selected')
  			.css({
- 			'background-color': '#FE2E64',
- 			'line-color': '#FE2E64',
- 			'target-arrow-color': '#FE2E64',
- 			'source-arrow-color': '#FE2E64',
- 			'opacity': 1
- 		})
- 			.selector('core')
- 			.css({
- 			'outside-texture-bg-color': 'white'
+     			'background-color': '#FE2E64',
+     			'line-color': '#FE2E64',
+     			'target-arrow-color': '#FE2E64',
+     			'source-arrow-color': '#FE2E64',
+     			'opacity': 1
+     		})
 
- 		})
+            .selector('core')
+            .css({
+                'outside-texture-bg-color': 'white'
+     		})
  	});
+    window.cy = cy;
  	allcy.load(data);
 
-// if graph contains more than 50 nodes load only root nodes 
- 	if (allcy.nodes().length > 50 && allcy.nodes().roots().length != 0 ) {
-			
-			var toAdd = allcy.nodes().roots().closedNeighborhood();
- 			allcy.nodes().roots().addClass("roots");
- 			
-			showNodesToExpand(toAdd);
-	 		cy.add(toAdd);
- 			cy.load(cy.elements('*').jsons());
+    // if graph contains more than 50 nodes load only root nodes
+ 	if (allcy.nodes().length > 50 && allcy.nodes().roots().length !== 0 ) {
+		var toAdd = allcy.nodes().roots().closedNeighborhood();
+		allcy.nodes().roots().addClass("roots");
+
+		showNodesToExpand(toAdd);
+ 		cy.add(toAdd);
+		cy.load(cy.elements('*').jsons());
 
  		cy.style()
  			.selector('.toBeExpaned')
  			.css({
+     			'width': 50,
+     			'height': 50
+     		})
+ 			.update();
 
- 			'width': 50,
- 			'height': 50
- 		})
- 			.update(); 			
- 			
  	} else {
-
- 		cy.add(data);
- 		cy.load(cy.elements('*').jsons());
+        cy.add(data);
+        cy.load(cy.elements('*').jsons());
  	}
- 	cy.boxSelectionEnabled(true);
-
-
  	checkBoxes();
 
-
- } // END create graph	
+} // END create graph
 
 
- //// parse function for matrix data
- function parseAndCreate(demoNodes, demoEdges) {
- 	var data = {
- 		nodes: demoNodes,
- 		edges: demoEdges
- 	};
- 	createGraph(data);
- }
+//// parse function for matrix data
+function parseTextMatrix(data) {
+    var nodes = [],
+        edges = [];
 
+    data.split( '\n' ).forEach( function( line ){
+        var columns = line.split( /,?\s+/ ),
+            sourceId = columns[0]; // split by comma or space
 
- ///// parsing function for json: for link/egde and "" issues
- function parseJson(dataToParse) {
+        nodes.push({
+            data: { id: sourceId }
+        });
 
- 	if (dataToParse.links == null) {
+        for( var i = 1; i < columns.length; i++ ){
+            edges.push({
+                data: {
+                    source  : sourceId,
+                    target  : columns[i]
+                }
+            });
+        }
+    });
 
- 		var links = dataToParse.edges;
- 	} else {
- 		var links = dataToParse.links;
- 		dataToParse.edges = links;
+	createGraph({
+        nodes: nodes,
+        edges: edges
+    });
+}
 
- 	}
+///// parsing function for json: for link/egde and "" issues
+function parseJson( data ) {
 
- 	var nodes = dataToParse.nodes;
-
- 	for (var i = 0; i < nodes.length; i++) {
-
- 		dataToParse.nodes[i].data = nodes[i];
- 		dataToParse.nodes[i].data.id = '"' + nodes[i].id + '"';
- 	}
-
-
- 	for (var i = 0; i < links.length; i++) {
-
- 		dataToParse.edges[i].data = links[i];
- 		dataToParse.edges[i].data.source = '"' + links[i].source + '"';
- 		dataToParse.edges[i].data.target = '"' + links[i].target + '"';
- 	}
-
- 	createGraph(dataToParse);
- }
+    if( data.hasOwnProperty( 'links' ) ){
+        data.edges = data.links;
+        delete data.links;
+    }
+	data.nodes = data.nodes.map( function _processNode( node ){
+        return {
+            data : $.extend( {}, node.data, {
+                id : node.id + ''
+            })
+        };
+    });
+    data.edges = data.edges.map( function _processEdge( edge ){
+        return {
+            data : $.extend( {}, edge.data, {
+                id      : edge.id || undefined,
+                source  : data.nodes[ edge.source ].data.id,
+                target  : data.nodes[ edge.target ].data.id
+            })
+        };
+    });
+	createGraph( data );
+}

config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js

@@ -34,7 +34,7 @@ $(function() { // on dom ready
 	});
 
 
-	//////// change the shape of the graph 
+	//////// change the shape of the graph
 	$('#selectShape').change(function() {
 
 		$("select option:selected").each(function() {
@@ -54,11 +54,11 @@ $(function() { // on dom ready
 		if ($('#showOutNode').is(":checked")) {
 			showOut = true;
 			cy.nodes().on("tapend", highlightOut);
-			
+
 		} else {
 			showOut = false;
 			cy.nodes().off("tapend", highlightOut);
-			
+
 			resetHighlightOut(showIn, showOut);
 		}
 	});
@@ -71,13 +71,13 @@ $(function() { // on dom ready
 		if ($('#showInNode').is(":checked")) {
 			showIn = true;
 			cy.nodes().on("tapend", highlightIn);
-			
+
 
 		} else {
 			showIn = false;
 			cy.nodes().off("tapend", highlightIn);
 			resetHighlightIn(showIn, showOut);
-			
+
 			cy.nodes().removeClass('connectedNodeIn');
 		}
 
@@ -101,12 +101,12 @@ $(function() { // on dom ready
 
 	});
 
-	//// disable/unable buttons 
+	//// disable/unable buttons
 	$(document).on('click', function() {
 
 		var selectedNode = cy.nodes(':selected');
 
-		if (selectedNode.outgoers().length == 0) {
+		if (selectedNode.outgoers().length === 0) {
 
 			$('.btn.colNode').prop('disabled', true);
 
@@ -149,7 +149,7 @@ $(function() { // on dom ready
 
 		var selectedNode = cy.nodes(':selected');
 
-		if (e.which == 101 && selectedNode.size() != 0) { // 101 for 'e' = expand
+		if (e.which === 101 && selectedNode.size() !== 0) { // 101 for 'e' = expand
 
 			if (selectedNode.hasClass('toBeExpaned')) {
 
@@ -162,20 +162,20 @@ $(function() { // on dom ready
 
 
 		}
-		if (e.which == 99 && selectedNode.size() != 0 && !selectedNode.hasClass('superNode') && selectedNode.outgoers().length != 0) { // 99 for 'c' = collapse
+		if (e.which === 99 && selectedNode.size() !== 0 && !selectedNode.hasClass('superNode') && selectedNode.outgoers().length !== 0) { // 99 for 'c' = collapse
 
 			colNode();
 
 		}
 
-		if (e.which == 100 && selectedNode.size() != 0) { // 100 for 'd' = delete
+		if (e.which === 100 && selectedNode.size() !== 0) { // 100 for 'd' = delete
 			deleteSelectedNodes();
 		}
 
 
 	});
 
-	/////////////// tool Panel movement 
+	/////////////// tool Panel movement
 
 	$(document).on('click', '.slider-arrow.show', function() {
 		$(".slider-arrow, .panel").animate({
@@ -234,13 +234,9 @@ $(function() { // on dom ready
 		// document.getElementById('cy').style.width="100%";
 		cy.resize();
 	});
+}); // on dom ready END
 
-
-
-
-}) // on dom ready END
-
-///////// finding outgoing Nodes		
+///////// finding outgoing Nodes
 function highlightOut() {
 
 	var selectedNode = this;
@@ -259,7 +255,7 @@ function highlightOut() {
 		})
 			.update();
 	} else {
-		
+
 		cy.nodes().not(this).removeClass('connectedNodeOut');
 		cy.nodes().not(this).removeClass('selectedNodeOut');
 		cy.edges().not(this).removeClass('connectedNodeOut');
@@ -290,7 +286,7 @@ function highlightOut() {
 	}
 }
 
-/////// reset highlighting of outgoing nodes 		
+/////// reset highlighting of outgoing nodes
 function resetHighlightOut(showIn, showOut) {
 
 	cy.style()
@@ -370,7 +366,7 @@ function highlightIn() {
 }
 
 
-/////// reset highlighting of incoming nodes 		
+/////// reset highlighting of incoming nodes
 function resetHighlightIn(showIn, showOut) {
 
 	cy.style()
@@ -401,7 +397,7 @@ function resetHighlightIn(showIn, showOut) {
 }
 
 
-////// export PNG 	
+////// export PNG
 function exportFunction() {
 
 	var pngPic = cy.png();
@@ -418,7 +414,6 @@ function downloadURI(uri, fname) {
 	link.click();
 	// Cleanup the DOM
 	document.body.removeChild(link);
-	delete link;
 }
 
 ///// restore Graph structure
@@ -449,7 +444,6 @@ function showNodeInfo(node) {
 	var j = 0;
 
 	for (var key in nodeContent) {
-
 		if (key == 'group' || key == 'data') {
 			continue;
 		}
@@ -458,10 +452,8 @@ function showNodeInfo(node) {
 		i++;
 		values[j] = nodeContent[key];
 		j++;
-
 	}
 
-
 	var childNodes = node.outgoers().nodes();
 	var childNum = childNodes.length;
 
@@ -472,16 +464,15 @@ function showNodeInfo(node) {
 	var table = createTable(fieldName, values, degree, parentNum, childNum);
 
