def test_torsiondrive_initial_final_molecule(torsiondrive_fixture,
fractal_compute_server):
""" With single initial molecule in torsion proc"""
torsion, client = torsiondrive_fixture
r = fractal_compute_server.storage.custom_query("torsiondrive",
"initial_molecules_ids",
torsion_id=torsion["id"])
assert r["meta"]["success"]
assert len(r["data"]) == 9
r = fractal_compute_server.storage.custom_query("torsiondrive",
"initial_molecules",
torsion_id=torsion["id"])
assert r["meta"]["success"]
assert len(r["data"]) == 9
mol = r["data"][0]
# Msgpack field
assert isinstance(msgpackext_loads(mol["geometry"]), np.ndarray) # TODO
# Sample fields in the molecule dict
assert all(
x in mol.keys()
for x in ["schema_name", "symbols", "geometry", "molecular_charge"])
r = fractal_compute_server.storage.custom_query("torsiondrive",
"final_molecules_ids",
torsion_id=torsion["id"])
assert r["meta"]["success"]
assert len(r["data"]) == 9
r = fractal_compute_server.storage.custom_query("torsiondrive",
"final_molecules",
torsion_id=torsion["id"])
assert r["meta"]["success"]
assert len(r["data"]) == 9
mol = r["data"][0]
def json_to_msgpack_table_altercolumns(table_name,
update_columns,
nullable_true=None):
if nullable_true is None:
nullable_true = set()
connection = op.get_bind()
table, cols = _intermediate_table(table_name, update_columns)
column_pairs, old_names, new_names = _get_colnames(update_columns)
num_records = connection.execute(
f"select count(*) from {table_name}").scalar()
old_columns = [getattr(table.c, x) for x in old_names]
new_columns = [getattr(table.c, x) for x in new_names]
logger.info(f"Checking converted columns...")
# Pull chunk to migrate
data = connection.execute(
sa.select([
table.c.id,
*old_columns,
*new_columns,
],
order_by=table.c.id.asc())).fetchall()
# ], limit=100, order_by=func.random())).fetchall()
col_names = ["id"] + old_names + new_names
for values in data:
row = {k: v for k, v in zip(col_names, values)}
# print(row["id"])
# print(row.keys())
# for k, v in row.items():
# print(k, v)
for name in old_names:
comp_data = msgpackext_loads(row[name + "_"])
# try:
# assert compare_recursive(comp_data, row[name])
# except AssertionError:
# assert compare_recursive(comp_data.ravel(), row[name], quiet=True)
# try:
# print(name, comp_data.dtype, comp_data)
# except:
# print(name, comp_data[0].dtype, comp_data)
# pass
# raise Exception()
logger.info(f"Dropping old columns and renaming new.")
# Drop old tables and swamp new ones in.
for old_name, new_name in column_pairs:
nullable = False
if old_name in nullable_true:
nullable = True
op.drop_column(table_name, old_name)
op.alter_column(table_name,
new_name,
new_column_name=old_name,
nullable=nullable)
def process_result_value(self, value, dialect):
if value is None:
return value
else:
return msgpackext_loads(value)
def process_result_value(self, value, dialect):
return msgpackext_loads(value)