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test_sqlalchemy.py
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test_sqlalchemy.py
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"""
Unit tests of the SQLAlchemt to PostgreSQL interface to MongoDB
Does not use portal or fractal server interfaces.
"""
from time import time
import pytest
from sqlalchemy.orm import joinedload
import qcfractal.interface as ptl
from qcfractal.services.services import TorsionDriveService
from qcfractal.storage_sockets.models import (
KVStoreORM,
MoleculeORM,
OptimizationHistory,
OptimizationProcedureORM,
ResultORM,
ServiceQueueORM,
TaskQueueORM,
TorsionDriveProcedureORM,
Trajectory,
)
from qcfractal.testing import sqlalchemy_socket_fixture as storage_socket
def session_delete_all(session, className):
rows = session.query(className).all()
for row in rows:
session.delete(row)
session.commit()
return len(rows)
@pytest.fixture(scope="function")
def session(storage_socket):
session = storage_socket.Session()
try:
yield session
session.commit()
except:
session.rollback()
raise
finally:
session.close()
@pytest.fixture
def molecules_H4O2(storage_socket):
water = ptl.data.get_molecule("water_dimer_minima.psimol")
water2 = ptl.data.get_molecule("water_dimer_stretch.psimol")
ret = storage_socket.add_molecules([water, water2])
yield list(ret["data"])
r = storage_socket.del_molecules(molecule_hash=[water.get_hash(), water2.get_hash()])
assert r == 2
@pytest.fixture
def kw_fixtures(storage_socket):
kw1 = ptl.models.KeywordSet(**{"values": {"something": "kwfixture"}})
ret = storage_socket.add_keywords([kw1])
yield list(ret["data"])
r = storage_socket.del_keywords(ret["data"][0])
assert r == 1
@pytest.mark.parametrize("compression", ptl.models.CompressionEnum)
@pytest.mark.parametrize("compression_level", [None, 1, 5])
def test_kvstore(session, compression, compression_level):
assert session.query(KVStoreORM).count() == 0
input_str = "This is some input "*10
kv = ptl.models.KVStore.compress(input_str, compression, compression_level)
log = KVStoreORM(**kv.dict())
session.add(log)
session.commit()
q = session.query(KVStoreORM).one()
# TODO - remove the exclude once all data is migrated in DB
# (there will be no "value" in the ORM anymore
kv2 = ptl.models.KVStore(**q.to_dict(exclude=["value"]))
assert kv2.get_string() == input_str
assert kv2.compression is compression
session_delete_all(session, KVStoreORM)
def test_old_kvstore(storage_socket, session):
'''
Tests retrieving old data from KVStore
TODO: Remove once entire migration is complete
'''
assert session.query(KVStoreORM).count() == 0
input_str = "This is some input "*10
# Manually create the ORM, setting only the 'value' member
# (This replicates what an existing database would have)
log = KVStoreORM(value=input_str)
session.add(log)
session.commit()
# Now query through the interface
q = storage_socket.get_kvstore([log.id])['data'][str(log.id)]
assert q.data.decode() == input_str
assert q.compression is ptl.models.CompressionEnum.none
assert q.compression_level == 0
session_delete_all(session, KVStoreORM)
def test_molecule_sql(storage_socket, session):
"""
Test the use of the ME class MoleculeORM
Note:
creation of a MoleculeORM using ME is not implemented yet
Should create a MoleculeORM using: mongoengine_socket.add_molecules
"""
num_mol_in_db = session.query(MoleculeORM).count()
# MoleculeORM.objects().delete()
assert num_mol_in_db == 0
water = ptl.data.get_molecule("water_dimer_minima.psimol")
water2 = ptl.data.get_molecule("water_dimer_stretch.psimol")
# Add MoleculeORM
ret = storage_socket.add_molecules([water, water2])
assert ret["meta"]["success"] is True
assert ret["meta"]["n_inserted"] == 2
ret = storage_socket.get_molecules()
assert ret["meta"]["n_found"] == 2
# Use the ORM class
water_mol = session.query(MoleculeORM).first()
assert water_mol.molecular_formula == "H4O2"
assert water_mol.molecular_charge == 0
# print(water_mol.dict())
#
# Query with fields in the model
result_list = session.query(MoleculeORM).filter_by(molecular_formula="H4O2").all()