 	$('#nodeInfoDiv').html("<p><strong>Node Description </p>" + table);
-	for (var i = 0; i < fieldName.length; i++) {
 
-		if (isValidUrl(values[i])) {
+	for (var strIndex = 0; strIndex < fieldName.length; strIndex++) {
 
+		if (isValidUrl(values[strIndex])) {
 			var e = document.createElement("div");
 			e.id = "linkDiv";
 			$('#nodeInfoDiv').append(e);
-			
+
 			var url = values[i];
-			
 			document.getElementById("linkDiv").innerHTML += "<br>" + fieldName[i] + "<br>";
 			$('<iframe id="iframeId" width = "240"/>').appendTo(document.getElementById("linkDiv")).prop('src', url);
 
@@ -490,40 +481,27 @@ function showNodeInfo(node) {
 	}
 }
 
-function isValidUrl(str) {
-	var pattern = new RegExp(/((([A-Za-z]{3,9}:(?:\/\/)?)(?:[\-;:&=\+\$,\w]+@)?[A-Za-z0-9\.\-]+|(?:www\.|[\-;:&=\+\$,\w]+@)[A-Za-z0-9\.\-]+)((?:\/[\+~%\/\.\w\-_]*)?\??(?:[\-\+=&;%@\.\w_]*)#?(?:[\.\!\/\\\w]*))?)/); // fragment locater
-	if (!pattern.test(str)) {
-
-		return false;
-	} else {
-		return true;
-	}
-}
-
 function createTable(fieldName, values, degree, parentNum, childNum) {
-
 	var table = "<table class='CSSTableGenerator'>";
-
 	for (var i = 0; i < fieldName.length; i++) {
-
-
 		if (isValidUrl(values[i])) {
 			i++;
 		}
-
 		table += "<tr>" + "<td>" + fieldName[i] + "</td>" + "<td>" + values[i] + "</td>" + "</tr>";
-
 	}
 	table += "<tr>" + "<td>" + "degree" + "</td>" + "<td>" + degree + "</td>" + "</tr>";
 	table += "<tr>" + "<td>" + "number of child nodes" + "</td>" + "<td>" + childNum + "</td>" + "</tr>";
 	table += "<tr>" + "<td>" + "number of parent nodes" + "</td>" + "<td>" + parentNum + "</td>" + "</tr>";
-
-
 	table += "</table>";
 	return table;
-
 }
 
+function isValidUrl(str) {
+	var pattern = new RegExp(/((([A-Za-z]{3,9}:(?:\/\/)?)(?:[\-;:&=\+\$,\w]+@)?[A-Za-z0-9\.\-]+|(?:www\.|[\-;:&=\+\$,\w]+@)[A-Za-z0-9\.\-]+)((?:\/[\+~%\/\.\w\-_]*)?\??(?:[\-\+=&;%@\.\w_]*)#?(?:[\.\!\/\\\w]*))?)/); // fragment locater
+	return pattern.test(str);
+}
+
+
 
 /////// delete selected nodes
 
@@ -539,7 +517,7 @@ function deleteSelectedNodes() {
 	cy.remove(edgesToRemove);
 
 }
-/////// restore Deleted Nodes 
+/////// restore Deleted Nodes
 function restoreDeletedNodes() {
 	nodesToRemove.restore();
 	edgesToRemove.restore();
@@ -550,7 +528,7 @@ function expandNodes(selectedNode) {
 
 	cy.nodes().unbind("tapend");
 	var selectedNodeId = selectedNode.id();
-	selectedNodeId = selectedNodeId.replace(/[^0-9\.]+/g, ""); // removing "" 
+	selectedNodeId = selectedNodeId.replace(/[^0-9\.]+/g, ""); // removing ""
 
 	var eles = allcy.nodes();
 
@@ -559,7 +537,7 @@ function expandNodes(selectedNode) {
 	showNodesToExpand(nodesToAdd);
 	cy.add(eles[selectedNodeId].outgoers());
 
-	selectedNode.removeClass('toBeExpaned'); 
+	selectedNode.removeClass('toBeExpaned');
 
 	$("select option:selected").each(function() {
 		shape = $(this).val();
@@ -583,7 +561,7 @@ function showNodesToExpand(toAdd) {
 
 		if (ele.outdegree() > 0 && !ele.hasClass('roots')) {
 			ele.addClass('toBeExpaned');
-		} 
+		}
 	});
 
 }
@@ -604,7 +582,7 @@ function checkBoxes() {
 		resetHighlightIn(showIn, showOut);
 		cy.nodes().removeClass('connectedNodeIn');
 	}
-	
+
 	if ($('#showOutNode').is(":checked")) {
 		showOut = true;
 		cy.nodes().on("tapend", highlightOut);

config/plugins/visualizations/graphviz/templates/graphviz.mako

@@ -6,12 +6,14 @@
     <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
 
     <title>${hda.name} | ${visualization_name}</title>
-<%
-    root = h.url_for( '/' )
-%>
-<script type="text/javascript" src="/static/scripts/libs/jquery/jquery.js"></script>
+    <%
+        root = h.url_for( '/' )
+    %>
+
+    <script type="text/javascript" src="/static/scripts/libs/jquery/jquery.js"></script>
+
     ${h.stylesheet_link( root + 'plugins/visualizations/graphviz/static/css/style.css' )}
-    
+
     ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/jquery.qtip.js' )}
     ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/cytoscape.min.js' )}
     ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/collapse.js' )}
@@ -25,63 +27,62 @@
     ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/wz_tooltip.js' )}
 
     <script>
+        function parseNodeEdge( data ){
+            data = data.data[0];
+            parseJson( data );
+        }
+
         $(document).ready(function() {
-        
-            var hdaId   = '${trans.security.encode_id( hda.id )}',
-            hdaExt  = '${hda.ext}',
-            dataUrl = "${h.url_for( controller='/datasets', action='index')}/" + hdaId + "/display?to_ext=" + hdaExt;
 
-			// var reader = new FileReader();
-			
-             $.ajax({
-                 'async': true,
-                 'global': false,
-                 'url': dataUrl,
-                 'dataType': "json",
-                 'success': function(data) {
-                     parseJson(data);
-                     //  createGraph(data);
-                 },
-                 'error': function(data) {
-                 
-							jQuery.get(dataUrl, function(data) {
-  		 				
-  							var lines = data.split('\n');
-                         var chars;
-                         for (var line = 0; line < lines.length; line++) {
-                             chars = lines[line].split(/,?\s+/); // split by comma or space
+            var hdaName = '${ hda.name | h }',
+                hdaId = '${trans.security.encode_id( hda.id )}',
+                hdaExt = '${hda.ext}',
+                rawUrl = '${h.url_for( controller="/datasets", action="index" )}',
+                apiUrl = '${h.url_for( "/" ) + "api/datasets"}',
+                dataUrl;
 
-                             demoNodes.push({
-                                 data: {
-                                     id: chars[0],
-                                     label: chars[0]
-                                 }
-                             });
+            function errorHandler( xhr, status, message ){
+                console.error(x, s, m);
+                alert("error loading data:\n" + m);
+            }
 
-                             for (var i = 1; i < chars.length; i++) {
-                                 demoEdges.push({
-                                     data: {
-                                         source: chars[0],
-                                         target: chars[i],
-                                         id: chars[0] + chars[i],
+            switch( hdaExt ){
+                case 'txt':
+                    dataUrl = rawUrl + '/' + hdaId + '/display?to_ext=txt';
+                    $.ajax(dataUrl, {
+                        dataType    : 'text',
+                        success     : parseTextMatrix,
+                        error       : errorHandler
+                    });
+                    break;
 
-                                     }
-                                 })
-                             }
-                         }
-					  
-  								parseAndCreate(demoNodes, demoEdges);
-  
-							});                     
-                     
-                  
-                 }
-             });
+                case 'json':
+                    dataUrl = rawUrl + '/' + hdaId + '/display?to_ext=json';
+                    $.ajax(dataUrl, {
+                        dataType    : 'json',
+                        success     : parseJson,
+                        error       : errorHandler
+                    });
+                    break;
 
-        } );
+                default:
+                    dataUrl = apiUrl + '/' + hdaId;
+                    $.ajax(dataUrl, {
+                        dataType    : 'json',
+                        success     : parseNodeEdge,
+                        error       : errorHandler,
+                        data : {
+                            data_type : 'raw_data',
+                            provider  : 'node-edge'
+                        }
+                    });
+            }
+        });
 
     </script>
     <div id="cy"></div>
+
+    <!-- left control panel for rendering controls, hiding nodes, etc. - initially hidden -->
     <div class="panel">
         <br>
         <div id="mainselection">
@@ -139,12 +140,10 @@
         <br>
         <br>
 
-
         <input type="button" class="btn delNode" name="deleteNodes" id="deleteNodes" value="Delete Selected Nodes " onclick="deleteSelectedNodes()" disabled="disabled">
         <br>
         <br>
 
-
         <input type="button" class="btn" name="restoreNodes" id="restoreNodes" value="Restore Deleted Nodes" onclick="restoreDeletedNodes()">
         <br>
         <br>
@@ -158,13 +157,16 @@
         <br>
         <br>
     </div>
-
+    <!-- button to show above panel -->
     <a href="javascript:void(0);" class="slider-arrow show">&raquo;</a>
-    <div id="nodeInfoDiv" class="nodePanel"> 
+
+    <!-- right control panel for displaying node data - initially hidden -->
+    <div id="nodeInfoDiv" class="nodePanel">
         <p> <strong>Node Description </strong></p>
         <br><br>
         <p> Please select a node </p>
     </div>
+    <!-- button to show above panel -->
     <a href="javascript:void(0);" class="slider-arrow-forNode show">&laquo;</a>
 </body>
 

lib/galaxy/datatypes/binary.py

@@ -73,7 +73,7 @@ class Binary( data.Data ):
         """Returns the mime type of the datatype"""
         return 'application/octet-stream'
 
-    def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
+    def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
         trans.response.set_content_type(dataset.get_mime())
         trans.log_event( "Display dataset id: %s" % str( dataset.id ) )
         trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size )

lib/galaxy/datatypes/data.py

@@ -312,7 +312,7 @@ class Data( object ):
         trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
         return open( dataset.file_name )
 
-    def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
+    def display_data(self, trans, data, preview=False, filename=None, to_ext=None, **kwd):
         """ Old display method, for transition - though still used by API and
         test framework. Datatypes should be very careful if overridding this
         method and this interface between datatypes and Galaxy will likely

lib/galaxy/datatypes/molecules.py

@@ -393,7 +393,7 @@ class OBFS(Binary):
             return "OpenBabel Fastsearch Index"
 
     def display_data(self, trans, data, preview=False, filename=None,
-                     to_ext=None, size=None, offset=None, **kwd):
+                     to_ext=None, **kwd):
         """Apparently an old display method, but still gets called.
 
