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import os
import pytest
from ase.db import connect
from ase import Atoms
import numpy as np
def test_sql_db_ext_tables(psycopg2):
DB_NAMES = ["test_ext_tables.db", "postgresql", "mysql", "mariadb"]
def get_db_name(name):
if name == 'postgresql':
if os.environ.get('POSTGRES_DB'): # gitlab-ci
name = 'postgresql://ase:ase@postgres:5432/testase'
else:
name = os.environ.get('ASE_TEST_POSTGRES_URL')
elif name == "mysql":
if os.environ.get('CI_PROJECT_DIR'): # gitlab-ci
name = 'mysql://root:ase@mysql:3306/testase_mysql'
else:
name = os.environ.get('MYSQL_DB_URL')
elif name == 'mariadb':
if os.environ.get('CI_PROJECT_DIR'): # gitlab-ci
name = 'mariadb://root:ase@mariadb:3306/testase_mysql'
else:
name = os.environ.get('MYSQL_DB_URL')
return name
def test_create_and_delete_ext_tab(db_name):
ext_tab = ["tab1", "tab2", "tab3"]
atoms = Atoms()
db = connect(name)
db.write(atoms)
for tab in ext_tab:
db._create_table_if_not_exists(tab, "INTEGER")
current_ext_tables = db._get_external_table_names()
for tab in ext_tab:
assert tab in current_ext_tables
db.delete_external_table("tab1")
assert "tab1" not in db._get_external_table_names()
def test_insert_in_external_tables(db_name):
atoms = Atoms()
db = connect(db_name)
# Now a table called insert_tab with schema datatype REAL should
# be created
uid = db.write(
atoms,
external_tables={
"insert_tab": {
"rate": 1.0,
"rate1": -
2.0}})
db.delete([uid])
# Hack: retrieve the connection
con = db._connect()
cur = con.cursor()
sql = "SELECT * FROM insert_tab WHERE ID=?"
cur.execute(sql, (uid,))
entries = [x for x in cur.fetchall()]
if db.connection is None:
con.close()
assert not entries
# Make sure that there are now entries in the
# external table with current uid
# Try to insert something that should not pass
# i.e. string value into the same table
with pytest.raises(ValueError):
db.write(atoms, external_tables={"insert_tab": {"rate": "something"}})
# Try to insert Numpy floats
db.write(atoms, external_tables={"insert_tab": {"rate": np.float32(1.0)}})
db.write(atoms, external_tables={"insert_tab": {"rate": np.float64(1.0)}})
# Make sure that we cannot insert a Numpy integer types into
# a float array
with pytest.raises(ValueError):
db.write(
atoms, external_tables={
"insert_tab": {
"rate": np.int32(1.0)}})
with pytest.raises(ValueError):
db.write(
atoms, external_tables={
"insert_tab": {
"rate": np.int64(1.0)}})
# Create a new table should have INTEGER types
db.write(atoms, external_tables={"integer_tab": {"rate": 1}})
# Make sure we can insert Numpy integers
db.write(atoms, external_tables={"integer_tab": {"rate": np.int32(1)}})
db.write(atoms, external_tables={"integer_tab": {"rate": np.int64(1)}})
# Make sure that we cannot insert float
with pytest.raises(ValueError):
db.write(
atoms, external_tables={
"integer_tab": {
"rate": np.float32(1)}})
with pytest.raises(ValueError):
db.write(
atoms, external_tables={
"integer_tab": {
"rate": np.float64(1)}})
# Make sure that ValueError is raised with mixed datatypes
with pytest.raises(ValueError):
db.write(
atoms,
external_tables={
"integer_tab": {
"rate": 1,
"rate2": 2.0}})
# Test that we cannot insert anything into a reserved table name
from ase.db.sqlite import all_tables
for tab_name in all_tables:
with pytest.raises(ValueError):
db.write(atoms, external_tables={tab_name: {"value": 1}})
def test_extract_from_table(db_name):
atoms = Atoms()
db = connect(db_name)
uid = db.write(
atoms,
external_tables={
"insert_tab": {
"rate": 12.0,
"rate1": -
10.0}})
row = db.get(id=uid)
assert abs(row["insert_tab"]["rate"] - 12.0) < 1E-8
assert abs(row["insert_tab"]["rate1"] + 10.0) < 1E-8
def test_write_atoms_row(db_name):
atoms = Atoms()
db = connect(db_name)
uid = db.write(
atoms, external_tables={"insert_tab": {"rate": 12.0, "rate1": -10.0},
"another_tab": {"somevalue": 1.0}})
row = db.get(id=uid)
# Hack: Just change the unique ID
row["unique_id"] = "uniqueIDTest"
db.write(row)
def test_external_table_upon_update(db_name):
db = connect(db_name)
no_features = 500
ext_table = dict((i, i) for i in range(no_features))
atoms = Atoms('Pb', positions=[[0, 0, 0]])
uid = db.write(atoms)
db.update(uid, external_tables={'sys': ext_table})
def test_external_table_upon_update_with_float(db_name):
db = connect(db_name)
ext_table = {'value1': 1.0, 'value2': 2.0}
atoms = Atoms('Pb', positions=[[0, 0, 0]])
uid = db.write(atoms)
db.update(uid, external_tables={'float_table': ext_table})
for db_name in DB_NAMES:
name = get_db_name(db_name)
if name is None:
continue
if db_name in ["postgresql", "mysql", "mariadb"]:
c = connect(name)
c.delete([row.id for row in c.select()])
test_create_and_delete_ext_tab(name)
test_insert_in_external_tables(name)
test_extract_from_table(name)
test_write_atoms_row(name)
test_external_table_upon_update(name)
test_external_table_upon_update_with_float(name)
if db_name not in ["postgresql", "mysql", "mariadb"]:
os.remove(name)
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