def test_inplace_v_not():
"""Test that client can copy a dictionary in which keys are BaseEntity objects."""
spec = ProcessSpec("A process spec", uids={'id': str(uuid4()), 'auto': str(uuid4())})
run1 = ProcessRun("A process run", spec=spec, uids={'id': str(uuid4()), 'auto': str(uuid4())})
run2 = ProcessRun("Another process run", spec=spec, uids={'id': str(uuid4())})
process_dict = {spec: [run1, run2]}
subbed = substitute_links(process_dict)
assert subbed != process_dict # This is true because the hashes change, even if objects equal
substitute_links(process_dict, inplace=True)
assert subbed == process_dict
def test_scope_substitution():
"""Test that the native id gets serialized, when specified."""
native_id = 'id1'
# Create measurement and material with two ids
mat = MaterialRun("A material", uids={
native_id: str(uuid4()), "an_id": str(uuid4()), "another_id": str(uuid4())})
meas = MeasurementRun("A measurement", material=mat, uids={
"some_id": str(uuid4()), native_id: str(uuid4()), "an_id": str(uuid4())})
# Turn the material pointer into a LinkByUID using native_id
subbed = substitute_links(meas, scope=native_id)
assert subbed.material == LinkByUID.from_entity(mat, scope=native_id)
# Put the measurement into a list and convert that into a LinkByUID using native_id
measurements_list = [meas]
subbed = substitute_links(measurements_list, scope=native_id)
assert subbed == [LinkByUID.from_entity(meas, scope=native_id)]
def test_object_key_substitution():
"""Test that client can copy a dictionary in which keys are BaseEntity objects."""
spec = ProcessSpec("A process spec", uids={'id': str(uuid4()), 'auto': str(uuid4())})
run1 = ProcessRun("A process run", spec=spec, uids={'id': str(uuid4()), 'auto': str(uuid4())})
run2 = ProcessRun("Another process run", spec=spec, uids={'id': str(uuid4())})
process_dict = {spec: [run1, run2]}
subbed = substitute_links(process_dict, scope='auto')
for key, value in subbed.items():
assert key == LinkByUID.from_entity(spec, scope='auto')
assert LinkByUID.from_entity(run1, scope='auto') in value
assert LinkByUID.from_entity(run2) in value
reverse_process_dict = {run2: spec}
subbed = substitute_links(reverse_process_dict, scope='auto')
for key, value in subbed.items():
assert key == LinkByUID.from_entity(run2)
assert value == LinkByUID.from_entity(spec, scope='auto')
def test_signature():
"""Exercise various permutations of the substitute_links sig."""
spec = ProcessSpec("A process spec", uids={'my': 'spec'})
with pytest.warns(DeprecationWarning):
run1 = ProcessRun("First process run", uids={'my': 'run1'}, spec=spec)
assert isinstance(substitute_links(run1, native_uid='my').spec, LinkByUID)
run2 = ProcessRun("Second process run", uids={'my': 'run2'}, spec=spec)
assert isinstance(substitute_links(run2, scope='my').spec, LinkByUID)
run3 = ProcessRun("Third process run", uids={'my': 'run3'}, spec=spec)
assert isinstance(substitute_links(run3, 'my').spec, LinkByUID)
with pytest.raises(ValueError): # Test deprecated auto-population
run4 = ProcessRun("Fourth process run", uids={'my': 'run4'}, spec=spec)
assert isinstance(substitute_links(run4, 'other', allow_fallback=False).spec, LinkByUID)
with pytest.warns(DeprecationWarning):
with pytest.raises(ValueError): # Test deprecated auto-population
run5 = ProcessRun("Fifth process run", uids={'my': 'run4'}, spec=spec)
assert isinstance(substitute_links(run5, scope="my", native_uid="my").spec, LinkByUID)
def test_substitution_without_id():
"""Test that trying to substitute links if uids haven't been assigned throws an error."""
mat = MaterialRun("A material with no id")
meas = MeasurementRun("A measurement with no id", material=mat)
with pytest.raises(ValueError):
substitute_links(meas), "subbed = substitute_links should fail if objects don't have uids"
with pytest.raises(ValueError):
substitute_links([meas, mat]), \
"subbed = substitute_links should fail if objects don't have uids"
with pytest.raises(ValueError):
substitute_links(meas.as_dict()), \
"subbed = substitute_links should fail if objects don't have uids"
# Create a dictionary in which either the key or value is missing a uid
meas.add_uid('id', str(uuid4()))
with pytest.raises(ValueError):
substitute_links({mat: meas}), \
"subbed = substitute_links should fail if objects don't have uids"
with pytest.raises(ValueError):
substitute_links({meas: mat}), \
"subbed = substitute_links should fail if objects don't have uids"
def test_material_soft_link():
"""Test that a measurement run can link to a material run, and that it survives serde."""
dye = MaterialRun("rhodamine",
file_links=FileLink(filename='a.csv', url='/a/path'))
assert dye.measurements == [], "default value of .measurements should be an empty list"
# The .measurements member should not be settable
with pytest.raises(AttributeError):
dye.measurements = [MeasurementRun("Dummy")]
absorbance = MeasurementRun(name="Absorbance",
uids={'id': str(uuid4())},
properties=[
Property(name='Abs at 500 nm',
value=NominalReal(0.1, ''))
])
assert absorbance.material is None, "Measurements should have None as the material by default"
absorbance.material = dye
assert absorbance.material == dye, "Material not set correctly for measurement"
assert dye.measurements == [
absorbance
], "Soft-link from material to measurement not created"
fluorescence = MeasurementRun(name="Fluorescence",
uids={'id': str(uuid4())},
properties=[
Property(name='PL counts at 550 nm',
value=NominalReal(30000, ''))
],
material=dye)
assert fluorescence.material == dye, "Material not set correctly for measurement"
assert dye.measurements == [absorbance, fluorescence], \
"Soft-link from material to measurements not created"
assert loads(dumps(absorbance)) == absorbance, \
"Measurement should remain unchanged when serialized"
assert loads(dumps(fluorescence)) == fluorescence, \
"Measurement should remain unchanged when serialized"
assert 'measurements' in repr(dye)
assert 'material' in repr(fluorescence)
assert 'material' in repr(absorbance)
subbed = substitute_links(dye)
assert 'measurements' in repr(subbed)
def body(obj: BaseEntity):
copy = substitute_links(loads(dumps(obj)))
result.append(json.loads(dumps(copy))["context"][0])