# 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)
SEE ALSO pa-gendata AUTHORS Matt Benedict, Mike Mundy ''' # 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)
''' # 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('newurl', nargs='?', default=None, help='New URL endpoint') 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:
Matt Benedict, Mike Mundy """ if __name__ == "__main__": parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, prog="pa_url", epilog=desc3) parser.add_argument("newurl", nargs="?", default=None, help="New URL endpoint") 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)