def test_add_dummy():
A = mw.Apparatus()
dummy = mw.Dummy(name="dummy")
A.add(dummy, mw.Vessel(), tube)
P = mw.Protocol(A)
with pytest.raises(ValueError):
P.add(dummy, active=1) # should be a bool!
def test_add_valve():
A = mw.Apparatus()
valve = mw.Valve(mapping={pump1: 1, pump2: 2})
bad_valve = mw.Valve()
A.add([pump1, pump2], [valve, bad_valve], tube)
P = mw.Protocol(A)
expected = [
dict(start=0, stop=None, component=valve, params={"setting": 1})
]
# directly pass the pump object
P.add(valve, setting=pump1)
assert P.procedures == expected
P.procedures = []
# using its name
P.add(valve, setting="pump1")
assert P.procedures == expected
P.procedures = []
# using its port number
P.add(valve, setting=1)
assert P.procedures == expected
with pytest.raises(ValueError):
P.add(valve, setting=3)
with pytest.raises(ValueError):
P.add(bad_valve, setting=3)
def test_compile():
P = mw.Protocol(A)
P.add([pump1, pump2], rate="10 mL/min", duration="5 min")
assert P._compile() == {
pump1: [
{
"params": {
"rate": "10 mL/min"
},
"time": 0
},
{
"params": {
"rate": "0 mL/min"
},
"time": 300
},
],
pump2: [
{
"params": {
"rate": "10 mL/min"
},
"time": mw._ureg.parse_expression("0 seconds"),
},
{
"params": {
"rate": "0 mL/min"
},
"time": 300
},
],
}
# if no stop times are given, duration inference should fail
P = mw.Protocol(A)
P.add([pump1, pump2], rate="10 mL/min")
with pytest.raises(RuntimeError):
P._compile()
def test_switching_rates():
# check switching between rates
P = mw.Protocol(A)
P.add([pump1, pump2], rate="10 mL/min", duration="5 min")
P.add(pump1, rate="5 mL/min", start="5 min", stop="10 min")
assert P._compile() == {
pump1: [
{
"params": {
"rate": "10 mL/min"
},
"time": 0
},
{
"params": {
"rate": "5 mL/min"
},
"time": 300
},
{
"params": {
"rate": "0 mL/min"
},
"time": 600
},
],
pump2: [
{
"params": {
"rate": "10 mL/min"
},
"time": 0
},
{
"params": {
"rate": "0 mL/min"
},
"time": 300
},
],
}
def test_json():
P = mw.Protocol(A)
P.add([pump1, pump2], rate="10 mL/min", duration="5 min")
assert json.loads(P.json()) == [
{
"start": 0,
"stop": 300,
"component": "pump1",
"params": {
"rate": "10 mL/min"
},
},
{
"start": 0,
"stop": 300,
"component": "pump2",
"params": {
"rate": "10 mL/min"
},
},
]
def test_yaml():
P = mw.Protocol(A)
P.add([pump1, pump2], rate="10 mL/min", duration="5 min")
assert yaml.safe_load(P.yaml()) == json.loads(P.json())
def test_conflicting_continuous_procedures():
P = mw.Protocol(A)
P.add(pump1, rate="5 mL/min")
P.add(pump1, rate="2 mL/min")
with pytest.raises(RuntimeError):
P._compile()
def test_overlapping_procedures():
P = mw.Protocol(A)
P.add(pump1, start="0 seconds", stop="5 seconds", rate="5 mL/min")
P.add(pump1, start="2 seconds", stop="5 seconds", rate="2 mL/min")
with pytest.raises(RuntimeError):
P._compile()
def test_add():
P = mw.Protocol(A)
procedure = {
"component": pump1,
"params": {
"rate": "10 mL/min"
},
"start": 0,
"stop": 300,
}
# test using duration
P.add(pump1, rate="10 mL/min", duration="5 min")
assert P.procedures[0] == procedure
# test adding with start and stop
P.procedures = []
P.add(pump1, rate="10 mL/min", start="0 min", stop="5 min")
assert P.procedures[0] == procedure
# test adding with start and stop as timedeltas
P.procedures = []
P.add(pump1,
rate="10 mL/min",
start=timedelta(seconds=0),
stop=timedelta(minutes=5))
assert P.procedures[0] == procedure
# test adding with duration as timedelta
P.procedures = []
P.add(pump1, rate="10 mL/min", duration=timedelta(minutes=5))
assert P.procedures[0] == procedure
P = mw.Protocol(A)
with pytest.raises(KeyError):
P.add(mw.Pump("not in apparatus"), rate="10 mL/min", duration="5 min")
# adding a class, not an instance of it
with pytest.raises(ValueError):
P.add(mw.Pump, rate="10 mL/min", duration="5 min")
# Not adding keyword args
with pytest.raises(RuntimeError):
P.add(pump1, duration="5 min")
# Invalid keyword for component
with pytest.raises(ValueError):
P.add(pump1, active=False, duration="5 min")
# Invalid dimensionality for kwarg
with pytest.raises(ValueError):
P.add(pump1, rate="5 mL", duration="5 min")
# No unit
with pytest.raises(ValueError):
P.add(pump1, rate="5", duration="5 min")
# Just the raw value without a unit
with pytest.raises(ValueError):
P.add(pump1, rate=5, duration="5 min")
# Providing stop and duration should raise error
with pytest.raises(RuntimeError):
P.add(pump1, rate="5 mL/min", stop="5 min", duration="5 min")
# stop time before start time
with pytest.raises(ValueError):
P.add([pump1, pump2], rate="10 mL/min", start="5 min", stop="4 min")
def test_unused_component():
# raise warning if component not used
P = mw.Protocol(A)
P.add(pump1, rate="10 mL/min", duration="5 min")
with pytest.warns(UserWarning, match="not used"):
P._compile()
def test_create_protocol():
# test naming
assert mw.Protocol(A, name="testing").name == "testing"
assert mw.Protocol(A).name == "Protocol_0"
assert mw.Protocol(A).name == "Protocol_1"
pump = mw.DummyPump(name="Dummy pump")
test = mw.DummySensor(name="test")
test2 = mw.DummySensor(name="test2")
test3 = mw.DummySensor(name="test3")
test4 = mw.BrokenDummySensor(name="test4")
tube = mw.Tube("1 foot", "1/16 in", "2/16 in", "PVC")
# create apparatus
A = mw.Apparatus()
A.add([a, b, c], pump, tube)
A.add(pump, [test, test2, test3, test4], tube)
P = mw.Protocol(A, name="testing execution")
P.add(pump, rate="5 mL/min", start="0 seconds", stop="1 secs")
P.add([test, test2, test3, test4], rate="5 Hz", start="0 secs", stop="1 secs")
# test both execution modes
for dry_run in [True, False]:
E = P.execute(confirm=True, dry_run=dry_run, log_file=None, data_file=None)
assert len(E.data["test"]) >= 5
if dry_run:
assert E.data["test"][0].data == "simulated read"
assert pump.rate == mw._ureg.parse_expression(pump._base_state["rate"])
# test fast forward
E = P.execute(confirm=True, dry_run=5, log_file=None, data_file=None)
assert len(E.data["test"]) >= 1