def _parse_value(val):
"""Example field-parsing logic."""
# If the string is complicated, split it up and try to get uncertainty and/or units
if isinstance(val, str) and len(val.split()) > 1:
toks = val.split()
mean = float(toks[0])
std = -1
if toks[1] in {"+-", "+/-"}:
std = float(toks[2])
try:
unit = units.parse_units(toks[-1])
except (ValueError, units.UndefinedUnitError):
print("Couldn't find {}".format(toks[-1]))
unit = ''
if std >= 0:
return NormalReal(mean=mean, std=std, units=unit)
else:
return NominalReal(mean, units=unit)
# if it is just a number wrap it in a nominal value
elif isinstance(val, (float, int)):
return NominalReal(val, '')
# if it is a single string, its either a single number of a category
elif isinstance(val, str):
try:
num = float(val)
return NominalReal(num, '')
except ValueError:
return DiscreteCategorical(val)
else:
raise ValueError("Couldn't parse {}".format(val))
def test_serialized_history():
"""Test the serialization of a complete material history."""
# Create several runs and specs linked together
buy_spec = LinkByUID("id", "pr723")
cookie_dough_spec = MaterialSpec("cookie dough spec", process=buy_spec)
buy_cookie_dough = ProcessRun("Buy cookie dough", uids={'id': '32283'}, spec=buy_spec)
cookie_dough = MaterialRun("cookie dough", process=buy_cookie_dough, spec=cookie_dough_spec)
bake = ProcessRun("bake cookie dough", conditions=[
Condition("oven temp", origin='measured', value=NominalReal(357, 'degF'))])
IngredientRun(material=cookie_dough,
process=bake, number_fraction=NominalReal(1, ''))
cookie = MaterialRun("cookie", process=bake, tags=["chocolate chip", "drop"])
MeasurementRun("taste", material=cookie, properties=[
Property("taste", value=DiscreteCategorical("scrumptious"))])
cookie_history = complete_material_history(cookie)
# There are 7 entities in the serialized list: cookie dough (spec & run), buy cookie dough,
# cookie dough ingredient, bake cookie dough, cookie, taste
assert len(cookie_history) == 7
for entity in cookie_history:
assert len(entity['uids']) > 0, "Serializing material history should assign uids."
# Check that the measurement points to the material
taste_dict = next(x for x in cookie_history if x.get('type') == 'measurement_run')
cookie_dict = next(x for x in cookie_history if x.get('name') == 'cookie')
scope = taste_dict.get('material').get('scope')
assert taste_dict.get('material').get('id') == cookie_dict.get('uids').get(scope)
# Check that both the material spec and the process run point to the same process spec.
# Because that spec was initially a LinkByUID, this also tests the methods ability to
# serialize a LinkByUID.
cookie_dough_spec_dict = next(x for x in cookie_history if x.get('type') == 'material_spec')
buy_cookie_dough_dict = next(x for x in cookie_history if x.get('name') == 'Buy cookie dough')
assert cookie_dough_spec_dict.get('process') == buy_spec.as_dict()
assert buy_cookie_dough_dict.get('spec') == buy_spec.as_dict()
def test_unit_normalization():
"""Make sure units are internally represented in a reasonable way."""
assert NominalReal(2.7, "newton / m^2").units == NominalReal(
2.7, "m^-1 newton / meter").units
val = NominalReal(2.7, "cm")
assert val.units == "centimeter"
assert val.dump()["units"] == "centimeter"
def ingest_table(material_run, table):
"""Ingest a material run into an existing table."""
for _, row in table.iterrows():
exp = MeasurementRun()
for prop_name in known_properties:
if prop_name in row:
exp.properties.append(Property(name=prop_name,
value=NominalReal(row[prop_name], '')))
for cond_name in known_conditions:
if cond_name in row:
exp.conditions.append(Condition(name=cond_name,
value=NominalReal(row[cond_name], '')))
exp.material = material_run
return material_run
def real_mapper(prop):
"""Mapping methods for RealBounds."""
