def db_connector(configuration_file, collection_config_key="mongo_encode_stats_collection"):
"""Connects to MongoDB instance
Parameters
----------
configuration_file: string
Path to configuration file
collection_config_key: string
Key used in config file for collection name under [mongo] section
Returns
-------
collection: mongodb collection
"""
config = ConfigurationParser(configuration_file)
mongo_config = config.get_section("mongo")
mongo_client = MongoClient(
"mongodb://{}:{}@{}/{}".format(
mongo_config["mongo_username"],
mongo_config["mongo_password"],
mongo_config["mongo_host"],
mongo_config["mongo_dbname"],
),
port=int(mongo_config["mongo_port"]),
)
db = mongo_client.moca_encode_tf
collection = db[mongo_config["mongo_encode_stats_collection"]]
return collection
def init_params(configuration_file):
config = ConfigurationParser(configuration_file)
server_config = config.get_section('server')
server_config = dict( (key.upper(), value) for key, value in list(server_config.items()))
for key, value in list(server_config.items()):
try:
# For integer
app.config[key] = int(value)
except ValueError:
app.config[key] = value
class TestConfigParser(unittest.TestCase):
"""Test configurationparser"""
def setUp(self):
self.config_file = 'tests/data/application.cfg'
self.parsed_config = ConfigurationParser(self.config_file)
def test_sections(self):
"""Test configuration sections"""
sections = self.parsed_config.get_all_sections()
assert 'binaries' in sections
def test_get_section(self):
"""Test configuration sections"""
section_dict = self.parsed_config.get_section('mongo')
assert 'mongo_host' in section_dict.keys()
def test_genomes(self):
"""Test configuration genomes"""
genomes = self.parsed_config.get_all_genomes()
assert 'hg19' in genomes
def setUp(self):
self.config_file = 'tests/data/application.cfg'
self.parsed_config = ConfigurationParser(self.config_file)
