def test_get_probanno(self):
''' Verify that we can successfully get a list of roleset probabilities from a valid ProbAnno object. '''
paClient = ProbabilisticAnnotation(self._config["probanno_url"], token=self._token)
probAnnoData = paClient.get_probanno( {
"probanno": self._config["probannoid"],
"probanno_workspace": self._config["test_ws"]
})
self.assertNotEqual(len(probAnnoData), 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')
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_get_probanno(self):
''' Verify that we can successfully get a list of roleset probabilities from a valid ProbAnno object. '''
paClient = ProbabilisticAnnotation(self._config["probanno_url"],
token=self._token)
probAnnoData = paClient.get_probanno({
"probanno":
self._config["probannoid"],
"probanno_workspace":
self._config["test_ws"]
})
self.assertNotEqual(len(probAnnoData), 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')
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_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"]))
# 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)
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
input['probanno'] = args.probanno
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
input['probanno_version'] = args.probannover
# 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_probanno(input)
except Exception as e:
print 'Error getting ProbAnno 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.
if args.roles:
print '\t'.join(['gene', 'role', 'likelihood'])
else:
print '\t'.join(['gene', 'annotation', 'likelihood'])
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
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'
])
default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
if args.newurl == None:
url = get_url()
print "Current URL: " + url
else:
url = set_url(args.newurl)
if args.noCheck:
print 'New URL set to: ' + url
exit(0)
try:
paClient = ProbabilisticAnnotation(url=url)
serverInfo = paClient.version()
if serverInfo[0] != 'probabilistic_annotation':
print url + ' is not a probabilistic annotation server'
exit(1)
print url + ' is valid and running %s v%s' % (serverInfo[0],
serverInfo[1])
except ProbAnnoServerError as e:
print 'Endpoint at %s returned error: %s' % (url, e)
exit(1)
except Exception as e:
print 'Could not get a valid response from endpoint at %s: %s' % (url,
e)
exit(1)
exit(0)
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)
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
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])
'''
# Main script function
if __name__ == "__main__":
# Parse arguments.
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
prog='pa-savedata',
epilog=desc3)
parser.add_argument('configFilePath',
help='path to configuration file',
action='store',
default=None)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Get the probabilistic_annotation section from the configuration file.
config = get_config(args.configFilePath)
# Create a DataParser object for working with the static database files.
dataParser = DataParser(config)
# Store the static database files in Shock.
paClient = ProbabilisticAnnotation(url=get_url())
dataParser.storeDatabaseFiles(paClient._headers['AUTHORIZATION'])
exit(0)
parser.add_argument(
"--no-check", help="do not check for a valid URL", action="store_true", dest="noCheck", default=False
)
usage = parser.format_usage()
parser.description = desc1 + " " + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
if args.newurl == None:
url = get_url()
print "Current URL: " + url
else:
url = set_url(args.newurl)
if args.noCheck:
print "New URL set to: " + url
exit(0)
try:
paClient = ProbabilisticAnnotation(url=url)
serverInfo = paClient.version()
if serverInfo[0] != "probabilistic_annotation":
print url + " is not a probabilistic annotation server"
exit(1)
print url + " is valid and running %s v%s" % (serverInfo[0], serverInfo[1])
except ProbAnnoServerError as e:
print "Endpoint at %s returned error: %s" % (url, e)
exit(1)
except Exception as e:
print "Could not get a valid response from endpoint at %s: %s" % (url, e)
exit(1)
exit(0)