         This allows us to format the data shown in the central pane via the "eye" icon.

lib/galaxy/datatypes/tabular.py

@@ -58,31 +58,23 @@ class TabularData( data.Text ):
         except:
             return False
 
-    def get_chunk(self, trans, dataset, chunk):
-        ck_index = int(chunk)
-        f = open(dataset.file_name)
-        initial_offset = (ck_index * trans.app.config.display_chunk_size)
-        f.seek(initial_offset)
-        # If we aren't at the start of the file, seek to next newline.  Do this better eventually.
-        if f.tell() != 0:
-            cursor = f.read(1)
-            while cursor and cursor != '\n':
+    def get_chunk(self, trans, dataset, offset=0, ck_size=None):
+        with open(dataset.file_name) as f:
+            f.seek(offset)
+            ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
+            if ck_data and ck_data[-1] != '\n':
                 cursor = f.read(1)
-        read_start_offset = f.tell()
-        prechunk_skip = read_start_offset - initial_offset
-        # We subtract the prechunk skip out of the primary chunk read to avoid
-        # shifting the chunk tail onto a line it shouldn't have.
-        ck_data = f.read(trans.app.config.display_chunk_size - prechunk_skip)
-        cursor = f.read(1)
-        while cursor and ck_data[-1] != '\n':
-            ck_data += cursor
-            cursor = f.read(1)
-        return dumps( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
+                while cursor and cursor != '\n':
+                    ck_data += cursor
+                    cursor = f.read(1)
+            last_read = f.tell()
+        return dumps( { 'ck_data': util.unicodify( ck_data ),
+                        'offset': last_read } )
 
-    def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
+    def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
         preview = util.string_as_bool( preview )
-        if chunk:
-            return self.get_chunk(trans, dataset, chunk)
+        if offset is not None:
+            return self.get_chunk(trans, dataset, offset, ck_size)
         elif to_ext or not preview:
             to_ext = to_ext or dataset.extension
             return self._serve_raw(trans, dataset, to_ext)

lib/galaxy/datatypes/text.py

@@ -127,19 +127,17 @@ class Ipynb( Json ):
             except:
                 return False
 
-    def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
+    def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
         config = trans.app.config
         trust = getattr( config, 'trust_ipython_notebook_conversion', False )
         if trust:
-            return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, chunk=chunk, **kwd)
+            return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, **kwd)
         else:
-            return super(Ipynb, self).display_data( trans, dataset, preview=preview, filename=filename, to_ext=to_ext, chunk=chunk, **kwd )
+            return super(Ipynb, self).display_data( trans, dataset, preview=preview, filename=filename, to_ext=to_ext, **kwd )
 
-    def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
+    def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
         preview = string_as_bool( preview )
-        if chunk:
-            return self.get_chunk(trans, dataset, chunk)
-        elif to_ext or not preview:
+        if to_ext or not preview:
             return self._serve_raw(trans, dataset, to_ext)
         else:
             ofile_handle = tempfile.NamedTemporaryFile(delete=False)
@@ -426,7 +424,7 @@ class SnpEffDb( Text ):
         # search data_dir/genome_version for files
         regulation_pattern = 'regulation_(.+).bin'
         #  annotation files that are included in snpEff by a flag
-        annotations_dict = {'nextProt.bin' : '-nextprot', 'motif.bin': '-motif'}
+        annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif'}
         regulations = []
         annotations = []
         genome_version = None

lib/galaxy/jobs/runners/kubernetes.py

@@ -75,7 +75,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         job_destination = job_wrapper.job_destination
 
         # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/
-        k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper)
+        k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag())
         k8s_job_obj = {
             "apiVersion": "extensions/v1beta1",
             "kind": "Job",
@@ -91,7 +91,14 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             "spec": self.__get_k8s_job_spec(job_wrapper)
         }
 
+        # Checks if job exists
+        job = Job(self._pykube_api, k8s_job_obj)
+        if job.exists():
+            job.delete()
         # Creates the Kubernetes Job
+        # TODO if a job with that ID exists, what should we do?
+        # TODO do we trust that this is the same job and use that?
+        # TODO or create a new job as we cannot make sure
         Job(self._pykube_api, k8s_job_obj).create()
 
         # define job attributes in the AsyncronousJobState for follow-up
@@ -103,9 +110,9 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         external_runjob_script = None
         return external_runjob_script
 
-    def __produce_unique_k8s_job_name(self, job_wrapper):
+    def __produce_unique_k8s_job_name(self, galaxy_internal_job_id):
         # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
-        return "galaxy-" + job_wrapper.get_id_tag()
+        return "galaxy-" + galaxy_internal_job_id
 
     def __get_k8s_job_spec(self, job_wrapper):
         """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template."""
@@ -118,7 +125,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         (see pod selector) and an appropriate restart policy."""
         k8s_spec_template = {
             "metadata": {
-                "labels": {"app": self.__produce_unique_k8s_job_name(job_wrapper)}
+                "labels": {"app": self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag())}
             },
             "spec": {
                 "volumes": self.__get_k8s_mountable_volumes(job_wrapper),
@@ -159,6 +166,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             # to assemble the command.
             # TODO possibly shell needs to be set by job_wrapper
             "command": ["/bin/bash", "-c", job_wrapper.runner_command_line],
+            "workingDir": job_wrapper.working_directory,
             "volumeMounts": [{
                 "mountPath": self.runner_params['k8s_persistent_volume_claim_mount_path'],
                 "name": self._galaxy_vol_name
@@ -204,9 +212,17 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id)
         if len(jobs.response['items']) == 1:
             job = Job(self._pykube_api, jobs.response['items'][0])
+            job_destination = job_state.job_wrapper.job_destination
             succeeded = 0
             active = 0
             failed = 0
+
+            max_pod_retrials = 1
+            if 'k8s_pod_retrials' in self.runner_params:
+                max_pod_retrials = int(self.runner_params['k8s_pod_retrials'])
+            if 'max_pod_retrials' in job_destination.params:
+                max_pod_retrials = int(job_destination.params['max_pod_retrials'])
+
             if 'succeeded' in job.obj['status']:
                 succeeded = job.obj['status']['succeeded']
             if 'active' in job.obj['status']:
@@ -223,16 +239,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 job_state.running = False
                 self.mark_as_finished(job_state)
                 return None
-
-            elif active > 0 or succeeded + active + failed == 0:
+            elif active > 0 and failed <= max_pod_retrials:
                 job_state.running = True
                 return job_state
-            elif failed > job_state.job_destination.params['max_pod_retrials']:
+            elif failed > max_pod_retrials:
                 self.__produce_log_file(job_state)
                 error_file = open(job_state.error_file, 'w')
                 error_file.write("Exceeded max number of Kubernetes pod retrials allowed for job\n")
                 error_file.close()
                 job_state.running = False
+                job_state.fail_message = "More pods failed than allowed. See stdout for pods details."
                 self.mark_as_failed(job_state)
                 job.scale(replicas=0)
                 return None
@@ -260,14 +276,46 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             self.mark_as_failed(job_state)
             return job_state
 
