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]