if 'uncertainty' in prop['scalars'][0]:
if prop['units'] == 'eV': # Arbitrarily convert to attojoules
mean = convert_units(value=float(prop['scalars'][0]['value']),
starting_unit=prop['units'],
final_unit='aJ'
)
std = convert_units(value=float(prop['scalars'][0]['value']),
starting_unit=prop['units'],
final_unit='aJ'
)
val = NormalReal(mean=mean,
units='aJ',
std=std
)
else:
val = NormalReal(mean=float(prop['scalars'][0]['value']),
units=prop['units'],
std=float(prop['scalars'][0]['uncertainty'])
)
else:
val = NominalReal(nominal=float(prop['scalars'][0]['value']),
units=prop['units']
)
return val
def test_access_data():
"""Demonstrate and test access patterns within the data island."""
binders = {
"Polyethylene Glycol 100M": 0.02,
"Sodium lignosulfonate": 0.004,
"Polyvinyl Acetate": 0.0001
}
powders = {"Al2O3": 0.96}
island = make_data_island(density=1.0,
bulk_modulus=300.0,
firing_temperature=750.0,
binders=binders,
powders=powders,
tag="Me")
# read the density value
assert (island.measurements[0].properties[0].value == NominalReal(1.0, ''))
# read the bulk modulus value
assert (island.measurements[0].properties[1].value == NormalReal(
300.0, 3.0, ''))
# read the firing temperature
assert (island.process.conditions[0].value == UniformReal(
749.5, 750.5, 'degC'))
assert (island.process.parameters[0].value == DiscreteCategorical(
{"hot": 1.0}))
# read the quantity of alumina
quantities = island.process.ingredients[0].material.process.conditions[
0].value.quantities
assert (list(keyfilter(lambda x: x == "Al2O3",
quantities).values())[0] == 0.96)
# check that the serialization results in the correct number of objects in the preface
# (note that neither measurements nor ingredients are serialized)
assert (len(json.loads(dumps(island))["context"]) == 26)
def test_serialize():
"""Serializing a nested object should be identical to individually serializing each piece."""
condition = Condition(name="A condition", value=NominalReal(7, ''))
parameter = Parameter(name="A parameter",
value=NormalReal(mean=17, std=1, units=''))
input_material = MaterialRun(tags="input")
process = ProcessRun(tags="A tag on a process run")
ingredient = IngredientRun(material=input_material, process=process)
material = MaterialRun(tags=["A tag on a material"], process=process)
measurement = MeasurementRun(tags="A tag on a measurement",
conditions=condition,
parameters=parameter,
material=material)
# serialize the root of the tree
native_object = json.loads(dumps(measurement))
# ingredients don't get serialized on the process
assert (len(native_object["context"]) == 5)
assert (native_object["object"]["type"] == LinkByUID.typ)
# serialize all of the nodes
native_batch = json.loads(
dumps([material, process, measurement, ingredient]))
assert (len(native_batch["context"]) == 5)
assert (len(native_batch["object"]) == 4)
assert (all(x["type"] == LinkByUID.typ for x in native_batch["object"]))
def test_invalid_assignment(caplog):
"""Test that invalid assignments throw the appropriate errors."""
with pytest.raises(TypeError):
Property(value=NominalReal(10, ''))
with pytest.raises(TypeError):
Property(name="property", value=10)
with pytest.raises(TypeError):
Property(name="property",
template=ProcessTemplate("wrong kind of template"))
with pytest.raises(ValueError):
Property(name="property", origin=None)
valid_prop = Property(name="property",
value=NominalReal(10, ''),
template=PropertyTemplate("template",
bounds=RealBounds(
0, 100, '')))
good_val = valid_prop.value
bad_val = NominalReal(-10.0, '')
assert len(caplog.records
) == 0, "Warning caught before logging tests were reached."
with validation_level(WarningLevel.IGNORE):
valid_prop.value = bad_val
assert len(caplog.records
) == 0, "Validation warned even though level is IGNORE."
assert valid_prop.value == bad_val, "IGNORE allowed the bad value to be set."
valid_prop.value = good_val
assert len(caplog.records
) == 0, "Validation warned even though level is IGNORE."
with validation_level(WarningLevel.WARNING):
valid_prop.value = bad_val
assert len(caplog.records
) == 1, "Validation didn't warn on out of bounds value."
assert valid_prop.value == bad_val, "WARNING allowed the bad value to be set."