+    def fail_job(self, job_state):
+        """
+        Kubernetes runner overrides fail_job (called by mark_as_failed) to rescue the pod's log files which are left as
+        stdout (pods logs are the natural stdout and stderr of the running processes inside the pods) and are
+        deleted in the parent implementation as part of the failing the job process.
+
+        :param job_state:
+        :return:
+        """
+
+        # First we rescue the pods logs
+        with open(job_state.output_file, 'r') as outfile:
+            stdout_content = outfile.read()
+
+        if getattr(job_state, 'stop_job', True):
+            self.stop_job(self.sa_session.query(self.app.model.Job).get(job_state.job_wrapper.job_id))
+        self._handle_runner_state('failure', job_state)
+        # Not convinced this is the best way to indicate this state, but
+        # something necessary
+        if not job_state.runner_state_handled:
+            job_state.job_wrapper.fail(
+                message=getattr(job_state, 'fail_message', 'Job failed'),
+                stdout=stdout_content, stderr='See stdout for pod\'s stderr.'
+            )
+            if job_state.job_wrapper.cleanup_job == "always":
+                job_state.cleanup()
+
     def __produce_log_file(self, job_state):
         pod_r = Pod.objects(self._pykube_api).filter(selector="app=" + job_state.job_id)
         logs = ""
         for pod_obj in pod_r.response['items']:
-            pod = Pod(self._pykube_api, pod_obj)
-            logs += "\n\n==== Pod " + pod.name + " log start ====\n\n"
-            logs += pod.logs(timestamps=True)
-            logs += "\n\n==== Pod " + pod.name + " log end   ===="
+            try:
+                pod = Pod(self._pykube_api, pod_obj)
+                logs += "\n\n==== Pod " + pod.name + " log start ====\n\n"
+                logs += pod.logs(timestamps=True)
+                logs += "\n\n==== Pod " + pod.name + " log end   ===="
+            except Exception as detail:
+                log.info("Could not write pod\'s " + pod_obj['metadata']['name'] +
+                         " log file due to HTTPError " + str(detail))
+
         logs_file_path = job_state.output_file
         logs_file = open(logs_file_path, mode="w")
         if isinstance(logs, text_type):
@@ -279,8 +327,9 @@ class KubernetesJobRunner(AsynchronousJobRunner):
     def stop_job(self, job):
         """Attempts to delete a dispatched job to the k8s cluster"""
         try:
-            jobs = Job.objects(self._pykube_api).filter(selector="app=" + job.job_runner_external_id)
-            if jobs.response['items'].len() >= 0:
+            jobs = Job.objects(self._pykube_api).filter(selector="app=" +
+                                                                 self.__produce_unique_k8s_job_name(job.get_id_tag()))
+            if len(jobs.response['items']) >= 0:
                 job_to_delete = Job(self._pykube_api, jobs.response['items'][0])
                 job_to_delete.scale(replicas=0)
             # TODO assert whether job parallelism == 0

lib/galaxy/managers/base.py

@@ -736,7 +736,7 @@ class ModelDeserializer( HasAModelManager ):
     """
     # TODO:?? a larger question is: which should be first? Deserialize then validate - or - validate then deserialize?
 
-    def __init__( self, app, **kwargs ):
+    def __init__( self, app, validator=None, **kwargs ):
         """
         Set up deserializers and validator.
         """
@@ -747,7 +747,7 @@ class ModelDeserializer( HasAModelManager ):
         self.deserializable_keyset = set([])
         self.add_deserializers()
         # a sub object that can validate incoming values
-        self.validate = ModelValidator( self.app )
+        self.validate = validator or ModelValidator( self.app )
 
     def add_deserializers( self ):
         """

lib/galaxy/managers/users.py

@@ -11,6 +11,7 @@ from galaxy import util
 from galaxy.managers import base
 from galaxy.managers import deletable
 from galaxy.managers import api_keys
+from galaxy.security import validate_user_input
 
 import logging
 log = logging.getLogger( __name__ )
@@ -26,7 +27,6 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
     # TODO: incorp BaseAPIController.validate_in_users_and_groups
     # TODO: incorp CreatesUsersMixin
     # TODO: incorp CreatesApiKeysMixin
-    # TODO: incorporate security/validate_user_input.py
     # TODO: incorporate UsesFormDefinitionsMixin?
 
     def create( self, webapp_name=None, **kwargs ):
@@ -288,6 +288,28 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
         })
 
 
+class UserDeserializer( base.ModelDeserializer ):
+    """
+    Service object for validating and deserializing dictionaries that
+    update/alter users.
+    """
+    model_manager_class = UserManager
+
+    def add_deserializers( self ):
+        super( UserDeserializer, self ).add_deserializers()
+        self.deserializers.update({
+            'username'  : self.deserialize_username,
+        })
+
+    def deserialize_username( self, item, key, username, trans=None, **context ):
+        # TODO: validate_user_input requires trans and should(?) raise exceptions
+        # move validation to UserValidator and use self.app, exceptions instead
+        validation_error = validate_user_input.validate_publicname( trans, username, user=item )
+        if validation_error:
+            raise base.ModelDeserializingError( validation_error )
+        return self.default_deserializer( item, key, username, trans=trans, **context )
+
+
 class CurrentUserSerializer( UserSerializer ):
     model_manager_class = UserManager
 

lib/galaxy/security/validate_user_input.py

@@ -11,6 +11,9 @@ log = logging.getLogger( __name__ )
 
 VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9\-]+$" )
 VALID_PUBLICNAME_SUB = re.compile( "[^a-z0-9\-]" )
+PUBLICNAME_MIN_LEN = 3
+PUBLICNAME_MAX_LEN = 255
+
 #  Basic regular expression to check email validity.
 VALID_EMAIL_RE = re.compile( "[^@]+@[^@]+\.[^@]+" )
 FILL_CHAR = '-'
@@ -41,16 +44,10 @@ def validate_publicname( trans, publicname, user=None ):
     # letters, numbers, and the '-' character.
     if user and user.username == publicname:
         return ''
-    if trans.webapp.name == 'tool_shed':
-        if len( publicname ) < 3:
-            return "Public name must be at least 3 characters in length"
-    else:
-        # DCT - TODO - Simplify logic if 3 chars is okay for publicname for
-        # galaxy as well as toolshed
-        if len( publicname ) < 3:
-            return "Public name must be at least 3 characters in length"
-    if len( publicname ) > 255:
-        return "Public name cannot be more than 255 characters in length"
+    if len( publicname ) < PUBLICNAME_MIN_LEN:
+        return "Public name must be at least %d characters in length" % ( PUBLICNAME_MIN_LEN )
+    if len( publicname ) > PUBLICNAME_MAX_LEN:
+        return "Public name cannot be more than %d characters in length" % ( PUBLICNAME_MAX_LEN )
     if not( VALID_PUBLICNAME_RE.match( publicname ) ):
         return "Public name must contain only lower-case letters, numbers and '-'"
     if trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first():

lib/galaxy/util/__init__.py

@@ -891,25 +891,33 @@ def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', default=None):
     return value
 
 
-def smart_str(s, encoding='utf-8', strings_only=False, errors='strict'):
+def smart_str(s, encoding=DEFAULT_ENCODING, strings_only=False, errors='strict'):
     """
     Returns a bytestring version of 's', encoded as specified in 'encoding'.
 
     If strings_only is True, don't convert (some) non-string-like objects.
 
     Adapted from an older, simpler version of django.utils.encoding.smart_str.
+
+    >>> assert smart_str(None) == b'None'
+    >>> assert smart_str(None, strings_only=True) is None
+    >>> assert smart_str(3) == b'3'
+    >>> assert smart_str(3, strings_only=True) == 3
+    >>> assert smart_str(b'a bytes string') == b'a bytes string'
+    >>> assert smart_str(u'a simple unicode string') == b'a simple unicode string'
+    >>> assert smart_str(u'à strange ünicode ڃtring') == b'\xc3\xa0 strange \xc3\xbcnicode \xda\x83tring'
+    >>> assert smart_str(b'\xc3\xa0n \xc3\xabncoded utf-8 string', encoding='latin-1') == b'\xe0n \xebncoded utf-8 string'
     """
     if strings_only and isinstance(s, (type(None), int)):
         return s
-    if not isinstance(s, string_types):
-        try:
-            return str(s)
-        except UnicodeEncodeError:
-            return text_type(s).encode(encoding, errors)
-    elif isinstance(s, text_type):
+    if not isinstance(s, string_types) and not isinstance(s, binary_type):
+        # In Python 2, s is not an instance of basestring
+        # In Python 3, s is not an instance of bytes or str
+        s = str(s)
+    if not isinstance(s, binary_type):
         return s.encode(encoding, errors)
-    elif s and encoding != 'utf-8':
-        return s.decode('utf-8', errors).encode(encoding, errors)
+    elif s and encoding != DEFAULT_ENCODING:
+        return s.decode(DEFAULT_ENCODING, errors).encode(encoding, errors)
     else:
         return s
 
@@ -1404,6 +1412,32 @@ def parse_int(value, min_val=None, max_val=None, default=None, allow_none=False)
             raise
 
 
+def parse_non_hex_float( s ):
+    """
+    Parse string `s` into a float but throw a `ValueError` if the string is in
+    the otherwise acceptable format `\d+e\d+` (e.g. 40000000000000e5.)
+
+    This can be passed into `json.loads` to prevent a hex string in the above
+    format from being incorrectly parsed as a float in scientific notation.
+
+    >>> parse_non_hex_float( '123.4' )
+    123.4
+    >>> parse_non_hex_float( '2.45e+3' )
+    2450.0
+    >>> parse_non_hex_float( '2.45e-3' )
+    0.00245
+    >>> parse_non_hex_float( '40000000000000e5' )
+    Traceback (most recent call last):
+        ...
+    ValueError: could not convert string to float: 40000000000000e5
+    """
+    f = float( s )
+    # successfully parsed as float if here - check for format in original string
+    if 'e' in s and not ( '+' in s or '-' in s ):
+        raise ValueError( 'could not convert string to float: ' + s )
+    return f
+
+
 def build_url( base_url, port=80, scheme='http', pathspec=None, params=None, doseq=False ):
     if params is None:
         params = dict()

lib/galaxy/web/framework/decorators.py

@@ -148,9 +148,10 @@ def expose_api( func, to_json=True, user_required=True ):
     return expose( _save_orig_fn( decorator, func ) )
 
