def test_material_attachment():
"""Test that a material can be attached to a measurement, and the connection survives serde."""
cake = MaterialRun('Final Cake')
mass = MeasurementRun('Weigh cake', material=cake)
mass_data = mass.dump()
mass_copy = MeasurementRun.build(mass_data)
assert mass_copy == mass
def test_soft_measurement_material_attachment():
"""Test that soft attachments are formed from materials to measurements."""
cake = MaterialRun("A cake")
smell_test = MeasurementRun("use your nose",
material=cake,
properties=[
Property(
name="Smell",
value=DiscreteCategorical("yummy"))
])
taste_test = MeasurementRun("taste", material=cake)
assert cake.measurements == [smell_test, taste_test]
def test_simple_deserialization(valid_data):
"""Ensure that a deserialized Measurement Run looks sane."""
measurement_run: MeasurementRun = MeasurementRun.build(valid_data)
assert measurement_run.uids == {'id': valid_data['uids']['id']}
assert measurement_run.name == 'Taste test'
assert measurement_run.notes is None
assert measurement_run.tags == []
assert measurement_run.conditions == []
assert measurement_run.parameters == []
assert measurement_run.properties[0] == Property('sweetness',
origin="measured",
value=NominalInteger(7))
assert measurement_run.properties[1] == Property('fluffiness',
origin="measured",
value=NominalInteger(10))
assert measurement_run.file_links == []
assert measurement_run.template is None
assert measurement_run.material == MaterialRun(
'sponge cake',
uids={'id': valid_data['material']['uids']['id']},
sample_type='experimental')
assert measurement_run.material.audit_info == AuditInfo(
**valid_data['material']['audit_info'])
assert measurement_run.material.dataset == UUID(
valid_data['material']['dataset'])
assert measurement_run.spec is None
assert measurement_run.typ == 'measurement_run'
assert measurement_run.audit_info == AuditInfo(**valid_data['audit_info'])
assert measurement_run.dataset == UUID(valid_data['dataset'])
def test_serialization(valid_data):
"""Ensure that a serialized Measurement Run looks sane."""
measurement_run: MeasurementRun = MeasurementRun.build(valid_data)
serialized = measurement_run.dump()
valid_data['material'].pop('audit_info')
valid_data['material'].pop('dataset')
valid_data.pop('audit_info')
valid_data.pop('dataset')
assert serialized == valid_data
def test_list_validation():
"""Test that lists are validated by gemd."""
with pytest.raises(ValueError):
# labels must be a list of string, but contains an int
IngredientSpec(labels=["Label 1", 17], name="foo")
ingredient = IngredientSpec(labels=["Label 1", "label 2"], name="foo")
with pytest.raises(TypeError):
# cannot append an int to a list of strings
ingredient.labels.append(17)
with pytest.raises(ValueError):
# list of conditions cannot contain a property
MeasurementRun("A measurement",
conditions=[Property("not a condition")])
def test_register_data_concepts(dataset):
"""Check that register routes to the correct collections"""
expected = {
MaterialTemplateCollection:
MaterialTemplate("foo"),
MaterialSpecCollection:
MaterialSpec("foo"),
MaterialRunCollection:
MaterialRun("foo"),
ProcessTemplateCollection:
ProcessTemplate("foo"),
ProcessSpecCollection:
ProcessSpec("foo"),
ProcessRunCollection:
ProcessRun("foo"),
MeasurementTemplateCollection:
MeasurementTemplate("foo"),
MeasurementSpecCollection:
MeasurementSpec("foo"),
MeasurementRunCollection:
MeasurementRun("foo"),
IngredientSpecCollection:
IngredientSpec("foo"),
IngredientRunCollection:
IngredientRun(),
PropertyTemplateCollection:
PropertyTemplate("bar", bounds=IntegerBounds(0, 1)),
ParameterTemplateCollection:
ParameterTemplate("bar", bounds=IntegerBounds(0, 1)),
ConditionTemplateCollection:
ConditionTemplate("bar", bounds=IntegerBounds(0, 1))
}
for collection, obj in expected.items():
assert len(obj.uids) == 0
registered = dataset.register(obj)
assert len(obj.uids) == 1
assert len(registered.uids) == 1
assert basename(dataset.session.calls[-1].path) == basename(
collection._path_template)
for pair in obj.uids.items():
assert pair[1] == registered.uids[pair[0]]
def test_register_all_data_concepts(dataset):
"""Check that register_all registers everything and routes to all collections"""
bounds = IntegerBounds(0, 1)
property_template = PropertyTemplate("bar", bounds=bounds)
parameter_template = ParameterTemplate("bar", bounds=bounds)
condition_template = ConditionTemplate("bar", bounds=bounds)
foo_process_template = ProcessTemplate(
"foo",
conditions=[[condition_template, bounds]],
parameters=[[parameter_template, bounds]])
foo_process_spec = ProcessSpec("foo", template=foo_process_template)
foo_process_run = ProcessRun("foo", spec=foo_process_spec)
foo_material_template = MaterialTemplate(
"foo", properties=[[property_template, bounds]])
