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SD2E / opil

The Open Protocol Interface Language (OPIL) is intended as a standard language for protocol interfaces
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How to get ParameterValue objects from an opil.ProtocolInterface #183

Open tramyn opened 3 years ago

tramyn commented 3 years ago

I want to get opil.ParameterValues from a strateos opil.ProtocolInterface (ex: CellFreeRiboswitches). I tried running the code below but unable to get desired information. What is the correct to do this?

Here is what I have tried so far. 

import opil
import sbol

file_path = 'CellFreeRiboswitches.xml'
opil_doc = opil.Document()
opil_doc.read(file_path, sbol3.RDF_XML)
opil_protocol_interfaces = [top_level for top_level in opil_doc.objects if isinstance(top_level, opil.ProtocolInterface)]
parameters = opil_protocol_interfaces[0].has_parameter
parameter_values = []
for parameter in parameters:
     if parameter.default_value:
          parameter_value = opil_doc.find(parameter.default_value)
          if parameter_value:
               parameter_values.append(parameter_value)
if len(parameter_values) == 0:
     raise Exception('Expecting ParameterValues but found none')
bbartley commented 3 years ago

This is easy. Notice that parameter.default_value returns a child ParameterValue object. For example:

for parameter in parameters:
     if parameter.default_value:
          print(parameter.default_value.identity)

http://strateos.com/CellFreeRiboswitches/MeasureParameter3/MeasureValue1
http://strateos.com/CellFreeRiboswitches/IntegerParameter1/IntegerValue1
http://strateos.com/CellFreeRiboswitches/MeasureParameter5/MeasureValue1
...

You may have been expecting a URI reference to a ParameterValue because that's how it was originally specified, but that turned out to be a bug in the specification. See discussion here: https://github.com/SD2E/opil/issues/73