def __init__(self, settings, debug_output): username = settings['omop_user'] password = settings['omop_passwd'] host = settings['omop_host'] port = settings['omop_port'] database = settings['omop_db'] engine = settings.get('omop_engine', 'postgresql') self._parents = {} self._codes = {} if settings['omop_use_alt_hierarchies']: if 'ccs_diag' in settings: self._codes['Condition_ICD9CM'] = {} self._parents['Condition_ICD9CM'] = util.read_CCS( util.get_file(settings['ccs_diag'], debug_output), self._codes['Condition_ICD9CM']) if 'ccs_proc' in settings: self._codes['Procedure_ICD9CM'] = {} self._parents['Procedure_ICD9CM'] = util.read_CCS( util.get_file(settings['ccs_proc'], debug_output), self._codes['Procedure_ICD9CM']) #self.schema = settings['omop_schema'] #self.db = sqlalchemy.create_engine('{0}://{1}:{2}@{3}:{4}/{5}'.format(engine, username, password, host, port, database)) self.schema = 'DIKB_DEV' self.db = sqlalchemy.create_engine( 'oracle://*****:*****@130.49.206.154:1521/dbmi01'.format( engine, username, password, host, port, database))
def __init__(self, settings, debug_output): username = settings['omop_user'] password = settings['omop_passwd'] host = settings['omop_host'] port = settings['omop_port'] database = settings['omop_db'] engine = settings.get('omop_engine', 'postgresql') self._parents = {} self._codes = {} if settings['omop_use_alt_hierarchies']: if 'ccs_diag' in settings: self._codes['Condition_ICD9CM'] = {} self._parents['Condition_ICD9CM'] = util.read_CCS(util.get_file(settings['ccs_diag'], debug_output), self._codes['Condition_ICD9CM']) if 'ccs_proc' in settings: self._codes['Procedure_ICD9CM'] = {} self._parents['Procedure_ICD9CM'] = util.read_CCS(util.get_file(settings['ccs_proc'], debug_output), self._codes['Procedure_ICD9CM']) self.schema = settings['omop_schema'] self.db = sqlalchemy.create_engine('{0}://{1}:{2}@{3}:{4}/{5}'.format(engine, username, password, host, port, database))
def init(self, settings): codes = getGlobalSymbols(settings) codes.update(getICD9(settings, False)) self._parents = util.read_CCS( get_file(settings, 'ccs_proc', 'code/ccs/multi_proc.txt'), codes) return codes
def init(self, settings): codes = getGlobalSymbols(settings) codes.update(getICD9(settings, False)) self._parents = util.read_CCS(get_file(settings, 'ccs_proc', 'code/ccs/multi_proc.txt'), codes) return codes