def test_annotate(self):
''' Run pa-annotate on a valid Genome object and verify that the job runs and returns a valid ProbAnno object in the expected time.'''
# Run the annotate() function to generate a ProbAnno object.
paClient = ProbabilisticAnnotation(self._config["probanno_url"],
token=self._token)
jobid = paClient.annotate({
"genome": self._config["genomeid"],
"genome_workspace": self._config["test_ws"],
"probanno": self._config["probannoid"],
"probanno_workspace": self._config["test_ws"]
})
# Allow time for the command to run.
time.sleep(float(self._config["runtime"]))
# Make sure the job has completed.
ujsClient = UserAndJobState(self._config['ujs_url'], token=self._token)
jobList = ujsClient.list_jobs([self._config['test_user']], 'CE')
jobCompleted = False
for job in jobList:
if jobid == job[0]:
jobCompleted = True
jobInfo = job
self.assertTrue(
jobCompleted, 'Job did not complete before timeout of %s seconds' %
(self._config['runtime']))
# See if the job ended in error.
details = ''
if jobInfo[11] == 1:
details = ujsClient.get_detailed_error(jobInfo[0])
self.assertEqual(jobInfo[11], 0, 'Job ended in error: %s' % (details))
# Look for the ProbAnno object in the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
try:
probannoObjectId = {
'workspace': self._config['test_ws'],
'name': self._config['probannoid']
}
objectList = wsClient.get_objects([probannoObjectId])
probannoObject = objectList[0]
self.assertEqual(
probannoObject['info'][1], self._config['probannoid'],
'ProbAnno object id %s is not %s' %
(probannoObject['info'][1], self._config['probannoid']))
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["probannoid"], self._config["test_ws"]))
def test_annotate(self):
''' Run pa-annotate on a valid Genome object and verify that the job runs and returns a valid ProbAnno object in the expected time.'''
# Run the annotate() function to generate a ProbAnno object.
paClient = ProbabilisticAnnotation(self._config["probanno_url"], token=self._token)
jobid = paClient.annotate( {
"genome": self._config["genomeid"],
"genome_workspace": self._config["test_ws"],
"probanno": self._config["probannoid"],
"probanno_workspace": self._config["test_ws"] } )
# Allow time for the command to run.
time.sleep(float(self._config["runtime"]))
# Make sure the job has completed.
ujsClient = UserAndJobState(self._config['ujs_url'], token=self._token)
jobList = ujsClient.list_jobs([ self._config['test_user'] ], 'CE')
jobCompleted = False
for job in jobList:
if jobid == job[0]:
jobCompleted = True
jobInfo = job
self.assertTrue(jobCompleted, 'Job did not complete before timeout of %s seconds' %(self._config['runtime']))
# See if the job ended in error.
details = ''
if jobInfo[11] == 1:
details = ujsClient.get_detailed_error(jobInfo[0])
self.assertEqual(jobInfo[11], 0, 'Job ended in error: %s' %(details))
# Look for the ProbAnno object in the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
try:
probannoObjectId = { 'workspace': self._config['test_ws'], 'name': self._config['probannoid'] }
objectList = wsClient.get_objects( [ probannoObjectId ] )
probannoObject = objectList[0]
self.assertEqual(probannoObject['info'][1], self._config['probannoid'], 'ProbAnno object id %s is not %s' %(probannoObject['info'][1], self._config['probannoid']))
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["probannoid"], self._config["test_ws"]))
# Create input parameters for annotate() function.
input = dict()
input['genome'] = args.genome
input['probanno'] = args.probanno
if args.genomews is None:
input['genome_workspace'] = user_workspace()
else:
input['genome_workspace'] = args.genomews
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Submit a job to annotate the specified genome.
try:
jobid = paClient.annotate(input)
print 'Probabilistic annotation job '+jobid+' successfully submitted'
except Exception as e:
print 'Error starting job: %s' %(e.message)
if args.showError:
traceback.print_exc(file=sys.stdout)
exit(1)
exit(0)
