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Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool.

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Daniel Blankenberg
2011-03-31 10:16:40 -04:00
parent 950b6e6abe
commit 955acd87e1
1 changed files with 7 additions and 5 deletions
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lib/galaxy/tools/actions/__init__.py
+7 -5
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@@ -133,16 +133,18 @@ class DefaultToolAction( object ):
else:
new_list.append( value )
return new_list
def wrap_values( inputs, input_values ):
def wrap_values( inputs, input_values, skip_missing_values = False ):
# Wrap tool inputs as necessary
for input in inputs.itervalues():
if input.name not in input_values and skip_missing_values:
continue
if isinstance( input, Repeat ):
for d in input_values[ input.name ]:
wrap_values( input.inputs, d )
wrap_values( input.inputs, d, skip_missing_values = skip_missing_values )
elif isinstance( input, Conditional ):
values = input_values[ input.name ]
current = values[ "__current_case__" ]
wrap_values( input.cases[current].inputs, values )
wrap_values( input.cases[current].inputs, values, skip_missing_values = skip_missing_values )
elif isinstance( input, DataToolParameter ):
input_values[ input.name ] = \
galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ],
@@ -254,7 +256,7 @@ class DefaultToolAction( object ):
if output.change_format:
if params is None:
params = make_dict_copy( incoming )
wrap_values( tool.inputs, params )
wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values )
for change_elem in output.change_format:
for when_elem in change_elem.findall( 'when' ):
check = when_elem.get( 'input', None )
@@ -304,7 +306,7 @@ class DefaultToolAction( object ):
# <outputs>
# <data format="input" name="output" label="Blat on ${<input_param>.name}" />
# </outputs>
wrap_values( tool.inputs, params )
wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values )
#tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined
params['tool'] = tool
params['on_string'] = on_text