 
-def __extract_payload_from_request(trans, func, kwargs):
-    content_type = trans.request.headers['content-type']
-    if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'):
+def __extract_payload_from_request( trans, func, kwargs ):
+
+    content_type = trans.request.headers[ 'content-type' ]
+    if content_type.startswith( 'application/x-www-form-urlencoded' ) or content_type.startswith( 'multipart/form-data' ):
         # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body
         # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which
         # are not a part of the request body. This is a problem because it's not possible to differentiate between values
@@ -158,13 +159,16 @@ def __extract_payload_from_request(trans, func, kwargs):
         # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from
         # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods.
         payload = kwargs.copy()
-        named_args, _, _, _ = inspect.getargspec(func)
+        named_args, _, _, _ = inspect.getargspec( func )
         for arg in named_args:
-            payload.pop(arg, None)
+            payload.pop( arg, None )
         for k, v in payload.iteritems():
-            if isinstance(v, string_types):
+            if isinstance( v, string_types ):
                 try:
-                    payload[k] = loads(v)
+                    # note: parse_non_hex_float only needed here for single string values where something like
+                    # 40000000000000e5 will be parsed as a scientific notation float. This is as opposed to hex strings
+                    # in larger JSON structures where quoting prevents this (further below)
+                    payload[ k ] = loads( v, parse_float=util.parse_non_hex_float )
                 except:
                     # may not actually be json, just continue
                     pass

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -278,7 +278,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
 
     @web.expose_api_raw_anonymous
     def display( self, trans, history_content_id, history_id,
-                 preview=False, filename=None, to_ext=None, chunk=None, raw=False, **kwd ):
+                 preview=False, filename=None, to_ext=None, raw=False, **kwd ):
         """
         GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display
         Displays history content (dataset).
@@ -297,7 +297,8 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
             if raw:
                 if filename and filename != 'index':
                     file_path = trans.app.object_store.get_filename( hda.dataset,
-                                                                     extra_dir=( 'dataset_%s_files' % hda.dataset.id ), alt_name=filename)
+                                                                     extra_dir=( 'dataset_%s_files' % hda.dataset.id ),
+                                                                     alt_name=filename)
                 else:
                     file_path = hda.file_name
                 rval = open( file_path )
@@ -306,7 +307,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
                 display_kwd = kwd.copy()
                 if 'key' in display_kwd:
                     del display_kwd["key"]
-                rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, chunk, **display_kwd )
+                rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, **display_kwd )
 
         except Exception as exception:
             log.error( "Error getting display data for dataset (%s) from history (%s): %s",

lib/galaxy/webapps/galaxy/api/users.py

@@ -27,6 +27,7 @@ class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cr
         super(UserAPIController, self).__init__(app)
         self.user_manager = users.UserManager(app)
         self.user_serializer = users.UserSerializer( app )
+        self.user_deserializer = users.UserDeserializer( app )
 
     @expose_api
     def index( self, trans, deleted='False', f_email=None, f_name=None, f_any=None, **kwd ):
@@ -175,8 +176,32 @@ class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cr
         return key
 
     @expose_api
-    def update( self, trans, **kwd ):
-        raise exceptions.NotImplemented()
+    def update( self, trans, id, payload, **kwd ):
+        """
+        update( self, trans, id, payload, **kwd )
+        * PUT /api/users/{id}
+            updates the values for the item with the given ``id``
+
+        :type id: str
+        :param id: the encoded id of the item to update
+        :type payload: dict
+        :param payload: a dictionary of new attribute values
+
+        :rtype: dict
+        :returns: an error object if an error occurred or a dictionary containing
+            the serialized item after any changes
+        """
+        current_user = trans.user
+        user_to_update = self.user_manager.by_id( self.decode_id( id ) )
+
+        # only allow updating other users if they're admin
+        editing_someone_else = current_user != user_to_update
+        is_admin = trans.api_inherit_admin or self.user_manager.is_admin( current_user )
+        if editing_someone_else and not is_admin:
+            raise exceptions.InsufficientPermissionsException( 'you are not allowed to update that user', id=id )
+
+        self.user_deserializer.deserialize( user_to_update, payload, user=current_user, trans=trans )
+        return self.user_serializer.serialize_to_view( user_to_update, view='detailed' )
 
     @expose_api
     @web.require_admin

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -232,11 +232,17 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
             return trans.app.object_store.file_ready(data.dataset)
 
     @web.expose
-    def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
+    def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
         data = self._check_dataset(trans, dataset_id)
         if not isinstance( data, trans.app.model.DatasetInstance ):
             return data
-        return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd)
+        # Ensure offset is an integer before passing through to datatypes.
+        if offset:
+            offset = int(offset)
+        # Ensure ck_size is an integer before passing through to datatypes.
+        if ck_size:
+            ck_size = int(ck_size)
+        return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)
 
     @web.expose
     def edit(self, trans, dataset_id=None, filename=None, hid=None, **kwd):

lib/galaxy/webapps/galaxy/controllers/tag.py

@@ -128,9 +128,9 @@ class TagsController ( BaseUIController, UsesTagsMixin ):
         # Create and return autocomplete data.
         ac_data = "#Header|Your Tags\n"
         for row in result_set:
-            tag = self.get_tag_handler( trans ).get_tag_by_id( trans, row[0] )
+            tag = self.get_tag_handler( trans ).get_tag_by_id( row[0] )
             # Exclude tags that are already applied to the item.
-            if ( item is not None ) and ( self.get_tag_handler( trans ).item_has_tag( trans, trans.user, item, tag ) ):
+            if ( item is not None ) and ( self.get_tag_handler( trans ).item_has_tag( trans.user, item, tag ) ):
                 continue
             # Add tag to autocomplete data. Use the most frequent name that user
             # has employed for the tag.
@@ -146,7 +146,7 @@ class TagsController ( BaseUIController, UsesTagsMixin ):
         tag_name_and_value = q.split( ":" )
         tag_name = tag_name_and_value[0]
         tag_value = tag_name_and_value[1]
-        tag = self.get_tag_handler( trans ).get_tag_by_name( trans, tag_name )
+        tag = self.get_tag_handler( trans ).get_tag_by_name( tag_name )
         # Don't autocomplete if tag doesn't exist.
         if tag is None:
             return ""

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

@@ -1 +1 @@
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static/maps/mvc/collection/collection-view-edit.js.map

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

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

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static/maps/mvc/history/hdca-li.js.map

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static/maps/mvc/history/hdca-model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"hdca-model.js","sources":["../../../src/mvc/history/hdca-model.js"],"names":["define","DC_MODEL","HISTORY_CONTENT","buildHDCASave","_super","attributes","options","this","isNew","url","urlRoot","get","type","call","hcontentMixin","HistoryContentMixin","ListDC","ListDatasetCollection","PairDC","PairDatasetCollection","ListPairedDC","ListPairedDatasetCollection","ListOfListsDC","ListOfListsDatasetCollection","HistoryListDatasetCollection","extend","defaults","_","clone","prototype","history_content_type","collection_type","model_class","initialize","model","save","toString","join","HistoryPairDatasetCollection","HistoryListPairedDatasetCollection","HistoryListOfListsDatasetCollection"],"mappings":"AAAAA,QACI,kCACA,oCACA,sBACD,SAAUC,EAAUC,GAEvB,YAmBA,SAASC,GAAeC,GACpB,MAAO,UAAgBC,EAAYC,GAO/B,MANIC,MAAKC,UACLF,EAAUA,MACVA,EAAQG,IAAMF,KAAKG,QAAUH,KAAKI,IAAK,cAAiB,YACxDN,EAAaA,MACbA,EAAWO,KAAO,sBAEfR,EAAOS,KAAMN,KAAMF,EAAYC,IAhB9C,GAAIQ,GAAgBZ,EAAgBa,oBAChCC,EAASf,EAASgB,sBAClBC,EAASjB,EAASkB,sBAClBC,EAAenB,EAASoB,4BACxBC,EAAgBrB,EAASsB,6BAoBzBC,EAA+BR,EAAOS,OAAQX,GAAgBW,QAG9DC,SAAWC,EAAEF,OAAQE,EAAEC,MAAOZ,EAAOa,UAAUH,WAC3CI,qBAAsB,qBACtBC,gBAAsB,OACtBC,YAAsB,wCAG1BC,WAAa,SAAUC,EAAO5B,GAC1BU,EAAOa,UAAUI,WAAWpB,KAAMN,KAAM2B,EAAO5B,GAC/CQ,EAAcmB,WAAWpB,KAAMN,KAAM2B,EAAO5B,IAIhD6B,KAAOhC,EAAea,EAAOa,UAAUM,MAGvCC,SAAW,WACN,OAAU,gCAAiC7B,KAAKI,IAAK,QAAU,KAAM0B,KAAM,OAShFC,EAA+BpB,EAAOO,OAAQX,GAAgBW,QAG9DC,SAAWC,EAAEF,OAAQE,EAAEC,MAAOV,EAAOW,UAAUH,WAC3CI,qBAAsB,qBACtBC,gBAAsB,SACtBC,YAAsB,wCAG1BC,WAAa,SAAUC,EAAO5B,GAC1BY,EAAOW,UAAUI,WAAWpB,KAAMN,KAAM2B,EAAO5B,GAC/CQ,EAAcmB,WAAWpB,KAAMN,KAAM2B,EAAO5B,IAIhD6B,KAAOhC,EAAee,EAAOW,UAAUM,MAGvCC,SAAW,WACN,OAAU,gCAAiC7B,KAAKI,IAAK,QAAU,KAAM0B,KAAM,OAOhFE,EAAqCnB,EAAaK,OAAQX,GAAgBW,QAE1EC,SAAWC,EAAEF,OAAQE,EAAEC,MAAOR,EAAaS,UAAUH,WACjDI,qBAAsB,qBACtBC,gBAAsB,cACtBC,YAAsB,wCAG1BC,WAAa,SAAUC,EAAO5B,GAC1Bc,EAAaS,UAAUI,WAAWpB,KAAMN,KAAM2B,EAAO5B,GACrDQ,EAAcmB,WAAWpB,KAAMN,KAAM2B,EAAO5B,IAIhD6B,KAAOhC,EAAeiB,EAAaS,UAAUM,MAG7CC,SAAW,WACN,OAAU,sCAAuC7B,KAAKI,IAAK,QAAU,KAAM0B,KAAM,OAOtFG,EAAsClB,EAAcG,OAAQX,GAAgBW,QAE5EC,SAAWC,EAAEF,OAAQE,EAAEC,MAAON,EAAcO,UAAUH,WAClDI,qBAAsB,qBACtBC,gBAAsB,YACtBC,YAAsB,wCAG1BC,WAAa,SAAUC,EAAO5B,GAC1BgB,EAAcO,UAAUI,WAAWpB,KAAMN,KAAM2B,EAAO5B,GACtDQ,EAAcmB,WAAWpB,KAAMN,KAAM2B,EAAO5B,IAIhD6B,KAAOhC,EAAemB,EAAcO,UAAUM,MAG9CC,SAAW,WACN,OAAU,uCAAwC7B,KAAKI,IAAK,QAAU,KAAM0B,KAAM,MAMvF,QACIb,6BAAsCA,EACtCc,6BAAsCA,EACtCC,mCAAsCA,EACtCC,oCAAsCA"}

