Merge remote-tracking branch 'tmcgowan/issue_3000' into dev

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

@@ -401,6 +401,7 @@ EditorFormView = Backbone.View.extend({
 
             window.make_popupmenu && make_popupmenu( $("#workflow-options-button"), {
                 "Save" : save_current_workflow,
+                "Save As": workflow_save_as,
                 "Run": function() {
                     window.location = self.urls.run_workflow;
                 },
@@ -412,6 +413,35 @@ EditorFormView = Backbone.View.extend({
                 "Close": close_editor
             });
 
+            /******************************************** Issue 3000*/
+            function workflow_save_as() {
+                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 () {
+                            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,
+                                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.");
+                            });
+                        },
+                        "Cancel": hide_modal
+                    });
+            };
+
             function edit_workflow_outputs(){
                 self.workflow.clear_active_node();
                 $('.right-content').hide();

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

@@ -526,7 +526,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
 
     @web.expose
     @web.require_login( "use Galaxy workflows" )
-    def copy( self, trans, id ):
+    def copy( self, trans, id, save_as_name=None ):
         # Get workflow to copy.
         stored = self.get_stored_workflow( trans, id, check_ownership=False )
         user = trans.get_user()
@@ -540,7 +540,10 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
 
         # Copy.
         new_stored = model.StoredWorkflow()
-        new_stored.name = "Copy of '%s'" % stored.name
+        if (save_as_name):
+            new_stored.name = '%s' % save_as_name
+        else:
+            new_stored.name = "Copy of '%s'" % stored.name
         new_stored.latest_workflow = stored.latest_workflow
         # Copy annotation.
         annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored )
@@ -592,6 +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

@@ -15,7 +15,8 @@
             'annotate_async'      : h.url_for( controller='workflow', action='annotate_async', id=trans.security.encode_id(stored.id) ),
             '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' )
+            'save_workflow'       : h.url_for(controller='workflow', action='save_workflow' ),
+            'workflow_save_as'    : h.url_for(controller='workflow', action='save_workflow_as') 
         },
         'workflows' : [{
             'id'                  : trans.security.encode_id( workflow.id ),