def cli(ctx, mongodb, username, password, host, port, logfile, loglevel,
config):
"""Manage Scout interactions."""
init_log(logger, logfile, loglevel)
mongo_configs = {}
configs = {}
if config:
logger.info("Use config file {0}".format(config))
configs = ConfigObj(config)
if mongodb:
mongo_configs['mongodb'] = mongodb
else:
mongo_configs['mongodb'] = configs.get('mongodb', 'variantDatabase')
logger.info("Setting mongodb to {0}".format(mongo_configs['mongodb']))
if host:
mongo_configs['host'] = host
else:
mongo_configs['host'] = configs.get('host', 'localhost')
logger.info("Setting host to {0}".format(mongo_configs['host']))
if port:
mongo_configs['port'] = port
else:
mongo_configs['port'] = int(configs.get('port', 27017))
logger.info("Setting port to {0}".format(mongo_configs['port']))
if username:
mongo_configs['username'] = username
else:
mongo_configs['username'] = configs.get('username')
if password:
mongo_configs['password'] = password
else:
mongo_configs['password'] = configs.get('password')
logger.info("Setting up a mongo adapter")
mongo_adapter = MongoAdapter()
logger.info("Connecting to database")
mongo_adapter.connect_to_database(
database=mongo_configs['mongodb'],
host=mongo_configs['host'],
port=mongo_configs['port'],
username=mongo_configs['username'],
password=mongo_configs['password']
)
mongo_configs['adapter'] = mongo_adapter
ctx.obj = mongo_configs
# We will use mongomock when mongoengine allows it
# from mongomock import MongoClient
from pymongo import MongoClient
from mongoengine import DoesNotExist
from configobj import ConfigObj
from vcf_parser import VCFParser
from scout.ext.backend import MongoAdapter
from scout.models import (Variant, Case, Event, Institute, PhenotypeTerm,
Institute, User)
from scout.commands import cli
from scout.log import init_log
root_logger = logging.getLogger()
init_log(root_logger, loglevel='INFO')
logger = logging.getLogger(__name__)
vcf_file = "tests/fixtures/337334.clinical.vcf"
one_variant = "tests/fixtures/337334.one_variant.clinical.vcf"
ped_file = "tests/fixtures/337334.ped"
scout_config = "tests/fixtures/scout_config_test.ini"
gene_list_file = "tests/fixtures/gene_lists/gene_list_test.txt"
madeline_file = "tests/fixtures/madeline.xml"
@pytest.fixture(scope='function')
def variant_file(request):
"""Get the path to a variant file"""
print('')
return vcf_file
research_sv_path,
clinical_snv_path,
clinical_sv_path,
ped_path,
load_path,
panel_path,
empty_sv_clinical_path,
)
from scout.models.hgnc_map import HgncGene
DATABASE = 'testdb'
REAL_DATABASE = 'realtestdb'
root_logger = logging.getLogger()
init_log(root_logger, loglevel='INFO')
LOG = logging.getLogger(__name__)
#############################################################
###################### App fixtures #########################
#############################################################
# use this app object to test CLI commands which use a test database
@pytest.fixture
def mock_app(real_populated_database):
mock_app = create_app(config=dict(TESTING=True,
DEBUG=True,
MONGO_DBNAME=REAL_DATABASE,
DEBUG_TB_ENABLED=False,
@click.option("-v", "--verbose", is_flag=True, help="Increase output verbosity.")
def delete_case(case_id, owner, mongo_db, username, password, port, host, verbose):
"""
Delete a case and all of its variants from the mongo database.
"""
logger = logging.getLogger("scout.commands.delete_case")
logger.info("Running delete_case")
if not mongo_db:
logger.warning("Please specify a database to wipe and populate" " with flag '-db/--mongo-db'.")
sys.exit(0)
if not case_id:
logger.warning("Please specify the id of the case that should be deleted" " with flag '-c/--case_id'.")
sys.exit(0)
if not owner:
logger.warning("Please specify the owner of the case that should be deleted" " with flag '-o/--owner'.")
sys.exit(0)
remove_case(case_id, owner, mongo_db, username, password, port, host, logger)
if __name__ == "__main__":
from scout.log import init_log
logger = logging.getLogger("scout")
init_log(logger, loglevel="DEBUG")
delete_case()
Delete a case and all of its variants from the mongo database.
"""
logger = logging.getLogger('scout.commands.delete_case')
logger.info("Running delete_case")
if not mongo_db:
logger.warning("Please specify a database to wipe and populate"\
" with flag '-db/--mongo-db'.")
sys.exit(0)
if not case_id:
logger.warning("Please specify the id of the case that should be deleted"\
" with flag '-c/--case_id'.")
sys.exit(0)
if not owner:
logger.warning("Please specify the owner of the case that should be deleted"\
" with flag '-o/--owner'.")
sys.exit(0)
remove_case(case_id, owner, mongo_db, username, password, port, host,
logger)
if __name__ == '__main__':
from scout.log import init_log
logger = logging.getLogger('scout')
init_log(logger, loglevel='DEBUG')
delete_case()
