def test_StepOperator_Ids(self):
# Check if step id and operator id matches each other
for f in self.jsonFiles:
with open(f) as xplanFile:
jsonData = json.load(xplanFile)
xplan_data = XplanDataParser(jsonData)
for step_obj in xplan_data.get_stepsList():
for oper_obj in step_obj.get_operatorList():
self.assertEqual(step_obj.get_id(), oper_obj.get_id())
def test_duplicateIds(self):
for f in self.jsonFiles:
unique_ids = []
duplic_ids = []
with open(f) as xplanFile:
jsonData = json.load(xplanFile)
xplan_data = XplanDataParser(jsonData)
for step_obj in xplan_data.get_stepsList():
if step_obj.get_id() not in unique_ids:
unique_ids.append(step_obj.get_id())
else:
duplic_ids.append(step_obj.get_id())
self.assertEqual(len(duplic_ids), 0)
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)
def test_Xplan_Keys(self):
for f in self.jsonFiles:
with open(f) as xplanFile:
jsonData = json.load(xplanFile)
xplan_data = XplanDataParser(jsonData)
expected_xplanKeys = ['id', 'name', 'experimentId', 'experimentLab', 'experimentSet', 'steps', 'initialState']
self.assertIsNotNone(xplan_data.get_xplanId())
self.assertIsNotNone(xplan_data.get_xplanName())
self.assertIsNotNone(xplan_data.get_experimentId())
self.assertIsNotNone(xplan_data.get_experimentLab())
self.assertIsNotNone(xplan_data.get_experimentSet())
self.assertTrue(set(xplan_data.get_xplanKeys()).issubset(set(expected_xplanKeys)))
expected_stepKeys = ['id', 'name', 'operator', 'description']
for step_obj in xplan_data.get_stepsList():
self.assertIsNotNone(step_obj.get_id())
self.assertIsNotNone(step_obj.get_name())
self.assertTrue(set(step_obj.get_keys()).issubset(set(expected_stepKeys)))
expected_operKeys = ['id', 'name', 'transformations', 'description', 'samples', 'manifest', 'measurements', 'type', 'instrument_configuration', '_comment', 'channels']
for oper_obj in step_obj.get_operatorList():
self.assertIsNotNone(oper_obj.get_id())
self.assertIsNotNone(oper_obj.get_name())
self.assertTrue(set(oper_obj.get_keys()).issubset(set(expected_operKeys)))
expected_operType = ['incubate', 'pick', 'streak', 'mix', 'spectrophotometry', 'dilute', 'transfer', 'flowCytometry', 'prepare_plasmids', 'transform', 'rnaSeq']
self.assertTrue(oper_obj.get_type() in expected_operType)
expected_agavePrefix = 'agave://data-sd2e-community/'
if oper_obj.get_instrumentConfig() is not None:
self.assertTrue(oper_obj.get_instrumentConfig().startswith(expected_agavePrefix))
expected_sbhPrefix = 'https://hub.sd2e.org/user/sd2e/'
for samp_obj in oper_obj.get_samplesList():
for uri in samp_obj.get_uriList():
isExpectedURI = uri.startswith(expected_sbhPrefix) or uri.startswith(expected_agavePrefix)
self.assertTrue(isExpectedURI)
expected_measKeys = ['file', 'source']
for meas_obj in oper_obj.get_measurementsList():
for file in meas_obj.get_filesList():
isExpectedURI = file.startswith(expected_sbhPrefix) or file.startswith(expected_agavePrefix)
self.assertTrue(isExpectedURI)
isExpectedURI = meas_obj.get_source().startswith(expected_sbhPrefix) or meas_obj.get_source().startswith(expected_agavePrefix)
self.assertTrue(isExpectedURI)
expected_chanKeys = ['name', 'calibration_file']
for chan_obj in oper_obj.get_channelsList():
self.assertTrue(set(chan_obj.get_keys()).issubset(set(expected_chanKeys)))
expected_sd2ePrefix = 'http://sd2e.org#'
expected_transfKeys = ['destination', 'source', 'volume', 'od600']
expected_measureKeys = ['IPTG_measure', 'Larabinose_measure', 'aTc_measure']
for transf_obj in oper_obj.get_transformationsList():
self.assertTrue(set(transf_obj.get_keys()).issubset(set(expected_transfKeys)))
isExpectedURI = transf_obj.get_destination().startswith(expected_sbhPrefix) or transf_obj.get_destination().startswith(expected_agavePrefix)
self.assertTrue(isExpectedURI)
for source in transf_obj.get_sourceList():
for uri in source.get_uriList():
isExpectedURI = uri.startswith(expected_sbhPrefix) or uri.startswith(expected_agavePrefix)
self.assertTrue(isExpectedURI)
for meas in source.get_measures():
self.assertTrue(meas in expected_measureKeys)