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){"use strict";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.listenTo(this.model,"change",function(a){_.has(a.changed,"deleted")?this.render():_.has(a.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$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"),f=c.wrapTemplate(['<div class="subtitle">','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<%        if( collection.collection_type === "list" ){ %>',d("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',d("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',d("a list of <%- countText %>dataset pairs"),"<% } %>","</div>"],"collection");return _.extend({},e.prototype.templates,{warnings:a,titleBar:b,subtitle:f})}();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)},_fetchModelDetails:function(){var a=this;return a.model.inReadyState()&&!a.model.hasDetails()?a.model.fetch({silent:!0}):jQuery.when()},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.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
+define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){"use strict";var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,e.prototype.initialize.call(this,a)},_setUpListeners:function(){e.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(a){_.has(a.changed,"deleted")?this.render():_.has(a.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$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"),f=c.wrapTemplate(['<div class="subtitle">','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<%        if( collection.collection_type === "list" ){ %>',d("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',d("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',d("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',d("a list of <%- countText %>dataset lists"),"<% } %>","</div>"],"collection");return _.extend({},e.prototype.templates,{warnings:a,titleBar:b,subtitle:f})}();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)},_fetchModelDetails:function(){var a=this;return a.model.inReadyState()&&!a.model.hasDetails()?a.model.fetch({silent:!0}):jQuery.when()},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/collection-view-edit.js

@@ -1,2 +1,2 @@
-define(["mvc/collection/collection-view","mvc/collection/collection-model","mvc/collection/collection-li-edit","mvc/base-mvc","utils/localization","ui/editable-text"],function(a,b,c,d,e){"use strict";var f=a.CollectionView,g=f.extend({DatasetDCEViewClass:c.DatasetDCEListItemEdit,NestedDCDCEViewClass:c.NestedDCDCEListItemEdit,initialize:function(a){f.prototype.initialize.call(this,a)},_setUpBehaviors:function(a){if(a=a||this.$el,f.prototype._setUpBehaviors.call(this,a),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){var b=this,c="> .controls .name";a.find(c).attr("title",e("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(a){var d=b.model.get("name");a&&a!==d?(b.$el.find(c).text(a),b.model.save({name:a}).fail(function(){b.$el.find(c).text(b.model.previous("name"))})):b.$el.find(c).text(d)}})}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),h=g.extend({DatasetDCEViewClass:c.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),i=h.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),j=i.extend({_setUpBehaviors:function(a){f.prototype._setUpBehaviors.call(this,a)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),k=g.extend({NestedDCDCEViewClass:c.NestedDCDCEListItemEdit.extend({foldoutPanelClass:j}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{CollectionViewEdit:g,ListCollectionViewEdit:h,PairCollectionViewEdit:i,ListOfPairsCollectionViewEdit:k}});
+define(["mvc/collection/collection-view","mvc/collection/collection-model","mvc/collection/collection-li-edit","mvc/base-mvc","utils/localization","ui/editable-text"],function(a,b,c,d,e){"use strict";var f=a.CollectionView,g=f.extend({DatasetDCEViewClass:c.DatasetDCEListItemEdit,NestedDCDCEViewClass:c.NestedDCDCEListItemEdit,initialize:function(a){f.prototype.initialize.call(this,a)},_setUpBehaviors:function(a){if(a=a||this.$el,f.prototype._setUpBehaviors.call(this,a),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){var b=this,c="> .controls .name";a.find(c).attr("title",e("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(a){var d=b.model.get("name");a&&a!==d?(b.$el.find(c).text(a),b.model.save({name:a}).fail(function(){b.$el.find(c).text(b.model.previous("name"))})):b.$el.find(c).text(d)}})}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),h=g.extend({DatasetDCEViewClass:c.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),i=h.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),j=i.extend({_setUpBehaviors:function(a){f.prototype._setUpBehaviors.call(this,a)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),k=g.extend({NestedDCDCEViewClass:c.NestedDCDCEListItemEdit.extend({foldoutPanelClass:j}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),l=g.extend({NestedDCDCEViewClass:c.NestedDCDCEListItemEdit.extend({foldoutPanelClass:j}),toString:function(){return"ListOfListsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{CollectionViewEdit:g,ListCollectionViewEdit:h,PairCollectionViewEdit:i,ListOfPairsCollectionViewEdit:k,ListOfListsCollectionViewEdit:l}});
 //# sourceMappingURL=../../../maps/mvc/collection/collection-view-edit.js.map

static/scripts/mvc/collection/collection-view.js

@@ -1,2 +1,2 @@
-define(["mvc/list/list-view","mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){"use strict";var f="collections",g=a.ModelListPanel,h=g.extend({_logNamespace:f,className:g.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.DatasetDCEListItemView,NestedDCDCEViewClass:c.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(a){g.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,this.panelStack=[],this.parentName=a.parentName,this.foldoutStyle=a.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(a){switch(a.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",a.get("element_type"))},_getItemViewOptions:function(a){var b=g.prototype._getItemViewOptions.call(this,a);return _.extend(b,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(a){var b=this;return g.prototype._setUpItemViewListeners.call(b,a),b.listenTo(a,{"expanded:drilldown":function(a,b){this._expandDrilldownPanel(b)},"collapsed:drilldown":function(a,b){this._collapseDrilldownPanel(b)}}),this},_expandDrilldownPanel:function(a){this.panelStack.push(a),this.$("> .controls").add(this.$list()).hide(),a.parentName=this.model.get("name"),this.$el.append(a.render().$el)},_collapseDrilldownPanel:function(){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});h.prototype.templates=function(){var a=d.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>"],"collection");return _.extend(_.clone(g.prototype.templates),{controls:a})}();var i=h.extend({DatasetDCEViewClass:c.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),j=i.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),k=h.extend({NestedDCDCEViewClass:c.NestedDCDCEListItemView.extend({foldoutPanelClass:j}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:h,ListCollectionView:i,PairCollectionView:j,ListOfPairsCollectionView:k}});
+define(["mvc/list/list-view","mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){"use strict";var f="collections",g=a.ModelListPanel,h=g.extend({_logNamespace:f,className:g.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.DatasetDCEListItemView,NestedDCDCEViewClass:c.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(a){g.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,this.panelStack=[],this.parentName=a.parentName,this.foldoutStyle=a.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(a){switch(a.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",a.get("element_type"))},_getItemViewOptions:function(a){var b=g.prototype._getItemViewOptions.call(this,a);return _.extend(b,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(a){var b=this;return g.prototype._setUpItemViewListeners.call(b,a),b.listenTo(a,{"expanded:drilldown":function(a,b){this._expandDrilldownPanel(b)},"collapsed:drilldown":function(a,b){this._collapseDrilldownPanel(b)}}),this},_expandDrilldownPanel:function(a){this.panelStack.push(a),this.$("> .controls").add(this.$list()).hide(),a.parentName=this.model.get("name"),this.$el.append(a.render().$el)},_collapseDrilldownPanel:function(){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});h.prototype.templates=function(){var a=d.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',e("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',e("a list of dataset lists"),"<% } %>","</div>","</div>","</div>"],"collection");return _.extend(_.clone(g.prototype.templates),{controls:a})}();var i=h.extend({DatasetDCEViewClass:c.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),j=i.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),k=h.extend({NestedDCDCEViewClass:c.NestedDCDCEListItemView.extend({foldoutPanelClass:j}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),l=h.extend({NestedDCDCEViewClass:c.NestedDCDCEListItemView.extend({foldoutPanelClass:j}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:h,ListCollectionView:i,PairCollectionView:j,ListOfPairsCollectionView:k,ListOfListsCollectionView:l}});
 //# sourceMappingURL=../../../maps/mvc/collection/collection-view.js.map

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

@@ -1,2 +1,2 @@
-define(["mvc/history/hdca-li","mvc/collection/collection-view-edit","ui/fa-icon-button","utils/localization"],function(a,b,c,d){"use strict";var e=a.HDCAListItemView,f=e.extend({_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return b.ListCollectionViewEdit;case"paired":return b.PairCollectionViewEdit;case"list:paired":return b.ListOfPairsCollectionViewEdit}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_renderPrimaryActions:function(){return this.log(this+"._renderPrimaryActions"),e.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()])},_renderDeleteButton:function(){var a=this,b=this.model.get("deleted");return c({title:d(b?"Dataset collection is already deleted":"Delete"),classes:"delete-btn",faIcon:"fa-times",disabled:b,onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemEdit("+a+")"}});return{HDCAListItemEdit:f}});
+define(["mvc/history/hdca-li","mvc/collection/collection-view-edit","ui/fa-icon-button","utils/localization"],function(a,b,c,d){"use strict";var e=a.HDCAListItemView,f=e.extend({_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return b.ListCollectionViewEdit;case"paired":return b.PairCollectionViewEdit;case"list:paired":return b.ListOfPairsCollectionViewEdit;case"list:list":return b.ListOfListsCollectionViewEdit}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_renderPrimaryActions:function(){return this.log(this+"._renderPrimaryActions"),e.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()])},_renderDeleteButton:function(){var a=this,b=this.model.get("deleted");return c({title:d(b?"Dataset collection is already deleted":"Delete"),classes:"delete-btn",faIcon:"fa-times",disabled:b,onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemEdit("+a+")"}});return{HDCAListItemEdit:f}});
 //# sourceMappingURL=../../../maps/mvc/history/hdca-li-edit.js.map

