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
