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"]))
class NarrativeJobProxy:
'''
Module Name:
NarrativeJobProxy
Module Description:
Very simple proxy that reauthenticates requests to the user_and_job_state
service as the narrative user.
DO NOT DEPLOY PUBLICALLY
'''
######## WARNING FOR GEVENT USERS #######
# Since asynchronous IO can lead to methods - even the same method -
# interrupting each other, you must be *very* careful when using global
# state. A method could easily clobber the state set by another while
# the latter method is running.
#########################################
#BEGIN_CLASS_HEADER
UPDATE_TOKEN_INTERVAL = 24 * 60 * 60 # 1 day in sec
# UPDATE_TOKEN_INTERVAL = 10
def _update_token(self):
if self._updating:
return
if (time.time() - self._updated_at < self.UPDATE_TOKEN_INTERVAL):
return
self._updating = True
print('Updating token at ' + str(time.time()))
try:
self._ujs = UserAndJobState(self._url, user_id=self._user,
password=self._pwd)
self._updated_at = time.time()
finally: # otherwise token will never be updated
self._updating = False
#END_CLASS_HEADER
# config contains contents of config file in a hash or None if it couldn't
# be found
def __init__(self, config):
#BEGIN_CONSTRUCTOR
self._user = config.get('narrative_user')
self._pwd = config.get('narrative_user_pwd')
if not self._user or not self._pwd:
raise ValueError(
'narrative user and/or narrative pwd missing from deploy.cfg')
self._url = config.get('ujs_url')
if not self._url:
raise ValueError('UJS url missing from deploy.cfg')
self._updated_at = - self.UPDATE_TOKEN_INTERVAL
self._updating = False
self._update_token()
#END_CONSTRUCTOR
pass
def ver(self, ctx):
# ctx is the context object
# return variables are: ver
#BEGIN ver
ver = '0.0.1'
#END ver
# At some point might do deeper type checking...
if not isinstance(ver, basestring):
raise ValueError('Method ver return value ' +
'ver is not type basestring as required.')
# return the results
return [ver]
def get_detailed_error(self, ctx, job):
# ctx is the context object
# return variables are: error
#BEGIN get_detailed_error
self._update_token()
error = self._ujs.get_detailed_error(job)
#END get_detailed_error
# At some point might do deeper type checking...
if not isinstance(error, basestring):
raise ValueError('Method get_detailed_error return value ' +
'error is not type basestring as required.')
# return the results
return [error]
def get_job_info(self, ctx, job):
# ctx is the context object
# return variables are: info
#BEGIN get_job_info
self._update_token()
info = self._ujs.get_job_info(job)
#END get_job_info
# At some point might do deeper type checking...
if not isinstance(info, list):
raise ValueError('Method get_job_info return value ' +
'info is not type list as required.')
# return the results
return [info]
class NarrativeJobProxy:
'''
Module Name:
NarrativeJobProxy
Module Description:
Very simple proxy that reauthenticates requests to the user_and_job_state
service as the narrative user.
DO NOT DEPLOY PUBLICALLY
'''
######## WARNING FOR GEVENT USERS #######
# Since asynchronous IO can lead to methods - even the same method -
# interrupting each other, you must be *very* careful when using global
# state. A method could easily clobber the state set by another while
# the latter method is running.
#########################################
#BEGIN_CLASS_HEADER
UPDATE_TOKEN_INTERVAL = 24 * 60 * 60 # 1 day in sec
# UPDATE_TOKEN_INTERVAL = 10
def _update_token(self):
if self._updating:
return
if (time.time() - self._updated_at < self.UPDATE_TOKEN_INTERVAL):
return
self._updating = True
print('Updating token at ' + str(time.time()))
try:
self._ujs = UserAndJobState(self._url,
user_id=self._user,
password=self._pwd)
self._updated_at = time.time()
finally: # otherwise token will never be updated
self._updating = False
#END_CLASS_HEADER
# config contains contents of config file in a hash or None if it couldn't
# be found
def __init__(self, config):
#BEGIN_CONSTRUCTOR
self._user = config.get('narrative_user')
self._pwd = config.get('narrative_user_pwd')
if not self._user or not self._pwd:
raise ValueError(
'narrative user and/or narrative pwd missing from deploy.cfg')
self._url = config.get('ujs_url')
if not self._url:
raise ValueError('UJS url missing from deploy.cfg')
self._updated_at = -self.UPDATE_TOKEN_INTERVAL
self._updating = False
self._update_token()
#END_CONSTRUCTOR
pass
def ver(self, ctx):
# ctx is the context object
# return variables are: ver
#BEGIN ver
ver = '0.0.1'
#END ver
# At some point might do deeper type checking...
if not isinstance(ver, basestring):
raise ValueError('Method ver return value ' +
'ver is not type basestring as required.')
# return the results
return [ver]
def get_detailed_error(self, ctx, job):
# ctx is the context object
# return variables are: error
#BEGIN get_detailed_error
self._update_token()
error = self._ujs.get_detailed_error(job)
#END get_detailed_error
# At some point might do deeper type checking...
if not isinstance(error, basestring):
raise ValueError('Method get_detailed_error return value ' +
'error is not type basestring as required.')
# return the results
return [error]
def get_job_info(self, ctx, job):
# ctx is the context object
# return variables are: info
#BEGIN get_job_info
self._update_token()
info = self._ujs.get_job_info(job)
#END get_job_info
# At some point might do deeper type checking...
if not isinstance(info, list):
raise ValueError('Method get_job_info return value ' +
'info is not type list as required.')
# return the results
return [info]
args = parser.parse_args()
# Get the status of the specified job.
ujsClient = UserAndJobState(args.ujsURL)
try:
info = job_info_dict(ujsClient.get_job_info(args.jobID))
except JobStateServerError as e:
print e.message
exit(1)
# Check if the job had an error.
if info['error']:
print "Job '%s' ended with error '%s' and no results are available." % (
args.jobID, info['status'])
print 'Error details:'
print ujsClient.get_detailed_error(args.jobID)
ujsClient.delete_job(args.jobID)
exit(1)
# Check if the job is complete.
if not info['complete']:
print "Job '%s' has status '%s' and is working on task %s of %s. Check again later." \
%(args.jobID, info['status'], info['total_progress'], info['max_progress'])
exit(1)
# Show job info.
if args.showTimes:
print 'Job started at %s and finished at %s' % (info['started'],
info['last_update'])
# Create a shock client.
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Get the status of the specified job.
ujsClient = UserAndJobState(args.ujsURL)
try:
info = job_info_dict(ujsClient.get_job_info(args.jobID))
except JobStateServerError as e:
print e.message
exit(1)
# Check if the job had an error.
if info['error']:
print "Job '%s' ended with error '%s' and no results are available." %(args.jobID, info['status'])
print 'Error details:'
print ujsClient.get_detailed_error(args.jobID)
ujsClient.delete_job(args.jobID)
exit(1)
# Check if the job is complete.
if not info['complete']:
print "Job '%s' has status '%s' and is working on task %s of %s. Check again later." \
%(args.jobID, info['status'], info['total_progress'], info['max_progress'])
exit(1)
# Show job info.
if args.showTimes:
print 'Job started at %s and finished at %s' %(info['started'], info['last_update'])
# Create a shock client.
shockClient = ShockClient(info['results']['shockurl'], ujsClient._headers['AUTHORIZATION'])
