def create_parser() -> FileAwareParser:
"""
Create a command line parser
:return: parser
"""
parser = FileAwareParser(
description="Clear data from FHIR observation fact table",
prog="removefacts",
use_defaults=False)
parser.add_argument("-ss",
"--sourcesystem",
metavar="SOURCE SYSTEM CODE",
help="Sourcesystem code")
parser.add_argument(
"-u",
"--uploadid",
metavar="UPLOAD IDENTIFIER",
help="Upload identifer -- uniquely identifies this batch",
type=int,
nargs='*')
add_connection_args(parser, strong_config_file=False)
parser.add_argument(
"-p",
"--testprefix",
metavar="SS PREFIX",
help=
f"Sourcesystem_cd prefix for test suite functions (Default: {default_test_prefix}"
)
parser.add_argument("--testlist",
help="List leftover test suite entries",
action="store_true")
parser.add_argument("--removetestlist",
help="Remove leftover test suite entries",
action="store_true")
return parser
def parse_args(argv: List[str]) -> Optional[argparse.Namespace]:
"""
Parse i2b2 connection arguments
:param argv: Arguments
:return: parsed arguments if success otherwise nothing
"""
parser = FileAwareParser(description="Iterate over table_access table",
prog="table_access")
add_connection_args(parser)
opts, _ = parser.parse_known_args(parser.decode_file_args(argv))
return opts
def test_decodefileargs1(self):
from i2b2model.sqlsupport.dbconnection import add_connection_args
parser = FileAwareParser()
parser.add_argument('-mv', '--metadatavoc', help="Unused")
add_connection_args(parser)
opts = parser.parse_args(
parser.decode_file_args(
f"--conf {os.path.join(self.conf_dir, 'db_conf')}".split()))
self.assertEqual("postgresql+psycopg2://localhost:5432/i2b2",
opts.crcdb)
self.assertEqual("postgresql+psycopg2://localhost:5433/i2b2",
opts.ontodb)
self.assertEqual("postgresql+psycopg2://localhost:5431/i2b2",
opts.dburl)
self.assertEqual('../tests/data/fhir_metadata_vocabulary',
opts.metadatavoc)
self.assertEqual('postgres', opts.user)
self.assertEqual('postgres', opts.password)
def test_decodefileargs2(self):
from i2b2model.sqlsupport.dbconnection import add_connection_args
parser = FileAwareParser()
add_connection_args(parser)
opts = process_parsed_args(
parser.parse_args(
parser.decode_file_args("--conf {}".format(
os.path.join(self.conf_dir, 'db_conf_2')).split())), None,
False)
self.assertEqual("postgresql+psycopg2://localhost:5431/i2b2",
opts.crcdb)
self.assertEqual("user2", opts.crcuser)
self.assertEqual("password1", opts.crcpassword)
self.assertEqual("postgresql+psycopg2://localhost:5433/i2b2",
opts.ontodb)
self.assertEqual("postgresql+psycopg2://localhost:5431/i2b2",
opts.dburl)
self.assertEqual('user1', opts.ontouser)
self.assertEqual('password1', opts.ontopassword)
def create_parser() -> FileAwareParser:
""" Create a parser for unit testing """
parser = FileAwareParser(description="Test connection")
parser.add_argument("-l",
"--load",
help="Load i2b2 SQL tables",
action="store_true")
parser.add_argument(
"-u",
"--uploadid",
metavar="Upload identifier",
help="Upload identifer -- uniquely identifies this batch",
type=int,
required=True)
return add_connection_args(parser)