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 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 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