assert len(result_list) == 2
assert result_list[0].molecular_multiplicity == 1
# Query with fields NOT in the model. works too!
result_list = session.query(MoleculeORM).filter_by(molecular_charge=0).all()
assert len(result_list) == 2
# get unique by hash and formula
one_mol = session.query(MoleculeORM).filter_by(
molecule_hash=water_mol.molecule_hash, molecular_formula=water_mol.molecular_formula
)
assert len(one_mol.all()) == 1
# Clean up
storage_socket.del_molecules(molecule_hash=[water.get_hash(), water2.get_hash()])
def test_services(storage_socket, session):
assert session.query(OptimizationProcedureORM).count() == 0
proc_data = {
"initial_molecule": None,
"keywords": None,
"program": "p7",
"qc_spec": {"basis": "b1", "program": "p1", "method": "m1", "driver": "energy"},
"status": "COMPLETE",
}
service_data = {
"tag": "tag1 tag2",
"hash_index": "123",
"status": "COMPLETE",
"optimization_program": "gaussian",
# extra fields
"torsiondrive_state": {},
"dihedral_template": "1",
"optimization_template": "2",
"molecule_template": "",
"logger": None,
"storage_socket": storage_socket,
"task_priority": 0,
}
procedure = OptimizationProcedureORM(**proc_data)
session.add(procedure)
session.commit()
assert procedure.id
service_pydantic = TorsionDriveService(**service_data)
doc = ServiceQueueORM(**service_pydantic.dict(include=set(ServiceQueueORM.__dict__.keys())))
doc.extra = service_pydantic.dict(exclude=set(ServiceQueueORM.__dict__.keys()))
doc.procedure_id = procedure.id
doc.priority = doc.priority.value # Special case where we need the value not the enum
session.add(doc)
session.commit()
session.delete(doc)
session.delete(procedure)
session.commit()
assert session.query(ServiceQueueORM).count() == 0
def test_results_sql(storage_socket, session, molecules_H4O2, kw_fixtures):
"""
Handling results throught the ME classes
"""
assert session.query(ResultORM).count() == 0
assert len(molecules_H4O2) == 2
assert len(kw_fixtures) == 1
page1 = {
"molecule": molecules_H4O2[0],
"method": "m1",
"basis": "b1",
"keywords": None,
"program": "p1",
"driver": "energy",
"status": "COMPLETE",
}
page2 = {
"molecule": molecules_H4O2[1],
"method": "m2",
"basis": "b1",
"keywords": kw_fixtures[0],
"program": "p1",
"driver": "energy",
"status": "COMPLETE",
}
result = ResultORM(**page1)
session.add(result)
session.commit()
# IMPORTANT: To be able to access lazy loading children use joinedload
ret = session.query(ResultORM).options(joinedload("molecule_obj")).filter_by(method="m1").first()
assert ret.molecule_obj.molecular_formula == "H4O2"
# Accessing the keywords_obj will issue a DB access
assert ret.keywords_obj == None
result2 = ResultORM(**page2)
session.add(result2)
session.commit()
ret = session.query(ResultORM).options(joinedload("molecule_obj")).filter_by(method="m2").first()
assert ret.molecule_obj.molecular_formula == "H4O2"
assert ret.method == "m2"
# clean up
session_delete_all(session, ResultORM)
def test_optimization_procedure(storage_socket, session, molecules_H4O2):
"""
Optimization procedure
"""
assert session.query(OptimizationProcedureORM).count() == 0
# assert Keywords.objects().count() == 0
data1 = {
"initial_molecule": molecules_H4O2[0],
"keywords": None,
"program": "p7",
"qc_spec": {"basis": "b1", "program": "p1", "method": "m1", "driver": "energy"},
"status": "COMPLETE",
}
result1 = {
"molecule": molecules_H4O2[0],
"method": "m1",
"basis": "b1",
"keywords": None,
"program": "p1",
"driver": "energy",
"status": "COMPLETE",
}
procedure = OptimizationProcedureORM(**data1)
session.add(procedure)
session.commit()
proc = session.query(OptimizationProcedureORM).options(joinedload("initial_molecule_obj")).first()
assert proc.initial_molecule_obj.molecular_formula == "H4O2"
assert proc.procedure == "optimization"
# add a trajectory result
result = ResultORM(**result1)
session.add(result)
session.commit()
assert result.id
# link result to the trajectory
proc.trajectory_obj = [Trajectory(opt_id=proc.id, result_id=result.id)]
session.commit()
proc = session.query(OptimizationProcedureORM).options(joinedload("trajectory_obj")).first()
assert proc.trajectory_obj
# clean up
session_delete_all(session, ResultORM)