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

@@ -1,2 +1,2 @@
-define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-view","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){"use strict";var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionView;case"paired":return c.PairCollectionView;case"list:paired":return c.ListOfPairsCollectionView}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("populated")?a.OK:a.RUNNING;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}});
+define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-view","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){"use strict";var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionView;case"paired":return c.PairCollectionView;case"list:paired":return c.ListOfPairsCollectionView;case"list:list":return c.ListOfListsCollectionView}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("populated")?a.OK:a.RUNNING;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/history/hdca-model.js

@@ -1,2 +1,2 @@
-define(["mvc/collection/collection-model","mvc/history/history-content-model","utils/localization"],function(a,b){"use strict";function c(a){return function(b,c){return this.isNew()&&(c=c||{},c.url=this.urlRoot+this.get("history_id")+"/contents",b=b||{},b.type="dataset_collection"),a.call(this,b,c)}}var d=b.HistoryContentMixin,e=a.ListDatasetCollection,f=a.PairDatasetCollection,g=a.ListPairedDatasetCollection,h=e.extend(d).extend({defaults:_.extend(_.clone(e.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){e.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(e.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),i=f.extend(d).extend({defaults:_.extend(_.clone(f.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){f.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(f.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),j=g.extend(d).extend({defaults:_.extend(_.clone(g.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){g.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(g.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:h,HistoryPairDatasetCollection:i,HistoryListPairedDatasetCollection:j}});
+define(["mvc/collection/collection-model","mvc/history/history-content-model","utils/localization"],function(a,b){"use strict";function c(a){return function(b,c){return this.isNew()&&(c=c||{},c.url=this.urlRoot+this.get("history_id")+"/contents",b=b||{},b.type="dataset_collection"),a.call(this,b,c)}}var d=b.HistoryContentMixin,e=a.ListDatasetCollection,f=a.PairDatasetCollection,g=a.ListPairedDatasetCollection,h=a.ListOfListsDatasetCollection,i=e.extend(d).extend({defaults:_.extend(_.clone(e.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){e.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(e.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),j=f.extend(d).extend({defaults:_.extend(_.clone(f.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){f.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(f.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),k=g.extend(d).extend({defaults:_.extend(_.clone(g.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){g.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(g.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}}),l=h.extend(d).extend({defaults:_.extend(_.clone(h.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(a,b){h.prototype.initialize.call(this,a,b),d.initialize.call(this,a,b)},save:c(h.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:i,HistoryPairDatasetCollection:j,HistoryListPairedDatasetCollection:k,HistoryListOfListsDatasetCollection:l}});
 //# sourceMappingURL=../../../maps/mvc/history/hdca-model.js.map

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

@@ -1,2 +1,2 @@
-define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){"use strict";var f="history",g=Backbone.Collection.extend(e.LoggableMixin).extend({_logNamespace:f,model:function(a,d){if("dataset"===a.history_content_type)return new b.HistoryDatasetAssociation(a,d);if("dataset_collection"===a.history_content_type){switch(a.collection_type){case"list":return new c.HistoryListDatasetCollection(a,d);case"paired":return new c.HistoryPairDatasetCollection(a,d);case"list:paired":return new c.HistoryListPairedDatasetCollection(a,d)}return{validationError:"Unknown collection_type: "+a.history_content_type}}return{validationError:"Unknown history_content_type: "+a.history_content_type}},initialize:function(a,b){b=b||{},this.historyId=b.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},running:function(){function a(a){return!a.inReadyState()}return new g(this.filter(a))},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},getVisible:function(a,b,c){c=c||[],this.debug("checking isVisible");var d=new g(this.filter(function(c){return c.isVisible(a,b)}));return _.each(c,function(a){_.isFunction(a)&&(d=new g(d.filter(a)))}),d},hidden:function(){function a(a){return a.hidden()}return new g(this.filter(a))},deleted:function(){function a(a){return a.get("deleted")}return new g(this.filter(a))},visibleAndUndeleted:function(){function a(a){return a.get("visible")&&!a.get("deleted")}return new g(this.filter(a))},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},fetch:function(a){return a=a||{},a.data=_.defaults(a.data||{},{v:"dev"}),Backbone.Collection.prototype.fetch.call(this,a)},fetchUpdated:function(a,b){return b=b||{},b.traditional=!0,b.data=[{name:"v",value:"dev"}],a&&(b.data=b.data.concat(this._filtersFromMap({"update_time-ge":a.toISOString()}))),b.merge=!0,b.remove=!1,this.fetch(b)},_filtersFromMap:function(a){var b=[];return _.each(a,function(a,c){b.push({name:"q",value:c}),b.push({name:"qv",value:a})}),b},fetchAllDetails:function(a){a=a||{};var b={details:"all"};return a.data=a.data?_.extend(a.data,b):b,this.fetch(a)},fetchCollectionCounts:function(a){return a=a||{},a.data=_.defaults({keys:["type_id","element_count"].join(","),q:"history_content_type",qv:"dataset_collection"},a.data||{}),a.merge=!0,a.remove=!1,this.fetch(a)},ajaxQueue:function(a,b){var c=jQuery.Deferred(),d=this.length,e=[];if(!d)return c.resolve([]),c;var f=this.chain().reverse().map(function(g,h){return function(){var i=a.call(g,b);i.done(function(a){c.notify({curr:h,total:d,response:a,model:g})}),i.always(function(a){e.push(a),f.length?f.shift()():c.resolve(e)})}}).value();return f.shift()(),c},isCopyable:function(a){var b=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return _.isObject(a)&&a.id&&_.contains(b,a.model_class)},copy:function(a){var b,c,d;_.isString(a)?(b=a,d="hda",c="dataset"):(b=a.id,d={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[a.model_class]||"hda",c="hdca"===d?"dataset_collection":"dataset");var e=this,f=jQuery.post(this.url(),{content:b,source:d,type:c}).done(function(a){e.add([a])}).fail(function(){e.trigger("error",e,f,{},"Error copying contents",{type:c,id:b,source:d})});return f},matches:function(a){return this.filter(function(b){return b.matches(a)})},createHDCA:function(a,b,d){var e=this,f={list:c.HistoryListDatasetCollection,paired:c.HistoryPairDatasetCollection},g=new f[b]({history_id:this.historyId,name:d,element_identifiers:a});return g.save().done(function(){e.add(g)}).fail(function(a,b,c){e.trigger("error",a,b,c)})},clone:function(){var a=Backbone.Collection.prototype.clone.call(this);return a.historyId=this.historyId,a},print:function(){var a=this;a.each(function(b){a.debug(b),b.elements&&a.debug("	 elements:",b.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:g}});
+define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){"use strict";var f="history",g=Backbone.Collection.extend(e.LoggableMixin).extend({_logNamespace:f,model:function(a,d){if("dataset"===a.history_content_type)return new b.HistoryDatasetAssociation(a,d);if("dataset_collection"===a.history_content_type){switch(a.collection_type){case"list":return new c.HistoryListDatasetCollection(a,d);case"paired":return new c.HistoryPairDatasetCollection(a,d);case"list:paired":return new c.HistoryListPairedDatasetCollection(a,d);case"list:list":return new c.HistoryListOfListsDatasetCollection(a,d)}var e="Unknown collection_type: "+a.collection_type;return console.warn(e,a),{validationError:e}}return{validationError:"Unknown history_content_type: "+a.history_content_type}},initialize:function(a,b){b=b||{},this.historyId=b.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},running:function(){function a(a){return!a.inReadyState()}return new g(this.filter(a))},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},getVisible:function(a,b,c){c=c||[],this.debug("checking isVisible");var d=new g(this.filter(function(c){return c.isVisible(a,b)}));return _.each(c,function(a){_.isFunction(a)&&(d=new g(d.filter(a)))}),d},hidden:function(){function a(a){return a.hidden()}return new g(this.filter(a))},deleted:function(){function a(a){return a.get("deleted")}return new g(this.filter(a))},visibleAndUndeleted:function(){function a(a){return a.get("visible")&&!a.get("deleted")}return new g(this.filter(a))},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},fetch:function(a){return a=a||{},a.data=_.defaults(a.data||{},{v:"dev"}),Backbone.Collection.prototype.fetch.call(this,a)},fetchUpdated:function(a,b){return b=b||{},b.traditional=!0,b.data=[{name:"v",value:"dev"}],a&&(b.data=b.data.concat(this._filtersFromMap({"update_time-ge":a.toISOString()}))),b.merge=!0,b.remove=!1,this.fetch(b)},_filtersFromMap:function(a){var b=[];return _.each(a,function(a,c){b.push({name:"q",value:c}),b.push({name:"qv",value:a})}),b},fetchAllDetails:function(a){a=a||{};var b={details:"all"};return a.data=a.data?_.extend(a.data,b):b,this.fetch(a)},fetchCollectionCounts:function(a){return a=a||{},a.data=_.defaults({keys:["type_id","element_count"].join(","),q:"history_content_type",qv:"dataset_collection"},a.data||{}),a.merge=!0,a.remove=!1,this.fetch(a)},ajaxQueue:function(a,b){var c=jQuery.Deferred(),d=this.length,e=[];if(!d)return c.resolve([]),c;var f=this.chain().reverse().map(function(g,h){return function(){var i=a.call(g,b);i.done(function(a){c.notify({curr:h,total:d,response:a,model:g})}),i.always(function(a){e.push(a),f.length?f.shift()():c.resolve(e)})}}).value();return f.shift()(),c},isCopyable:function(a){var b=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return _.isObject(a)&&a.id&&_.contains(b,a.model_class)},copy:function(a){var b,c,d;_.isString(a)?(b=a,d="hda",c="dataset"):(b=a.id,d={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[a.model_class]||"hda",c="hdca"===d?"dataset_collection":"dataset");var e=this,f=jQuery.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:b,source:d,type:c})}).done(function(a){e.add([a])}).fail(function(){e.trigger("error",e,f,{},"Error copying contents",{type:c,id:b,source:d})});return f},matches:function(a){return this.filter(function(b){return b.matches(a)})},createHDCA:function(a,b,d){var e=this,f={list:c.HistoryListDatasetCollection,paired:c.HistoryPairDatasetCollection},g=new f[b]({history_id:this.historyId,name:d,element_identifiers:a});return g.save().done(function(){e.add(g)}).fail(function(a,b,c){e.trigger("error",a,b,c)})},clone:function(){var a=Backbone.Collection.prototype.clone.call(this);return a.historyId=this.historyId,a},print:function(){var a=this;a.each(function(b){a.debug(b),b.elements&&a.debug("	 elements:",b.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:g}});
 //# sourceMappingURL=../../../maps/mvc/history/history-contents.js.map

