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import os
import pytest
from ase.db import connect
from ase import Atoms
from ase.calculators.emt import EMT
from ase.build import molecule
@pytest.fixture(scope='module')
def url():
pytest.importorskip('pymysql')
on_ci_server = 'CI_PROJECT_DIR' in os.environ
if on_ci_server:
db_url = 'mysql://root:ase@mysql:3306/testase_mysql'
# HOST = 'mysql'
# USER = 'root'
# PASSWD = 'ase'
# DB_NAME = 'testase_mysql'
else:
db_url = os.environ.get('MYSQL_DB_URL')
# HOST = os.environ.get('MYSQL_HOST', None)
# USER = os.environ.get('MYSQL_USER', None)
# PASSWD = os.environ.get('MYSQL_PASSWD', None)
# DB_NAME = os.environ.get('MYSQL_DB_NAME', None)
if db_url is None:
msg = ('Not on GitLab CI server. To run this test '
'host, username, password and database name '
'must be in the environment variables '
'MYSQL_HOST, MYSQL_USER, MYSQL_PASSWD and '
'MYSQL_DB_NAME, respectively.')
pytest.skip(msg)
return db_url
@pytest.fixture
def db(url):
return connect(url)
@pytest.fixture
def h2o():
return molecule('H2O')
def test_connect(db):
db.delete([row.id for row in db.select()])
def test_write_read(db):
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, 1.1)])
uid = db.write(co, tag=1, type='molecule')
co_db = db.get(id=uid)
atoms_db = co_db.toatoms()
assert len(atoms_db) == 2
assert atoms_db[0].symbol == co[0].symbol
assert atoms_db[1].symbol == co[1].symbol
assert co_db.tag == 1
assert co_db.type == 'molecule'
def test_write_read_with_calculator(db, h2o):
calc = EMT(dummy_param=2.4)
h2o.calc = calc
uid = db.write(h2o)
h2o_db = db.get(id=uid).toatoms(attach_calculator=True)
calc_db = h2o_db.calc
assert calc_db.parameters['dummy_param'] == 2.4
# Check that get_atoms function works
db.get_atoms(H=2)
def test_update(db, h2o):
h2o = molecule('H2O')
uid = db.write(h2o, type='molecule')
db.update(id=uid, type='oxide')
atoms_type = db.get(id=uid).type
assert atoms_type == 'oxide'
def test_delete(db, h2o):
h2o = molecule('H2O')
uid = db.write(h2o, type='molecule')
# Make sure that we can get the value
db.get(id=uid)
db.delete([uid])
with pytest.raises(KeyError):
db.get(id=uid)
def test_read_write_bool_key_value_pair(db, h2o):
# Make sure we can read and write boolean key value pairs
uid = db.write(h2o, is_water=True, is_solid=False)
row = db.get(id=uid)
assert row.is_water
assert not row.is_solid
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