Submit label and annotation separate from other inputs to avoid futur…

…e conflicts

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

@@ -708,27 +708,37 @@ define([
                     if ( content.inputs && content.inputs.length > 0 ) {
                         content.inputs.unshift({
                             type    : 'text',
-                            name    : 'label',
+                            name    : '__label',
                             label   : 'Label',
                             value   : node.label,
-                            help    : 'Add a step label.'
+                            help    : 'Add a step label.',
+                            onchange: function( label ) {
+                                node.label = label;
+                                form.trigger( 'change' );
+                            }
                         });
                         content.inputs.push({
                             type    : 'text',
-                            name    : 'annotation',
+                            name    : '__annotation',
                             label   : 'Annotation',
                             value   : node.annotation,
                             area    : true,
-                            help    : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'
+                            help    : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.',
+                            onchange: function( annotation ) {
+                                node.annotation = annotation;
+                                form.trigger( 'change' );
+                            }
                         });
                         content.onchange = function() {
                             Utils.request({
                                 type    : 'POST',
                                 url     :  Galaxy.root + 'api/workflows/build_module',
                                 data    : {
-                                    id      : node.id,
-                                    type    : node.type,
-                                    inputs  : form.data.create()
+                                    id          : node.id,
+                                    type        : node.type,
+                                    inputs      : form.data.create(),
+                                    label       : node.label,
+                                    annotation  : node.annotation
                                 },
                                 success : function( data ) {
                                     node.update_field_data( data );

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -359,8 +359,8 @@ def build_module( self, trans, payload={} ):
         """
         type = payload.get( 'type' )
         inputs = payload.get( 'inputs', {} )
-        annotation = inputs.get( 'annotation', '' )
-        label = inputs.get( 'label', '' )
+        annotation = payload.get( 'annotation', '' )
+        label = payload.get( 'label', '' )
         tool_id = payload.get( 'tool_id' )
         content_id = payload.get( 'content_id' )
         if tool_id:

lib/galaxy/workflow/modules.py

@@ -237,7 +237,7 @@ def from_dict( Class, trans, d, **kwds ):
         elif "content_id" in d:
             content_id = d["content_id"]
             module.subworkflow = SubWorkflowModule.subworkflow_from_content_id( trans, content_id )
-        module.label = d.get("label", None) or None
+        module.label = d.get( "label", None ) or None
         return module
 
     @classmethod
@@ -288,12 +288,11 @@ def get_data_outputs( self ):
         outputs = []
         for workflow_output in self.subworkflow.workflow_outputs:
             output_step = workflow_output.workflow_step
-            label = name = workflow_output.label
-            if name is None:
-                name = "%s:%s" % (output_step.order_index, workflow_output.output_name)
-                label = name
+            label = workflow_output.label
+            if label is None:
+                label = "%s:%s" % (output_step.order_index, workflow_output.output_name)
             output = dict(
-                name=name,
+                name=label,
                 label=label,
                 extensions=['input'],  # TODO
             )