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):
"""loqusdb: manage a local variant count database."""
# configure root logger to print to STDERR
loglevel = LEVELS.get(max(verbose, 1), "INFO")
coloredlogs.install(level=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)
if password:
pwd = '******'
else:
pwd = None
logger.info('uri={0}{1}:{2}@{3}:{4}/{5}'.format(
conn_host, username, pwd, host, port, database))
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 frequency(context, bulk, remove):
"""Upload or remove variants to/from frequency database."""
loqusdb_auth = context.obj.get("loqusdb", {})
adapter = LoqusdbAdapter()
adapter.connect(**loqusdb_auth)
mip_case = context.obj["case"]
if mip_case.is_old:
logger.warn("unsupported MIP version for frequency: %s", mip_case.version)
else:
vcf_path = mip_case.research_vcf
case_group_id = group_id(mip_case)
# we only care about "rare" variants
ped_path = mip_case.configs.pedigree
try:
affected_inds = affected_individuals(ped_path)
except FrequencyError as error:
logger.warn("LOQUSDB: {}".format(error.message))
if "affected_inds" in locals():
with open(vcf_path, "r") as vcf_stream:
try:
if remove:
count = delete_variants(adapter, vcf_stream, case_group_id, affected_inds)
logger.info("removed {} variants".format(count))
else:
load_variants(
adapter, case_group_id, affected_inds, vcf_stream, bulk_insert=bulk, vcf_path=vcf_path
)
except CaseError as error:
logger.warn("LOQUSDB: {}".format(error.message))
def parse_payload(db, payload, config, force=False):
"""Upload frequency to the database."""
loqusdb_auth = config['LOQUSDB_AUTH']
adapter = LoqusdbAdapter()
adapter.connect(**loqusdb_auth)
case_id = payload['case_id']
mip_analysis = load_analysis(payload['family_dir'])
if mip_analysis.is_old:
logger.warn("unsupported MIP version for frequency: %s",
mip_analysis.version)
else:
vcf_path, affected = parse_mip(mip_analysis)
if affected:
upload(adapter, vcf_path, affected, case_id, force=force)
def cli(ctx, database, username, password, authdb, port, host, uri, verbose,
config, test, genome_build):
"""loqusdb: manage a local variant count database."""
loglevel = "INFO"
if verbose:
loglevel = "DEBUG"
coloredlogs.install(level=loglevel)
LOG.info("Running loqusdb version %s", __version__)
configs = {}
if config:
try:
configs = yaml.safe_load(config)
except yaml.YAMLError as err:
LOG.warning(err)
ctx.abort()
uri = configs.get('uri') or uri
if test:
uri = "mongomock://"
try:
client = get_client(
host=configs.get('host') or host,
port=configs.get('port') or port,
username=configs.get('username') or username,
password=configs.get('password') or password,
authdb=authdb or database or 'loqusdb',
uri=uri,
)
except DB_Error as err:
LOG.warning(err)
ctx.abort()
database = configs.get('db_name') or database
if not database:
database = 'loqusdb'
if uri:
uri_info = uri_parser.parse_uri(uri)
database = uri_info.get('database')
adapter = MongoAdapter(client, db_name=database)
genome_build = genome_build or configs.get('genome_build') or GRCH37
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
ctx.obj['version'] = __version__
ctx.obj['genome_build'] = genome_build
def mongo_adapter(request, mongo_client):
"""Return a mongo adapter"""
adapter = MongoAdapter()
adapter.connect(database='test', client=mongo_client)
return adapter
def loqusdb_adapter(mongo_client):
adapter = MongoAdapter()
adapter.connect(database='test', client=mongo_client)
return adapter
def mongo_adapter(request, mongo_client):
"""Return a mongo adapter"""
adapter = MongoAdapter()
adapter.connect(database='test', client=mongo_client)
return adapter
def test_connect_uri(mongo_client):
adapter = MongoAdapter()
uri = "{0}".format("mongodb://localhost")
adapter.connect(uri=uri)
assert True
def test_connect(mongo_client):
adapter = MongoAdapter()
db_name = 'test'
adapter.connect(database=db_name, client=mongo_client)
assert True
def test_init_app(mongo_client):
app = FlaskApp()
app.config['LOQUSDB_URI'] = "mongodb://localhost"
adapter = MongoAdapter()
adapter.init_app(app)
assert True
def real_mongo_adapter(request, real_mongo_client):
"""Return a mongo adapter"""
db_name = REAL_DATABASE
adapter = MongoAdapter(real_mongo_client, db_name)
return adapter
def mongo_adapter(request, mongo_client):
"""Return a mongo adapter"""
db_name = TEST_DATABASE
adapter = MongoAdapter(mongo_client, db_name)
return adapter
def test_init_app(mongo_client):
app = MockFlaskApp()
adapter = MongoAdapter()
adapter.init_app(app)
assert adapter.db_name == app.config['MONGO_DBNAME']
def test_connect(mongo_client):
adapter = MongoAdapter()
db_name = 'test'
adapter.connect(database=db_name, client=mongo_client)
assert True
def test_connect_uri(mongo_client):
adapter = MongoAdapter()
uri = "{0}".format("mongodb://localhost")
adapter.connect(uri=uri)
assert True