foo_material_spec = MaterialSpec("foo",
template=foo_material_template,
process=foo_process_spec)
foo_material_run = MaterialRun("foo",
spec=foo_material_spec,
process=foo_process_run)
baz_template = MaterialTemplate("baz")
foo_measurement_template = MeasurementTemplate(
"foo",
conditions=[[condition_template, bounds]],
parameters=[[parameter_template, bounds]],
properties=[[property_template, bounds]])
foo_measurement_spec = MeasurementSpec("foo",
template=foo_measurement_template)
foo_measurement_run = MeasurementRun("foo",
spec=foo_measurement_spec,
material=foo_material_run)
foo_ingredient_spec = IngredientSpec("foo",
material=foo_material_spec,
process=foo_process_spec)
foo_ingredient_run = IngredientRun(spec=foo_ingredient_spec,
material=foo_material_run,
process=foo_process_run)
baz_run = MeasurementRun("baz")
# worst order possible
expected = {
foo_ingredient_run: IngredientRunCollection,
foo_ingredient_spec: IngredientSpecCollection,
foo_measurement_run: MeasurementRunCollection,
foo_measurement_spec: MeasurementSpecCollection,
foo_measurement_template: MeasurementTemplateCollection,
foo_material_run: MaterialRunCollection,
foo_material_spec: MaterialSpecCollection,
foo_material_template: MaterialTemplateCollection,
foo_process_run: ProcessRunCollection,
foo_process_spec: ProcessSpecCollection,
foo_process_template: ProcessTemplateCollection,
baz_template: MaterialTemplateCollection,
baz_run: MeasurementRunCollection,
property_template: PropertyTemplateCollection,
parameter_template: ParameterTemplateCollection,
condition_template: ConditionTemplateCollection
}
for obj in expected:
assert len(obj.uids) == 0 # All should be without ids
registered = dataset.register_all(expected.keys())
assert len(registered) == len(expected)
seen_ids = set()
for obj in expected:
assert len(obj.uids) == 1 # All should now have exactly 1 id
for pair in obj.uids.items():
assert pair not in seen_ids # All ids are different
seen_ids.add(pair)
for obj in registered:
for pair in obj.uids.items():
assert pair in seen_ids # registered items have the same ids
call_basenames = [
call.path.split('/')[-2] for call in dataset.session.calls
]
collection_basenames = [
basename(collection._path_template)
for collection in expected.values()
]
assert set(call_basenames) == set(collection_basenames)
assert len(set(call_basenames)) == len(
call_basenames) # calls are batched internally
# spot check order. Does not check every constraint
assert call_basenames.index(
basename(
IngredientRunCollection._path_template)) > call_basenames.index(
basename(IngredientSpecCollection._path_template))
assert call_basenames.index(basename(
MaterialRunCollection._path_template)) > call_basenames.index(
basename(MaterialSpecCollection._path_template))
assert call_basenames.index(
basename(
MeasurementRunCollection._path_template)) > call_basenames.index(
basename(MeasurementSpecCollection._path_template))
assert call_basenames.index(basename(
ProcessRunCollection._path_template)) > call_basenames.index(
basename(ProcessSpecCollection._path_template))
assert call_basenames.index(basename(
MaterialSpecCollection._path_template)) > call_basenames.index(
basename(MaterialTemplateCollection._path_template))
assert call_basenames.index(
basename(
MeasurementSpecCollection._path_template)) > call_basenames.index(
basename(MeasurementTemplateCollection._path_template))
assert call_basenames.index(basename(
ProcessSpecCollection._path_template)) > call_basenames.index(
basename(ProcessTemplateCollection._path_template))
assert call_basenames.index(basename(
MaterialSpecCollection._path_template)) > call_basenames.index(
basename(ProcessSpecCollection._path_template))
assert call_basenames.index(basename(
MaterialSpecCollection._path_template)) > call_basenames.index(
basename(MeasurementSpecCollection._path_template))
assert call_basenames.index(
basename(MeasurementTemplateCollection._path_template)
) > call_basenames.index(
basename(ConditionTemplateCollection._path_template))
assert call_basenames.index(
basename(MeasurementTemplateCollection._path_template)
) > call_basenames.index(
basename(ParameterTemplateCollection._path_template))
assert call_basenames.index(
basename(
MaterialTemplateCollection._path_template)) > call_basenames.index(
basename(PropertyTemplateCollection._path_template))
def test_serialization(valid_data):
"""Ensure that a serialized Measurement Run looks sane."""
measurement_run: MeasurementRun = MeasurementRun.build(valid_data)
serialized = measurement_run.dump()
assert serialized == valid_data
def test_object_validation():
"""Test that an object pointing to another object is validated."""
meas = MeasurementRun("A measurement")
with pytest.raises(TypeError):
MaterialRun("A cake", process=meas)