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 __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