def test_calculate(self):
''' Run pa-calculate on a valid ProbAnno object and verify that the job runs and returns a valid RxnProbs object.'''
# Run the calculate() function to generate a RxnProbs object.
paClient = ProbabilisticAnnotation(self._config["probanno_url"], token=self._token)
rxnprobsMetadata = paClient.calculate( {
"probanno": self._config["probannoid"],
"probanno_workspace": self._config["test_ws"],
"rxnprobs": self._config["rxnprobsid"],
"rxnprobs_workspace": self._config["test_ws"]
} )
# Look for the RxnProbs object in the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
try:
rxnprobsObjectId = { 'workspace': self._config['test_ws'], 'name': self._config['rxnprobsid'] }
objectList = wsClient.get_objects( [ rxnprobsObjectId ] )
rxnprobsObject = objectList[0]
self.assertEqual(rxnprobsObject['info'][1], self._config['rxnprobsid'], 'RxnProbs object id %s is not %s' %(rxnprobsObject['info'][1], self._config['rxnprobsid']))
except WorkspaceServerError as e:
traceback.print_exc(file=sys.stderr)
self.fail(msg = "The expected object %s did not get created in the workspace %s!\n" %(self._config["rxnprobsid"], self._config["test_ws"]))
def test_calculate(self):
''' Run pa-calculate on a valid ProbAnno object and verify that the job runs and returns a valid RxnProbs object.'''
# Run the calculate() function to generate a RxnProbs object.
paClient = ProbabilisticAnnotation(self._config["probanno_url"],
token=self._token)
rxnprobsMetadata = paClient.calculate({
"probanno":
self._config["probannoid"],
"probanno_workspace":
self._config["test_ws"],
"rxnprobs":
self._config["rxnprobsid"],
"rxnprobs_workspace":
self._config["test_ws"]
})
# Look for the RxnProbs object in the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
try:
rxnprobsObjectId = {
'workspace': self._config['test_ws'],
'name': self._config['rxnprobsid']
}
objectList = wsClient.get_objects([rxnprobsObjectId])
rxnprobsObject = objectList[0]
self.assertEqual(
rxnprobsObject['info'][1], self._config['rxnprobsid'],
'RxnProbs object id %s is not %s' %
(rxnprobsObject['info'][1], self._config['rxnprobsid']))
except WorkspaceServerError as e:
traceback.print_exc(file=sys.stderr)
self.fail(
msg=
"The expected object %s did not get created in the workspace %s!\n"
% (self._config["rxnprobsid"], self._config["test_ws"]))
input['probanno'] = args.probanno
input['rxnprobs'] = args.rxnprobs
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
if args.rxnprobsws is None:
input['rxnprobs_workspace'] = user_workspace()
else:
input['rxnprobs_workspace'] = args.rxnprobsws
input['template_model'] = args.template
input['template_workspace'] = args.templatews
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Calculate reaction probabilities from probabilistic annotation.
try:
objectInfo = paClient.calculate(input)
print 'RxnProbs successfully generated in workspace:'
printObjectInfo(objectInfo)
except Exception as e:
print 'Error calculating reaction probabilities: %s' %(e.message)
if args.showError:
traceback.print_exc(file=sys.stdout)
exit(1)
exit(0)
