def _view_job(meth, job_id):
"""Views a job.
:param job_id: A job id
:type job_id: kbtypes.Unicode
:ui_name job_id: A job id
:rtype: kbtypes.Unicode
:return: job info
"""
meth.stages = 2
meth.advance("Fetching job info")
ujs = UserAndJobState(url=service.URLS.user_and_job_state, token=meth.token)
job_info = ujs.get_job_info(job_id)
meth.advance("Done!")
return json.dumps(job_info)
def _view_job(meth, job_id):
"""Views a job.
:param job_id: A job id
:type job_id: kbtypes.Unicode
:ui_name job_id: A job id
:rtype: kbtypes.Unicode
:return: job info
"""
meth.stages = 2
meth.advance("Fetching job info")
ujs = UserAndJobState(url=service.URLS.user_and_job_state,
token=meth.token)
job_info = ujs.get_job_info(job_id)
meth.advance("Done!")
return json.dumps(job_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]
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]
dest='showTimes',
default=False)
parser.add_argument('--ujs-url',
help='url for user and job state service',
action='store',
dest='ujsURL',
default='https://kbase.us/services/userandjobstate')
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
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']:
if __name__ == "__main__":
# Parse options.
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, prog='cbd-getmatrix', epilog=desc3)
parser.add_argument('jobID', help='path to file with list of input sequence files', action='store', default=None)
parser.add_argument('outputPath', help='path to output csv file', action='store', default=None)
parser.add_argument('--show-times', help='show job start and end timestamps', action='store_true', dest='showTimes', default=False)
parser.add_argument('--ujs-url', help='url for user and job state service', action='store', dest='ujsURL', default='https://kbase.us/services/userandjobstate')
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
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." \
