Originating workflow must be unchanged, load save as workflow to editor on save.

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

@@ -413,21 +413,30 @@ EditorFormView = Backbone.View.extend({
                 "Close": close_editor
             });
 
+            /******************************************** Issue 3000*/
             function workflow_save_as() {
-                var body = $('<lable>Save as name: <input type="text" id="workflow_rename"></label>');
+                var body = $('<form><label style="display:inline-block; width: 100%;">Save as name: </label><input type="text" id="workflow_rename" style="width: 80%;" autofocus/>' + 
+                '<br><label style="display:inline-block; width: 100%;">Annotation: </label><input type="text" id="wf_annotation" style="width: 80%;" /></form>');
                     window.show_modal("Save As a New Workflow", body, {
                         "OK": function () {
-                            self.rename_name = $('#workflow_rename').val();
-                            save_current_workflow(null, function() {
+                            var rename_name = $('#workflow_rename').val().length > 0 ? $('#workflow_rename').val() : "SavedAs_" + self.workflow.name;
+                            var rename_annotation = $('#wf_annotation').val().length > 0 ? $('#wf_annotation').val() : "";
                             $.ajax({
-                                url: self.urls.workflow_save_as + "&save_as_name=" + self.rename_name,
-                                type: "GET",
-                            }).done(function(){
-                                window.location.href = self.urls.workflow_index;
+                                url: self.urls.workflow_save_as,
+                                type: "POST",
+                                data: {
+                                    workflow_name: rename_name,
+                                    workflow_annotation: rename_annotation,
+                                    workflow_data: function() { return JSON.stringify( self.workflow.to_simple() ); }
+                                }
+                            }).done(function(id){
+                                window.onbeforeunload = undefined;
+                                window.location = "/workflow/editor?id=" + id;
+                                hide_modal();
                             }).fail(function(){
+                                hide_modal();
                                 alert("Saving this workflow failed. Please contact this site's administrator.");
-                            })});
-                            hide_modal();
+                            });
                         },
                         "Cancel": hide_modal
                     });

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -595,6 +595,50 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
                            value="",
                            help="A description of the workflow; annotation is shown alongside shared or published workflows." )
 
+    @web.json
+    def save_workflow_as(self, trans, workflow_name, workflow_data, workflow_annotation=""):
+        """
+            Creates a new workflow based on Save As command. It is a new workflow, but
+            is created with workflow_data already present.
+        """
+        user = trans.get_user()
+        if workflow_name is not None:
+            workflow_contents_manager = workflows.WorkflowContentsManager(trans.app)
+            stored_workflow = model.StoredWorkflow()
+            stored_workflow.name = workflow_name
+            stored_workflow.user = user
+            self.create_item_slug(trans.sa_session, stored_workflow)
+            workflow = model.Workflow()
+            workflow.name = workflow_name
+            workflow.stored_workflow = stored_workflow
+            stored_workflow.latest_workflow = workflow
+            # Add annotation.
+            workflow_annotation = sanitize_html( workflow_annotation, 'utf-8', 'text/html' )
+            self.add_item_annotation( trans.sa_session, trans.get_user(), stored_workflow, workflow_annotation )
+            
+            # Persist
+            session = trans.sa_session
+            session.add( stored_workflow )
+            session.flush()
+
+            try:
+                workflow, errors = workflow_contents_manager.update_workflow_from_dict(
+                    trans,
+                    stored_workflow,
+                    workflow_data,
+                )
+            except workflows.MissingToolsException as e:
+                return dict(
+                    name=e.workflow.name,
+                    message="This workflow includes missing or invalid tools. "
+                        "It cannot be saved until the following steps are removed or the missing tools are enabled.",
+                    errors=e.errors,
+                )
+            return (trans.security.encode_id(stored_workflow.id))
+        else:
+            #This is an error state, 'save as' must have a workflow_name
+            log.exception("Error in Save As workflow: no name.")
+
     @web.expose
     def delete( self, trans, id=None ):
         """

templates/webapps/galaxy/workflow/editor.mako

@@ -16,7 +16,7 @@
             'get_new_module_info' : h.url_for(controller='workflow', action='get_new_module_info' ),
             'workflow_index'      : h.url_for( controller='workflow', action='index' ),
             'save_workflow'       : h.url_for(controller='workflow', action='save_workflow' ),
-            'workflow_save_as'    : h.url_for(controller='workflow', action='copy', id=trans.security.encode_id(stored.id)) 
+            'workflow_save_as'    : h.url_for(controller='workflow', action='save_workflow_as') 
         },
         'workflows' : [{
             'id'                  : trans.security.encode_id( workflow.id ),