templates/admin/impersonate.mako

@@ -29,6 +29,7 @@
      *  queries (term, below) */
     $("#email_select").select2({
         placeholder: "Select a user",
+	width: "33%",
         ajax: {
             url: "${h.url_for(controller="/api/users", action="index")}",
             dataType: 'json',
@@ -44,7 +45,7 @@
               $.each(data, function(index, item){
                     results.push({
                       id: item.email,
-                      text: item.email
+                      text: item.username + " : " + item.email
                     });
               });
               return {

templates/ind_share_base.mako

@@ -92,7 +92,7 @@
                         <label>
                             Email address of user to share with
                         </label>
-                        <div style="float: left; width: 250px; margin-right: 10px;">
+                        <div style="float: left; width: 100%;  margin-right: 10px;">
                             <input type="hidden" id="email_select" name="email" >
                             </input>
                         </div>
@@ -131,6 +131,7 @@
 
     $("#email_select").select2({
         placeholder: "Select a user",
+	width: "33%",
         multiple: false,
         initSelection: function(element, callback) {
             var data = [];

test/api/test_users.py

@@ -1,3 +1,5 @@
+import json
+from requests import put
 from base import api
 
 TEST_USER_EMAIL = "user_for_users_index_test@bx.psu.edu"
@@ -18,7 +20,64 @@ class UsersApiTestCase( api.ApiTestCase ):
 
     def test_index_only_self_for_nonadmins( self ):
         self._setup_user( TEST_USER_EMAIL )
-        with self._different_user( ):
+        with self._different_user():
             all_users_response = self._get( "users" )
             # Non admin users can only see themselves
             assert len( all_users_response.json() ) == 1
+
+    def test_show( self ):
+        user = self._setup_user( TEST_USER_EMAIL )
+        with self._different_user( email=TEST_USER_EMAIL ):
+            show_response = self.__show( user )
+            self._assert_status_code_is( show_response, 200 )
+            self.__assert_matches_user( user, show_response.json() )
+
+    def test_update( self ):
+        new_name = 'linnaeus'
+        user = self._setup_user( TEST_USER_EMAIL )
+        not_the_user = self._setup_user( 'email@example.com' )
+        with self._different_user( email=TEST_USER_EMAIL ):
+
+            # working
+            update_response = self.__update( user, username=new_name )
+            self._assert_status_code_is( update_response, 200 )
+            update_json = update_response.json()
+            self.assertEqual( update_json[ 'username' ], new_name )
+
+            # too short
+            update_response = self.__update( user, username='mu' )
+            self._assert_status_code_is( update_response, 400 )
+
+            # not them
+            update_response = self.__update( not_the_user, username=new_name )
+            self._assert_status_code_is( update_response, 403 )
+
+            # non-existent
+            no_user_id = self.security.encode_id( 100 )
+            update_url = self._api_url( "users/%s" % ( no_user_id ), use_key=True )
+            update_response = put( update_url, data=json.dumps( dict( username=new_name ) ) )
+            self._assert_status_code_is( update_response, 404 )
+
+    def test_admin_update( self ):
+        new_name = 'flexo'
+        user = self._setup_user( TEST_USER_EMAIL )
+
+        update_url = self._api_url( "users/%s" % ( user[ "id" ] ), params=dict( key=self.master_api_key ) )
+        update_response = put( update_url, data=json.dumps( dict( username=new_name ) ) )
+        self._assert_status_code_is( update_response, 200 )
+        update_json = update_response.json()
+        self.assertEqual( update_json[ 'username' ], new_name )
+
+    def __show( self, user ):
+        return self._get( "users/%s" % ( user[ 'id' ] ) )
+
+    def __update( self, user, **new_data ):
+        update_url = self._api_url( "users/%s" % ( user[ "id" ] ), use_key=True )
+        # TODO: Awkward json.dumps required here because of https://trello.com/c/CQwmCeG6
+        body = json.dumps( new_data )
+        return put( update_url, data=body )
+
+    def __assert_matches_user( self, userA, userB ):
+        self._assert_has_keys( userB, "id", "username", "total_disk_usage" )
+        assert userA[ "id" ] == userB[ "id" ]
+        assert userA[ "username" ] == userB[ "username" ]

test/unit/managers/test_UserManager.py

@@ -1,5 +1,8 @@
 # -*- coding: utf-8 -*-
 """
+User Manager testing.
+
+Executable directly using: python -m test.unit.managers.test_UserManager
 """
 import imp
 import os
@@ -12,6 +15,7 @@ import sqlalchemy
 from six import string_types
 
 from galaxy import exceptions, model
+from galaxy.managers import base as base_manager
 from galaxy.managers import histories, users
 
 from .base import BaseTestCase
@@ -215,6 +219,45 @@ class CurrentUserSerializerTestCase( BaseTestCase ):
         self.assertIsJsonifyable( serialized )
 
 
+# =============================================================================
+class UserDeserializerTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( UserDeserializerTestCase, self ).set_up_managers()
+        self.deserializer = users.UserDeserializer( self.app )
+
+    def _assertRaises_and_return_raised( self, exception_class, fn, *args, **kwargs ):
+        try:
+            fn( *args, **kwargs )
+        except exception_class as exception:
+            self.assertTrue( True )
+            return exception
+        assert False, '%s not raised' % ( exception_class.__name__ )
+
+    def test_username_validation( self ):
+        user = self.user_manager.create( **user2_data )
+
+        # self.log( "usernames can be unicode" ) #TODO: nope they can't
+        # self.deserializer.deserialize( user, { 'username': 'Σίσυφος' }, trans=self.trans )
+
+        self.log( "usernames must be long enough and with no non-hyphen punctuation" )
+        exception = self._assertRaises_and_return_raised( base_manager.ModelDeserializingError,
+            self.deserializer.deserialize, user, { 'username': 'ed' }, trans=self.trans )
+        self.assertTrue( 'Public name must be at least' in str( exception ) )
+        self.assertRaises( base_manager.ModelDeserializingError, self.deserializer.deserialize,
+            user, { 'username': 'f.d.r.' }, trans=self.trans )
+
+        self.log( "usernames must be unique" )
+        self.user_manager.create( **user3_data )
+        self.assertRaises( base_manager.ModelDeserializingError, self.deserializer.deserialize,
+            user, { 'username': 'user3' }, trans=self.trans )
+
+        self.log( "username should be updatable" )
+        new_name = 'double-plus-good'
+        self.deserializer.deserialize( user, { 'username': new_name }, trans=self.trans )
+        self.assertEqual( self.user_manager.by_id( user.id ).username, new_name )
+
+
 # =============================================================================
 class AdminUserFilterParserTestCase( BaseTestCase ):
 
@@ -237,5 +280,4 @@ class AdminUserFilterParserTestCase( BaseTestCase ):
 
 # =============================================================================
 if __name__ == '__main__':
-    # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()

tools/stats/gsummary.xml

@@ -1,9 +1,15 @@
-<tool id="Summary_Statistics1" name="Summary Statistics" version="1.1.0">
+<tool id="Summary_Statistics1" name="Summary Statistics" version="1.1.1">
   <description>for any numerical column</description>
   <edam_topics>
     <edam_topic>topic_2269</edam_topic>
   </edam_topics>
-  <command interpreter="python">gsummary.py $input $out_file1 "$cond"</command>
+  <requirements>
+    <requirement type="package" version="2.7.8">rpy2</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1" level="fatal" />
+  </stdio>
+  <command>ptyhon $__tool_directory__/gsummary.py "$input" "$out_file1" "$cond"</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Summary statistics on" help="Dataset missing? See TIP below"/>
     <param name="cond" size="30" type="text" value="c5" label="Column or expression" help="See syntax below">
@@ -13,10 +19,6 @@
   <outputs>
     <data format="tabular" name="out_file1" />
   </outputs>
-  <requirements>
-    <requirement type="package" version="2.15.1">R</requirement>
-    <requirement type="package">rpy</requirement>
-  </requirements>
   <tests>
     <test>
       <param name="input" value="1.bed"/>