def cli(ctx, conn_host, database, username, password, port, host, verbose,
logfile, backend):
"""loqusdb: manage a local variant count database."""
# configure root logger to print to STDERR
loglevel = LEVELS.get(min(verbose,1), "INFO")
init_log(
logger = logger,
filename = logfile,
loglevel = loglevel
)
# mongo uri looks like:
#mongodb://[username:password@]host1[:port1][,host2[:port2],...[,hostN[:portN]]][/[database][?options]]
uri = None
if username and password:
uri = "{0}{1}:{2}@{3}:{4}/{5}".format(
conn_host, username, password, host, port, database
)
logger.info('uri={0}'.format(uri))
adapter = MongoAdapter()
adapter.connect(
host=host,
port=port,
database=database,
uri=uri
)
ctx.obj = {}
ctx.obj['db'] = database
ctx.obj['user'] = username
ctx.obj['password'] = password
ctx.obj['port'] = port
ctx.obj['host'] = host
ctx.obj['adapter'] = adapter
def cli(ctx, conn_host, database, username, password, port, host, verbose,
logfile, backend):
"""loqusdb: manage a local variant count database."""
# configure root logger to print to STDERR
loglevel = LEVELS.get(max(verbose, 1), "INFO")
init_log(logger=logger, filename=logfile, loglevel=loglevel)
# mongo uri looks like:
#mongodb://[username:password@]host1[:port1][,host2[:port2],...[,hostN[:portN]]][/[database][?options]]
uri = None
if username and password:
uri = "{0}{1}:{2}@{3}:{4}/{5}".format(conn_host, username, password,
host, port, database)
logger.info('uri={0}'.format(uri))
adapter = MongoAdapter()
adapter.connect(host=host, port=port, database=database, uri=uri)
ctx.obj = {}
ctx.obj['db'] = database
ctx.obj['user'] = username
ctx.obj['password'] = password
ctx.obj['port'] = port
ctx.obj['host'] = host
ctx.obj['adapter'] = adapter
import logging
import pytest
from mongomock import MongoClient
from pymongo import MongoClient as RealMongoClient
from loqusdb.plugins import MongoAdapter
from loqusdb.log import init_log
logger = logging.getLogger('.')
init_log(logger, loglevel='DEBUG')
@pytest.fixture(scope='function')
def mongo_client(request):
"""Return a mongomock client"""
client = MongoClient()
return client
# @pytest.fixture(scope='function')
# def real_mongo_client(request):
# """Return a mongo client"""
# client = RealMongoClient()
#
# def teardown():
# client.drop_database('test')
#
# request.addfinalizer(teardown)
# return client
@pytest.fixture(scope='function')
def mongo_adapter(request, mongo_client):
import logging
import pytest
from mongomock import MongoClient
from pymongo import MongoClient as RealMongoClient
from ped_parser import FamilyParser
from loqusdb.plugins import MongoAdapter
from loqusdb.log import init_log
logger = logging.getLogger('.')
init_log(logger, loglevel='DEBUG')
class Variant(object):
"""Mock a cyvcf variant
Default is to return a variant with three individuals high genotype
quality.
"""
def __init__(self,
chrom='1',
pos=80000,
ref='A',
alt='C',
end=None,
gt_quals=[60, 60, 60],
gt_types=[1, 1, 0]):
super(Variant, self).__init__()
self.CHROM = chrom
import cyvcf2
import pytest
from loqusdb.build_models.case import build_case
from loqusdb.build_models.variant import build_variant
from loqusdb.log import init_log
from loqusdb.models import Case
from loqusdb.plugins.mongo.adapter import MongoAdapter
from loqusdb.utils.load import update_case
from mongomock import MongoClient as MockClient
from ped_parser import FamilyParser
from pymongo import MongoClient
logger = logging.getLogger(".")
init_log(logger, loglevel="DEBUG")
REAL_DATABASE = "loqus-test"
TEST_DATABASE = "test"
class CyvcfVariant(object):
"""Mock a cyvcf variant
Default is to return a variant with three individuals high genotype
quality.
"""
def __init__(
self,
chrom="1",
pos=80000,
