def post(self):
"""Load a case into Scout."""
variant_threshold = request.form.get('variant_threshold', 5000)
variant_type = request.form.get('variant_type', 'clinical')
vcf_config = (request.form.get('vcf_config') or
current_app.config['SCOUT_VCF_CONFIG'])
mongo_info = current_app.config['SCOUT_MONGODB_SETTINGS']
mongo_auth = {}
for key, value in iteritems(mongo_info):
if key == 'db':
mongo_auth['mongo_db'] = value
else:
mongo_auth[key] = value
scout_config_path = request.form['scout_config']
scout_config = ConfigParser(scout_config_path)
load_mongo_db(scout_config, vcf_config, variant_type=variant_type,
variant_number_threshold=variant_threshold, **mongo_auth)
return jsonify(success=True)
def load_case(
self, scout_config_path, variant_type="clinical", vcf_config=None, variant_threshold=5000, mongo_auth=None
):
"""Load a case into Scout."""
vcf_config = vcf_config or self.config["scout"]["vcf_config"]
if mongo_auth is None:
# adapt to scout input
mongo_info = self.config["scout"]["auth"]
mongo_auth = {}
for key, value in iteritems(mongo_info):
if key == "db":
mongo_auth["mongo_db"] = value
else:
mongo_auth[key] = value
scout_config = ConfigParser(scout_config_path)
vcf = load_mongo_db(
scout_config,
vcf_config,
variant_type=variant_type,
variant_number_threshold=variant_threshold,
**mongo_auth
)
return vcf
def load(vcf_file, ped_file, scout_config_file, vcf_config_file, family_type,
mongo_db, username, variant_type, madeline, coverage_report, password,
owner, port, host, verbose, rank_score_threshold,
variant_number_threshold):
"""
Load the mongo database.
Command line arguments will override what's in the config file.
"""
# Check if vcf file exists and that it has the correct naming:
logger = logging.getLogger(__name__)
scout_configs = {}
scout_validation_file = os.path.join(BASE_PATH,
'config_spec/scout_config.ini')
logger.info("Running load_mongo")
if scout_config_file:
scout_configs = ConfigParser(scout_config_file,
configspec=scout_validation_file)
logger.info("Using scout config file {0}".format(scout_config_file))
if vcf_file:
scout_configs['load_vcf'] = vcf_file
logger.info("Using command line specified vcf {0}".format(vcf_file))
scout_configs['igv_vcf'] = vcf_file
if ped_file:
logger.info(
"Using command line specified ped file {0}".format(ped_file))
scout_configs['ped'] = ped_file
if madeline:
logger.info(
"Using command line specified madeline file {0}".format(madeline))
scout_configs['madeline'] = madeline
if coverage_report:
logger.info("Using command line specified coverage report {0}".format(
coverage_report))
scout_configs['coverage_report'] = coverage_report
if owner:
logger.info("Using command line specified owner {0}".format(institute))
scout_configs['owner'] = owner
if not scout_configs.get('load_vcf', None):
logger.warning(
"Please provide a vcf file.(Use flag '-vcf/--vcf_file')")
sys.exit(0)
# Check that the ped file is provided:
if not scout_configs.get('ped', None):
logger.warning(
"Please provide a ped file.(Use flag '-ped/--ped_file')")
sys.exit(0)
# Check that the config file is provided:
if not vcf_config_file:
logger.warning(
"Please provide a vcf config file.(Use flag '-config/--config_file')"
)
sys.exit(0)
my_vcf = load_mongo_db(scout_configs,
vcf_config_file,
family_type,
mongo_db=mongo_db,
username=username,
password=password,
variant_type=variant_type,
port=port,
host=host,
rank_score_threshold=rank_score_threshold,
variant_number_threshold=variant_number_threshold)
