def test_get_all_available(self):
"""should return a listing of all the available databases on the
indicated server"""
available = get_db_name()
# make sure we have a compara db present -- a crude check on
# correctness
one_valid = False
for db in available:
if db.Type == "compara":
one_valid = True
break
self.assertEqual(one_valid, True)
# now check that when we request available under a specific version
# that we only receive valid ones back
available = get_db_name(release="46")
for db in available:
self.assertEqual(db.Release, '46')
def test_get_all_available(self):
"""should return a listing of all the available databases on the
indicated server"""
available = get_db_name()
# make sure we have a compara db present -- a crude check on
# correctness
one_valid = False
for db in available:
if db.Type == "compara":
one_valid = True
break
self.assertEqual(one_valid, True)
# now check that when we request available under a specific version
# that we only receive valid ones back
available = get_db_name(release="46")
for db in available:
self.assertEqual(db.Release, '46')
def test_getdb(self):
"""should discover human entries correctly"""
for name, db_name in [("human", "homo_sapiens_core_49_36k"),
("mouse", "mus_musculus_core_49_37b"),
("rat", "rattus_norvegicus_core_49_34s"),
("platypus", "ornithorhynchus_anatinus_core_49_1f")]:
result = get_db_name(species=name, db_type="core", release='49')
self.assertEqual(len(result), 1)
result = result[0]
self.assertEqual(result.Name, db_name)
self.assertEqual(result.Release, '49')
def test_getdb(self):
"""should discover human entries correctly"""
for name, db_name in [("human", "homo_sapiens_core_49_36k"),
("mouse", "mus_musculus_core_49_37b"),
("rat", "rattus_norvegicus_core_49_34s"),
("platypus",
"ornithorhynchus_anatinus_core_49_1f")]:
result = get_db_name(species=name, db_type="core", release='49')
self.assertEqual(len(result), 1)
result = result[0]
self.assertEqual(result.Name, db_name)
self.assertEqual(result.Release, '49')
def __init__(self, account, species=None, db_type=None, release=None,
pool_recycle=None, division=None):
self._tables = {}
self.db_name = get_db_name(account=account, species=species,
release=release, db_type=db_type, division=division)
if not self.db_name:
raise RuntimeError, "%s db doesn't exist for '%s' on '%s'" % \
(db_type, species, account.host)
else:
self.db_name = self.db_name[0]
self._db = DbConnection(account=account, db_name=self.db_name,
pool_recycle=pool_recycle)
self._meta = sql.MetaData(self._db)
self.Type = db_type
def __init__(self, account, species=None, db_type=None, release=None,
pool_recycle=None, division=None):
self._tables = {}
self.db_name = get_db_name(account=account, species=species,
release=release, db_type=db_type, division=division)
if not self.db_name:
raise RuntimeError("%s db doesn't exist for '%s' on '%s'" % \
(db_type, species, account.host))
else:
self.db_name = self.db_name[0]
self._db = DbConnection(account=account, db_name=self.db_name,
pool_recycle=pool_recycle)
self._meta = sql.MetaData(self._db)
self.Type = db_type
