if __name__ == "__main__":
# Parse options.
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, prog='pa_checkjob', epilog=desc3)
parser.add_argument('-j', '--jobID', help='job ID', action='store', dest='jobID', default=None)
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 list of jobs for the user.
if 'KB_AUTH_USER_ID' in os.environ:
userID = os.environ.get('KB_AUTH_USER_ID')
else:
auth = _read_inifile()
userID = auth['user_id']
ujsClient = UserAndJobState(args.ujsURL)
try:
jobList = ujsClient.list_jobs([ userID ], 'RCE')
except JobStateServerError as e:
print e.message
exit(1)
# See if the user has any jobs in the list.
if len(jobList) == 0:
print 'There are no jobs for you.'
exit(1)
# Print info about the specific job if requested.
if args.jobID is not None:
def __init__(self, args):
_authdata = _read_inifile()
self.wsClient = workspaceService("http://kbase.us/services/workspace/")
self.token = _authdata['token']
self.args = args
default=None)
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 list of jobs for the user.
if 'KB_AUTH_USER_ID' in os.environ:
userID = os.environ.get('KB_AUTH_USER_ID')
else:
auth = _read_inifile()
userID = auth['user_id']
ujsClient = UserAndJobState(args.ujsURL)
try:
jobList = ujsClient.list_jobs([userID], 'RCE')
except JobStateServerError as e:
print 'Error getting job list: ' + e.message
exit(1)
# See if the user has any jobs in the list.
if len(jobList) == 0:
print 'There are no jobs for you.'
exit(1)
# Print info about the specific job if requested.
if args.jobID is not None:
default='http://kbase.us/services/workspace/')
args = parser.parse_args()
if args.probanno is None:
args.probanno = args.genome + '.probanno'
if args.probannows is None:
args.probannows = args.workspace
if args.rxnprobs is None:
args.rxnprobs = args.genome + '.rxnprobs'
if args.rxnprobsws is None:
args.rxnprobsws = args.workspace
if args.phenosimsetws is None:
args.phenosimsetws = args.workspace
# Create the clients for the services we need.
authdata = _read_inifile()
token = authdata['token']
wsClient = workspaceService(args.wsurl)
# Build roles to reactions dictionary.
step = 1
print "+++ Step %d: Build reactions to roles dictionary +++" % (step)
if not os.path.exists(rolesToRxnsFileName):
os.system(
"all_roles_used_in_models | roles_to_complexes | get_relationship_HasStep -to id >%s"
% (rolesToRxnsFileName))
rolesToReactions = dict()
reactionsToRoles = dict()
# Each line of the file has four fields: (1) role, (2) hypothetical flag, (3) complex id, (4) reaction id
rolesToRxnsFile = open(rolesToRxnsFileName, 'r')
for line in rolesToRxnsFile:
parser.add_argument('--ws-url', help='url for workspace service', action='store', dest='wsurl', default='http://kbase.us/services/workspace/')
args = parser.parse_args()
if args.probanno is None:
args.probanno = args.genome + '.probanno'
if args.probannows is None:
args.probannows = args.workspace
if args.rxnprobs is None:
args.rxnprobs = args.genome + '.rxnprobs'
if args.rxnprobsws is None:
args.rxnprobsws = args.workspace
if args.phenosimsetws is None:
args.phenosimsetws = args.workspace
# Create the clients for the services we need.
authdata = _read_inifile()
token = authdata['token']
wsClient = workspaceService(args.wsurl)
# Build roles to reactions dictionary.
step = 1
print "+++ Step %d: Build reactions to roles dictionary +++" %(step)
if not os.path.exists(rolesToRxnsFileName):
os.system("all_roles_used_in_models | roles_to_complexes | get_relationship_HasStep -to id >%s" %(rolesToRxnsFileName))
rolesToReactions = dict()
reactionsToRoles = dict()
# Each line of the file has four fields: (1) role, (2) hypothetical flag, (3) complex id, (4) reaction id
rolesToRxnsFile = open(rolesToRxnsFileName, 'r')
for line in rolesToRxnsFile:
fields = line.strip('\r\n').split('\t')
reaction = fields[3]
