def parse_args():
"""
This function expands the default argument list defined in cdr_cleaner.args_parser
:return: an expanded argument list object
"""
import cdr_cleaner.args_parser as parser
argument_parser = parser.get_argument_parser()
argument_parser.add_argument(
'-y',
'--year_threshold',
dest='year_threshold',
action='store',
help='The year threshold applied to domain tables except observation',
required=False,
default=DEFAULT_YEAR_THRESHOLD)
argument_parser.add_argument('-o',
'--observation_year_threshold',
dest='observation_year_threshold',
action='store',
help='The threshold applied to observation',
required=False,
default=OBSERVATION_DEFAULT_YEAR_THRESHOLD)
return argument_parser.parse_args()
def parse_args():
"""
Expands the default argument list defined in cdr_cleaner.args_parser
:return: an expanded argument list object
"""
import cdr_cleaner.args_parser as parser
argument_parser = parser.get_argument_parser()
argument_parser.add_argument(
'-c',
'--combined_dataset_id',
dest='combined_dataset_id',
action='store',
help='The combined dataset used to generate the deid dataset',
required=True)
return argument_parser.parse_args()
def parse_args():
"""
Expands the default argument list defined in cdr_cleaner.args_parser
:return: an expanded argument list object
"""
import cdr_cleaner.args_parser as parser
argument_parser = parser.get_argument_parser()
argument_parser.add_argument(
'-m',
'--mapping_dataset_id',
dest='mapping_dataset_id',
action='store',
help=
'The dataset containing mapping tables, typically the combined_dataset',
required=True)
return argument_parser.parse_args()
def get_parser():
"""
Create a parser which raises invalid enum errors
:return: parser
"""
from cdr_cleaner import args_parser
engine_parser = args_parser.get_argument_parser()
engine_parser.add_argument(
'-a',
'--data_stage',
required=True,
dest='data_stage',
action='store',
type=DataStage,
choices=list([s for s in DataStage if s is not DataStage.UNSPECIFIED]),
help='Specify the dataset')
return engine_parser
if add_handler:
handler = logging.StreamHandler()
handler.setLevel(logging.INFO)
formatter = logging.Formatter(
'%(asctime)s - %(levelname)s - %(name)s - %(message)s')
handler.setFormatter(formatter)
logging.getLogger('').addHandler(handler)
if __name__ == '__main__':
import cdr_cleaner.args_parser as ap
# import cdr_cleaner.clean_cdr_engine as clean_engine
from constants.cdr_cleaner.clean_cdr_engine import FILENAME
from utils import bq
parser = ap.get_argument_parser()
parser.add_argument(
'--cope_survey_dataset',
action='store',
dest='cope_survey_dataset_id',
help=('Dataset containing the mapping table provided by RDR team. '
'These maps questionnaire_response_ids to cope_months.'),
required=True)
parser.add_argument(
'--cope_survey_table',
action='store',
dest='cope_survey_table',
required=True,
help='Name of the table cotaining the cope survey mapping information')
parser.add_argument(
'--mapping_dataset',
raise NotImplementedError("Please fix me.")
def get_sandbox_tablenames(self):
"""
Generates list of sandbox table names created by this rule.
"""
return [
self.sandbox_table_for(table) for table in self.affected_tables
]
if __name__ == '__main__':
import cdr_cleaner.args_parser as parser
import cdr_cleaner.clean_cdr_engine as clean_engine
ext_parser = parser.get_argument_parser()
ARGS = ext_parser.parse_args()
if ARGS.list_queries:
clean_engine.add_console_logging()
query_list = clean_engine.get_query_list(
ARGS.project_id, ARGS.dataset_id, ARGS.sandbox_dataset_id,
[(RemoveEhrDataWithoutConsent, )])
for query in query_list:
LOGGER.info(query)
else:
clean_engine.add_console_logging(ARGS.console_log)
clean_engine.clean_dataset(ARGS.project_id, ARGS.dataset_id,
ARGS.sandbox_dataset_id, ARGS.cutoff_date,
[(RemoveEhrDataWithoutConsent, )])
select_query[cdr_consts.DESTINATION_DATASET] = sandbox_dataset_id
queries.append(select_query)
update_query = dict()
update_query[cdr_consts.QUERY] = UPDATE_NEGATIVE_PPI_QUERY.format(
project_id=project_id, dataset_id=dataset_id)
queries.append(update_query)
return queries
if __name__ == '__main__':
import cdr_cleaner.args_parser as parser
import cdr_cleaner.clean_cdr_engine as clean_engine
ARGS = parser.get_argument_parser().parse_args()
if ARGS.list_queries:
clean_engine.add_console_logging()
query_list = clean_engine.get_query_list(ARGS.project_id,
ARGS.dataset_id,
ARGS.sandbox_dataset_id,
[(get_update_ppi_queries,)])
for query in query_list:
LOGGER.info(query)
else:
clean_engine.add_console_logging(ARGS.console_log)
clean_engine.clean_dataset(ARGS.project_id, ARGS.dataset_id,
ARGS.sandbox_dataset_id,
[(get_update_ppi_queries,)])
