def __init__(self, genomeId, context=None, communityIndex='0'):
''' Initialize object.
@param genomeId: Genome ID string for genome being annotated
@param context: User context when used in a server
@param communityIndex: Index number of model in a community model
@return Nothing
'''
# Save the genome ID (used for messages and temporary file names).
self.genomeId = genomeId
self.communityIndex = communityIndex
# Get the configuration variables.
serviceName = os.environ.get('KB_SERVICE_NAME', 'ProbModelSEED')
cfg = ConfigParser()
cfg.read(os.path.join(os.environ.get('KB_TOP'), 'deployment.cfg'))
self.config = dict()
for nameval in cfg.items(serviceName):
self.config[nameval[0]] = nameval[1]
# Use the context from the server or build a context when used outside of a server.
if context is not None:
self.ctx = context
else:
self.ctx = dict()
self.ctx['client_ip'] = '127.0.0.1'
self.ctx['user_id'] = '-'
self.ctx['module'] = serviceName
self.ctx['method'] = '-'
self.ctx['call_id'] = '-'
# Create a logger.
self.logger = log.log(serviceName,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.config['mlog_log_file'])
self.logger.set_log_level(int(self.config['mlog_log_level']))
# Create a ProbAnnotationParser object for working with the static database files.
self.dataParser = ProbAnnotationParser(self.config)
# Get the static database files. If the files do not exist and they are downloaded
# from Shock, it can take a few minutes before they are ready.
self.dataParser.getDatabaseFiles(self.logger, '')
# Create a work directory for storing temporary files.
if not os.path.exists(self.config['work_dir']):
os.makedirs(self.config['work_dir'], 0775)
self.workFolder = tempfile.mkdtemp(dir=self.config['work_dir'],
prefix='')
return
config = dict()
for nameval in cfg.items(serviceName):
config[nameval[0]] = nameval[1]
# Create a logger.
logger = log.log(serviceName,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=config['mlog_log_file'])
logger.set_log_level(int(config['mlog_log_level']))
# Create a ProbAnnotationParser object for working with the static data files.
dataParser = ProbAnnotationParser(config)
# Load the static data files from Shock.
if args.action == 'load':
print 'Started loading data files from Shock ...'
dataParser.writeStatusFile('running')
try:
dataParser.loadDatabaseFiles(logger)
dataParser.writeStatusFile('ready')
print 'Finished loading data files'
except:
dataParser.writeStatusFile('failed')
print 'Failed to load static data files from Shock'
traceback.print_exc(file=sys.stderr)
exit(1)
