def setup_database(request):
"""Setup the mongo adapter"""
print('')
logger.info("Setting up database")
host = 'localhost'
port = 27017
db_name = 'testdatabase'
client = MongoClient(
host=host,
port=port,
)
#Initialize an adapter
adapter = MongoAdapter()
#Connect to the test database
adapter.connect_to_database(
database=db_name,
host=host,
port=port
)
logger.info("Database setup")
def teardown():
print('\n')
logger.info('Teardown database')
client.drop_database(db_name)
logger.info('Teardown done')
request.addfinalizer(teardown)
return adapter
def scout(context):
"""Update sample information for samples from Scout."""
db = context.obj["db"]
mongo_auth = context.obj["SCOUT_AUTH"]
mongo_adapter = MongoAdapter()
mongo_adapter.connect_to_database(**mongo_auth)
process_scout(db, mongo_adapter)
def archive(context):
"""Update sample information for samples from Scout."""
db = context.obj["db"]
mip_root = context.obj["MIP_ANALYSIS_ROOT"]
mongo_auth = context.obj["SCOUT_AUTH"]
mongo_adapter = MongoAdapter()
mongo_adapter.connect_to_database(**mongo_auth)
process_archive(db, mongo_adapter, mip_root)
def queue(context):
"""Add stuff to the queue."""
db = context.obj['db']
mongo_auth = context.obj['SCOUT_AUTH']
mongo_adapter = MongoAdapter()
mongo_adapter.connect_to_database(**mongo_auth)
analyze.trigger(db, context.obj['MIP_CUST_ROOTS'])
visualize.trigger(db, mongo_adapter)
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
def setup_loaded_database(request):
"""Setup a mongo databse with loaded variants"""
print('')
logger.info("Setting up database and populate it")
host = 'localhost'
port = 27017
db_name = 'testdatabase'
client = MongoClient(
host=host,
port=port,
)
#Initialize an adapter
adapter = MongoAdapter()
#Connect to the test database
adapter.connect_to_database(
database=db_name,
host=host,
port=port
)
scout_configs = ConfigObj(scout_config)
case = adapter.add_case(
case_lines=open(scout_configs['ped'], 'r'),
case_type='ped',
owner=scout_configs['owner'],
scout_configs=scout_configs
)
adapter.add_variants(
vcf_file=scout_configs['load_vcf'],
variant_type='clinical',
case=case,
)
logger.info("Database setup")
def teardown():
print('\n')
logger.info('Teardown database')
client.drop_database(db_name)
logger.info('Teardown done')
request.addfinalizer(teardown)
return adapter
