Allow renaming of uploaded files in toolbox tests by including a <edit_attributes type="name" value="new dataset name" /> child tag. A rename directive is automatically assigned (no xml changes required) to uploaded composite datasets, so that they can be identified uniquely.

lib/galaxy/tools/__init__.py

@@ -510,6 +510,7 @@ class Tool:
         store in `self.tests`.
         """
         self.tests = []
+        composite_data_names_counter = 0 #composite datasets need a unique name: each test occurs in a fresh history, but we'll keep it unique per set of tests
         for i, test_elem in enumerate( tests_elem.findall( 'test' ) ):
             name = test_elem.get( 'name', 'Test-%d' % (i+1) )
             maxseconds = int( test_elem.get( 'maxseconds', '120' ) )
@@ -524,6 +525,28 @@ class Tool:
                     else:
                         value = None
                     attrib['children'] = list( param_elem.getchildren() )
+                    if attrib['children']:
+                        #at this time, we can assume having children only occurs on DataToolParameter test items
+                        #but this could change and would cause the below parsing to change based upon differences in children items
+                        attrib['metadata'] = []
+                        attrib['composite_data'] = []
+                        attrib['edit_attributes'] = []
+                        composite_data_name = None #composite datasets need to be renamed uniquely
+                        for child in attrib['children']:
+                            if child.tag == 'composite_data':
+                                attrib['composite_data'].append( child )
+                                if composite_data_name is None:
+                                    #generate a unique name; each test uses a fresh history
+                                    composite_data_name = '_COMPOSITE_RENAMED %i_' % ( composite_data_names_counter )
+                                    composite_data_names_counter += 1
+                            elif child.tag == 'metadata':
+                                attrib['metadata'].append( child )
+                            elif child.tag == 'metadata':
+                                attrib['metadata'].append( child )
+                            elif child.tag == 'edit_attributes':
+                                attrib['edit_attributes'].append( child )
+                        if composite_data_name:
+                            attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) #composite datasets need implicit renaming; inserted at front of list so explicit declarations take precedence
                     test.add_param( attrib.pop( 'name' ), value, attrib )
                 for output_elem in test_elem.findall( "output" ):
                     attrib = dict( output_elem.attrib )

lib/galaxy/tools/test.py

@@ -30,12 +30,15 @@ class ToolTestBuilder( object ):
                     if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ):
                         self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value)
             elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files:
-                if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) == 0:
+                name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ]
+                if name_change:
+                    name_change = name_change[-1].get( 'value' ) #only the last name change really matters
+                if value is None and not name_change:
                     assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name
                 else:
-                    self.required_files.append( ( value, extra ) )
-                    if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) > 0:
-                        value = extra.get( 'ftype' )
+                    self.required_files.append( ( value, extra ) ) #these files will be uploaded
+                    if name_change:
+                        value = name_change #change value for select to renamed uploaded file for e.g. composite dataset
         except Exception, e:
             log.debug( "Error in add_param for %s: %s" % ( name, e ) )
         self.inputs.append( ( name, value, extra ) )

test/functional/test_toolbox.py

@@ -33,10 +33,22 @@ class ToolTestCase( TwillTestCase ):
         # Upload any needed files
         for fname, extra in testdef.required_files:
             children = extra.get( 'children', [] )
-            metadata = [ child for child in children if child.tag == 'metadata' ]
-            composite_data = [ child for child in children if child.tag == 'composite_data' ]
+            metadata = extra.get( 'metadata', [] )
+            composite_data = extra.get( 'composite_data', [] )
             self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ), metadata = metadata, composite_data = composite_data )
             print "Uploaded file: ", fname, ", ftype: ", extra.get( 'ftype', 'auto' ), ", extra: ", extra
+            #Post upload attribute editing
+            edit_attributes = extra.get( 'edit_attributes', [] )
+            #currently only renaming is supported
+            for edit_att in edit_attributes:
+                if edit_att.get( 'type', None ) == 'name':
+                    new_name = edit_att.get( 'value', None )
+                    assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag'
+                    hda_id = self.get_history_as_data_list()[-1].get( 'id' )
+                    self.edit_hda_attribute_info( hda_id, new_name = new_name )
+                    print "Renamed uploaded file to:", new_name
+                else:
+                    raise Exception( 'edit_attributes type (%s) is unimplemented' % edit_att.get( 'type', None ) )
         # We need to handle the case where we've uploaded a valid compressed file since the upload
         # tool will have uncompressed it on the fly.
         all_inputs = {}