def test_get_ensembl_account(self):
"""return an HostAccount with correct port"""
for release in [48, "48", None]:
act_new = get_ensembl_account(release=ENSEMBL_RELEASE)
self.assertEqual(act_new.port, 5306)
for release in [45, "45"]:
act_old = get_ensembl_account(release=45)
self.assertEqual(act_old.port, 3306)
def test_active_connections(self):
"""connecting to a database on a specified server should be done once
only, but same database on a different server should be done"""
ensembl_acct = get_ensembl_account(release="46")
engine1 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h")
engine2 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h")
self.assertEqual(engine1, engine2)
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "BSD"
__version__ = "3.0a1"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
if "ENSEMBL_ACCOUNT" in os.environ:
args = os.environ["ENSEMBL_ACCOUNT"].split()
host, username, password = args[0:3]
kwargs = {}
if len(args) > 3:
kwargs["port"] = int(args[3])
account = HostAccount(host, username, password, **kwargs)
else:
account = get_ensembl_account(release=ENSEMBL_RELEASE)
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(species="chicken",
release=ENSEMBL_RELEASE,
account=account)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels("chicken")
chicken_feature_levels = ChickenFeatureLevels(
feature_types=["gene", "cpg", "est"],
core_db=self.chicken.CoreDb,
otherfeature_db=self.chicken.OtherFeaturesDb,
)
def test_pool_recycle_option(self):
"""excercising ability to specify a pool recycle option"""
ensembl_acct = get_ensembl_account(release="56")
engine1 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h",
pool_recycle=1000)