class CGDTestCase(unittest.TestCase):
"""
Test connection, loading, and querying of CGD snapshot
CGDTestCase is an integration test using the Travis CI
testing environment to test with a mysql database
The database is created and populated in the .travis.yml file
"""
def setUp(self):
database = 'cgd_test'
user = '******'
self.cgd_test = CGD(database, user)
self.connection, self.cursor = self.cgd_test._connect_to_database()
return
def tearDown(self):
self.cgd_test._disconnect_from_database(self.cursor, self.connection)
self.cgd_test = None
return
def test_queries(self):
"""
Just checking that these run without errors, probably needs
do so some actual checking of things
:return:
"""
self.cgd_test.check_if_db_is_empty(self.cursor)
# test queries
self.cgd_test.execute_query(self.cursor, self.cgd_test.static_files['disease_drug_variant_query']['file'])
self.cgd_test.execute_query(self.cursor, self.cgd_test.static_files['variant_protein_query']['file'])
self.cgd_test.execute_query(self.cursor, self.cgd_test.static_files['variant_cdna_query']['file'])
self.cgd_test.execute_query(self.cursor, self.cgd_test.static_files['genotypes_with_no_protein_cdna_mapping']['file'])
self.cgd_test.execute_query(self.cursor, self.cgd_test.static_files['fusion_copy_any_mutation_genotypes']['file'])
return
def test_fetch(self):
""".
Just checking that we can fetch sources without errors
:return:
"""
self.cgd_test.fetch()
return
def test_parse(self):
"""
Just checking that we can parse sources without errors
:return:
"""
self.cgd_test.parse()
return
def main():
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
parser = argparse.ArgumentParser(
description='Cancer Knowledge Base Graph'
' Generator',
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('--host',
'-H',
type=str,
default="localhost",
help='Location of MySQL Server')
parser.add_argument('--database', '-D', type=str, help='Name of database')
parser.add_argument('--user', '-u', help='Username')
parser.add_argument('--password', '-p', help='Password')
parser.add_argument('--config',
'-c',
help='Config file, see example '
'formatting in conf directory')
args = parser.parse_args()
# Config file overrides command line credentials
# We need to refactor the Dipper config.py so it is reusable here
if args.config is not None:
credentials = json.load(open(args.config, 'r'))
args.host = credentials['dbauth']['cgd']['host']
args.database = credentials['dbauth']['cgd']['database']
args.user = credentials['dbauth']['cgd']['user']
args.password = credentials['dbauth']['cgd']['password']
if args.password is None:
if sys.stdin.isatty():
args.password = getpass.getpass(prompt="Enter your password: "******"Enter your password: ")
# Parse test source
cgd = CGD(args.database, args.user, args.password, args.host)
cgd.fetch(False)
cgd.parse()
cgd.write(format='turtle')
return