session_delete_all(session, OptimizationProcedureORM)
def test_torsiondrive_procedure(storage_socket, session):
"""
Torsiondrive procedure
"""
assert session.query(TorsionDriveProcedureORM).count() == 0
# assert Keywords.objects().count() == 0
# molecules = MoleculeORM.objects(molecular_formula='H4O2')
# assert molecules.count() == 2
data1 = {
# "molecule": molecules[0],
"keywords": None,
"program": "p9",
"qc_spec": {"basis": "b1", "program": "p1", "method": "m1", "driver": "energy"},
"status": "COMPLETE",
}
torj_proc = TorsionDriveProcedureORM(**data1)
session.add(torj_proc)
session.commit()
# Add optimization_history
opt_proc = OptimizationProcedureORM(**data1)
opt_proc2 = OptimizationProcedureORM(**data1)
session.add_all([opt_proc, opt_proc2])
session.commit()
assert opt_proc.id
opt_hist = OptimizationHistory(torsion_id=torj_proc.id, opt_id=opt_proc.id, key="20")
opt_hist2 = OptimizationHistory(torsion_id=torj_proc.id, opt_id=opt_proc2.id, key="20")
torj_proc.optimization_history_obj = [opt_hist, opt_hist2]
session.commit()
torj_proc = session.query(TorsionDriveProcedureORM).options(joinedload("optimization_history_obj")).first()
assert torj_proc.optimization_history == {"20": [str(opt_proc.id), str(opt_proc2.id)]}
# clean up
session_delete_all(session, OptimizationProcedureORM)
session_delete_all(session, TorsionDriveProcedureORM)
def test_add_task_queue(storage_socket, session, molecules_H4O2):
"""
Simple test of adding a task using the SQL classes
in QCFractal, tasks should be added using storage_socket
"""
assert session.query(TaskQueueORM).count() == 0
# TaskQueueORM.objects().delete()
page1 = {
"molecule": molecules_H4O2[0],
"method": "m1",
"basis": "b1",
"keywords": None,
"program": "p1",
"driver": "energy",
}
# add a task that reference results
result = ResultORM(**page1)
session.add(result)
session.commit()
task = TaskQueueORM(base_result_obj=result, spec={"something": True})
session.add(task)
session.commit()
ret = session.query(TaskQueueORM)
assert ret.count() == 1
task = ret.first()
assert task.status == "WAITING"
assert task.base_result_obj.status == "INCOMPLETE"
# cleanup
session_delete_all(session, TaskQueueORM)
session_delete_all(session, ResultORM)
def test_results_pagination(storage_socket, session, molecules_H4O2, kw_fixtures):
"""
Test results pagination
"""
assert session.query(ResultORM).count() == 0
result_template = {
"molecule": molecules_H4O2[0],
"method": "m1",
"basis": "b1",
"keywords": kw_fixtures[0],
"program": "p1",
"driver": "energy",
}
# Save ~ 1 msec/doc in ME, 0.5 msec/doc in SQL
# ------------------------------------------
t1 = time()
total_results = 1000
first_half = int(total_results / 2)
limit = 100
skip = 50
for i in range(first_half):
result_template["basis"] = str(i)
r = ResultORM(**result_template)
session.add(r)
result_template["method"] = "m2"
for i in range(first_half, total_results):
result_template["basis"] = str(i)
r = ResultORM(**result_template)
session.add(r)
session.commit() # must commit outside the loop, 10 times faster
total_time = (time() - t1) * 1000 / total_results
print("Inserted {} results in {:.2f} msec / doc".format(total_results, total_time))
# query (~ 0.13 msec/doc) in ME, and ~0.02 msec/doc in SQL
# ----------------------------------------
t1 = time()
ret1 = session.query(ResultORM).filter_by(method="m1")
ret2 = session.query(ResultORM).filter_by(method="m2").limit(limit) # .offset(skip)
data1 = [d.to_dict() for d in ret1]
data2 = [d.to_dict() for d in ret2]
# count is total, but actual data size is the limit
assert ret1.count() == first_half
assert len(data1) == first_half
# assert ret2.count() == total_results - first_half
# assert len(ret2) == limit
# assert len(data2) == limit
#
# assert int(data2[0]['basis']) == first_half + skip
#
# # get the last page when with fewer than limit are remaining
# ret = session.query(ResultORM).filter_by(method='m1').limit(limit).offset(int(first_half - limit / 2))
# assert len(ret) == limit / 2
total_time = (time() - t1) * 1000 / total_results
print("Query {} results in {:.3f} msec /doc".format(total_results, total_time))
# cleanup
session_delete_all(session, ResultORM)