def quick_output(format, format_source=None, change_format_xml=None):
test_output = ToolOutput( "test_output" )
test_output.format = format
test_output.format_source = format_source
if change_format_xml:
test_output.change_format = XML(change_format_xml)
else:
test_output.change_format = None
return test_output
def quick_output(format, format_source=None, change_format_xml=None):
test_output = ToolOutput("test_output")
test_output.format = format
test_output.format_source = format_source
if change_format_xml:
test_output.change_format = XML(change_format_xml)
else:
test_output.change_format = None
return test_output
def execute( self, trans, incoming={}, set_output_hid=True, history=None, **kwargs ):
"""
Overrides Tool.execute() to dynamically add more output elements
"""
if incoming.has_key('extra_output'):
try:
extra_output = json.loads(urllib.unquote(incoming['extra_output']))
if isinstance(extra_output, list):
if len(self.outputs) > 1:
for k in self.outputs.keys():
if k != 'output':
del self.outputs[k]
for item in extra_output:
output = ToolOutput(item[0])
output.format = item[1]
output.change_format = None
output.format_source = None
output.metadata_source = ""
output.parent = None
output.label = item[2] if len(item) > 2 and item[2] != None else item[0]
output.count = 1
output.filters = []
output.from_work_dir = None
output.hidden = item[3] if len(item) > 3 else False
output.tool = self
output.actions = ToolOutputActionGroup( output, None )
output.dataset_collector_descriptions = [DEFAULT_DATASET_COLLECTOR_DESCRIPTION]
self.outputs[ output.name ] = output
except:
log.exception('Could not add extra output elements')
return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs )