def setUpClass(cls):
print("Running " + cls.__name__)
yeastGates_json = 'example/xplan/yeastGates-Q0-v2.json'
yeastGates_sbol = 'example/sbol/yeastGates-Q0-v2.xml'
om_path = 'example/om/om-2.0.rdf'
cls.sbolDoc = Document()
cls.sbolDoc.read(yeastGates_sbol)
with open(yeastGates_json) as jsonFile:
jsonData = json.load(jsonFile)
cls.converted_sbol = xbol.convert_xplan_to_sbol(jsonData, SBOLNamespace.HTTPS_HS, om_path, True)
cls.xplan_data = XplanDataParser(jsonData)
def setUpClass(cls):
print("Running " + cls.__name__)
rule30_json = 'example/xplan/yg_t3.json'
om_path = 'example/om/om-2.0.rdf'
with open(rule30_json) as jsonFile:
jsonData = json.load(jsonFile)
cls.xplanData = XplanDataParser(jsonData)
cls.sbolDoc = xbol.convert_xplan_to_sbol(jsonData,
SBOLNamespace.HTTPS_HS,
om_path, True)
# print(cls.sbolDoc.writeString())
print(cls.sbolDoc)
cls.sbol_idDict = SBOLTestUtil(cls.xplanData)
cls.attachments_tl = []
cls.experiments_tl = []
cls.experimentalData_tl = []
cls.implementations_tl = []
cls.measures_tl = []
cls.units_tl = []
for topLevel in cls.sbolDoc:
if topLevel.type == SBOLNamespace.ATTACHMENT_NS:
cls.attachments_tl.append(topLevel)
elif topLevel.type == SBOLNamespace.EXPERIMENT_NS:
cls.experiments_tl.append(topLevel)
elif topLevel.type == SBOLNamespace.EXPERIMENTAL_DATA_NS:
cls.experimentalData_tl.append(topLevel)
elif topLevel.type == SBOLNamespace.IMPLEMENTATION_NS:
cls.implementations_tl.append(topLevel)
elif topLevel.type == SBOLNamespace.MEASURE_NS:
cls.measures_tl.append(topLevel)
elif topLevel.type == SBOLNamespace.UNIT_NS:
cls.units_tl.append(topLevel)
elif topLevel.type == SBOLNamespace.ACTIVITY_NS:
continue #No need to store this when I can directly access through sbolDoc
else:
print("Warning! Unexpected SBOL object was found: " +
topLevel.type)
