def test_get_rxnprobs(self):
''' Verify that we can successfully get a list of rxnprobs data from a valid RxnProbs object.'''
paClient = ProbabilisticAnnotation(self._config["probanno_url"], token=self._token)
rxnProbsData = paClient.get_rxnprobs( {
"rxnprobs": self._config["rxnprobsid"],
"rxnprobs_workspace": self._config["test_ws"]
})
self.assertNotEqual(len(rxnProbsData), 0, 'Length of output array is zero')
def test_get_rxnprobs(self):
''' Verify that we can successfully get a list of rxnprobs data from a valid RxnProbs object.'''
paClient = ProbabilisticAnnotation(self._config["probanno_url"],
token=self._token)
rxnProbsData = paClient.get_rxnprobs({
"rxnprobs":
self._config["rxnprobsid"],
"rxnprobs_workspace":
self._config["test_ws"]
})
self.assertNotEqual(len(rxnProbsData), 0,
'Length of output array is zero')
input['rxnprobs'] = args.rxnprobs
if args.rxnprobsws is None:
input['rxnprobs_workspace'] = user_workspace()
else:
input['rxnprobs_workspace'] = args.rxnprobsws
input['rxnprobs_version'] = args.rxnprobsver
input['sort_field'] = args.sortField
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Get the raw data from the server.
try:
output = paClient.get_rxnprobs(input)
except Exception as e:
print 'Error getting RxnProbs object: %s' % (e.message)
if args.showError:
traceback.print_exc(file=sys.stdout)
exit(1)
# Format the data as a table of tab delimited fields.
print '\t'.join([
'reaction_id', 'probability', 'complex_diagnostic', 'complex_details',
'putative_GPR'
])
for rxnprob in output:
print '%s\t%f\t%s\t%s\t%s' % (rxnprob[0], rxnprob[1], rxnprob[2],
rxnprob[3], rxnprob[4])
input['rxnprobs'] = args.rxnprobs
if args.rxnprobsws is None:
input['rxnprobs_workspace'] = user_workspace()
else:
input['rxnprobs_workspace'] = args.rxnprobsws
input['rxnprobs_version'] = args.rxnprobsver
input['sort_field'] = args.sortField
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Get the raw data from the server.
try:
output = paClient.get_rxnprobs(input)
except Exception as e:
print 'Error getting RxnProbs object: %s' %(e.message)
if args.showError:
traceback.print_exc(file=sys.stdout)
exit(1)
# Format the data as a table of tab delimited fields.
print '\t'.join(['reaction_id', 'probability', 'complex_diagnostic', 'complex_details', 'putative_GPR'])
for rxnprob in output:
print '%s\t%f\t%s\t%s\t%s' %(rxnprob[0], rxnprob[1], rxnprob[2], rxnprob[3], rxnprob[4])
exit(0)
