Merge branch 'dev' into remove_reload_buttons

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

@@ -40,10 +40,23 @@ TODO:
                 },
 
                 render: function() {
-                    this.$el
+                    this.dragStartHandler = _.bind(this._dragstart, this);
+                    this.dragEndHandler = _.bind(this._dragend, this);
+                    var handle = this.$el
                         .attr("data-element-id", this.element.id)
                         .attr("draggable", true)
-                        .html(this.template({ element: this.element }));
+                        .html(this.template({ element: this.element }))
+                        .get(0);
+                    handle.addEventListener(
+                        "dragstart",
+                        this.dragStartHandler,
+                        false
+                    );
+                    handle.addEventListener(
+                        "dragend",
+                        this.dragEndHandler,
+                        false
+                    );
                     if (this.selected) {
                         this.$el.addClass("selected");
                     }
@@ -102,8 +115,6 @@ TODO:
                     "click .name": "_clickName",
                     "click .discard": "_clickDiscard",
 
-                    dragstart: "_dragstart",
-                    dragend: "_dragend",
                     dragover: "_sendToParent",
                     drop: "_sendToParent"
                 },

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

@@ -46,17 +46,28 @@ currPanel.once( 'rendered', function(){
             ),
 
             render: function() {
-                this.$el
+                this.dragStartHandler = _.bind(this._dragstart, this);
+                this.dragEndHandler = _.bind(this._dragend, this);
+                var handle = this.$el
                     .attr("draggable", true)
                     .data("pair", this.pair)
                     .html(this.template({ pair: this.pair }))
-                    .addClass("flex-column-container");
+                    .addClass("flex-column-container")
+                    .get(0);
+                handle.addEventListener(
+                    "dragstart",
+                    this.dragStartHandler,
+                    false
+                );
+                handle.addEventListener(
+                    "dragend",
+                    this.dragEndHandler,
+                    false
+                );
                 return this;
             },
 
             events: {
-                dragstart: "_dragstart",
-                dragend: "_dragend",
                 dragover: "_sendToParent",
                 drop: "_sendToParent"
             },

lib/galaxy/jobs/__init__.py

@@ -991,7 +991,7 @@ def fail(self, message, exception=False, stdout="", stderr="", exit_code=None):
                 etype, evalue, tb = sys.exc_info()
 
             outputs_to_working_directory = util.asbool(self.get_destination_configuration("outputs_to_working_directory", False))
-            if outputs_to_working_directory:
+            if outputs_to_working_directory and not self.__link_file_check():
                 for dataset_path in self.get_output_fnames():
                     try:
                         shutil.move(dataset_path.false_path, dataset_path.real_path)

lib/galaxy/tools/parameters/grouping.py

@@ -211,6 +211,11 @@ def get_composite_dataset_name(self, context):
         dataset_name = context.get('files_metadata|base_name', None)
         if dataset_name is None:
             dataset_name = context.get('files_metadata', {}).get('base_name', None)
+        if dataset_name is None:
+            filenames = list()
+            for composite_file in context.get('files', []):
+                filenames.append(composite_file.get('file_data', {}).get('filename', ''))
+            dataset_name = os.path.commonprefix(filenames).rstrip('.') or None
         if dataset_name is None:
             dataset_name = 'Uploaded Composite Dataset (%s)' % self.get_file_type(context)
         return dataset_name