valid_prop.value = good_val
assert len(
caplog.records) == 1, "Validation DID warn on a valid value."
with validation_level(WarningLevel.FATAL):
with pytest.raises(ValueError):
valid_prop.value = bad_val
assert valid_prop.value == good_val, "FATAL didn't allow the bad value to be set."
with validation_level(WarningLevel.FATAL):
with pytest.raises(ValueError):
valid_prop.template = PropertyTemplate("template",
bounds=RealBounds(0, 1, ''))
assert valid_prop.value == good_val, "FATAL didn't allow the bad value to be set."
def test_invalid_assignment():
"""Invalid assignments to `process` or `material` throw a TypeError."""
with pytest.raises(TypeError):
IngredientSpec(name="name", material=NominalReal(3, ''))
with pytest.raises(TypeError):
IngredientSpec(name="name", process="process")
with pytest.raises(TypeError):
IngredientSpec() # Name is required
def test_deserialize():
"""Round-trip serde should leave the object unchanged."""
condition = Condition(name="A condition", value=NominalReal(7, ''))
parameter = Parameter(name="A parameter", value=NormalReal(mean=17, std=1, units=''))
measurement = MeasurementRun(tags="A tag on a measurement", conditions=condition,
parameters=parameter)
copy_meas = GEMDJson().copy(measurement)
assert(copy_meas.conditions[0].value == measurement.conditions[0].value)
assert(copy_meas.parameters[0].value == measurement.parameters[0].value)
assert(copy_meas.uids["auto"] == measurement.uids["auto"])
def test_attribute_serde():
"""An attribute with a link to an attribute template should be copy-able."""
prop_tmpl = PropertyTemplate(name='prop_tmpl',
bounds=RealBounds(0, 2, 'm'))
prop = Property(name='prop', template=prop_tmpl, value=NominalReal(1, 'm'))
meas_spec = MeasurementSpec("a spec")
meas = MeasurementRun("a measurement", spec=meas_spec, properties=[prop])
assert loads(dumps(prop)) == prop
assert loads(dumps(meas)) == meas
assert isinstance(prop.template, PropertyTemplate)
def test_invalid_assignment():
"""Test that invalid assignments throw the appropriate errors."""
with pytest.raises(ValueError):
Property(value=NominalReal(10, ''))
with pytest.raises(TypeError):
Property(name="property", value=10)
with pytest.raises(TypeError):
Property(name="property",
template=ProcessTemplate("wrong kind of template"))
with pytest.raises(ValueError):
Property(name="property", origin=None)
def test_build():
"""Test that build recreates the material."""
spec = MaterialSpec(
"A spec",
properties=PropertyAndConditions(
property=Property("a property", value=NominalReal(3, ''))),
tags=["a tag"])
mat = MaterialRun(name="a material", spec=spec)
mat_dict = mat.as_dict()
mat_dict['spec'] = mat.spec.as_dict()
assert MaterialRun.build(mat_dict) == mat
def test_equality():
"""Test that equality check works as expected."""
spec = MaterialSpec(
"A spec",
properties=PropertyAndConditions(
property=Property("a property", value=NominalReal(3, ''))),
tags=["a tag"])
mat1 = MaterialRun("A material", spec=spec)
mat2 = MaterialRun("A material", spec=spec, tags=["A tag"])
assert mat1 == deepcopy(mat1)
assert mat1 != mat2
assert mat1 != "A material"
def test_material_attachment():
"""
Attach a material run to an ingredient run.
Check that the ingredient can be built, and that the connection survives ser/de.
"""
flour = MaterialRun("flour", sample_type='unknown')
flour_ingredient = IngredientRun(material=flour,
absolute_quantity=NominalReal(500, 'g'))
flour_ingredient_copy = IngredientRun.build(flour_ingredient.dump())
assert flour_ingredient_copy == flour_ingredient
def test_material_run():
"""
Test the ability to create a MaterialRun that is linked to a MaterialSpec.
Make sure all enumerated values are respected, and check consistency after
serializing and deserializing.
"""
# Define a property, and make sure that an inappropriate value for origin throws ValueError
with pytest.raises(ValueError):
prop = Property(name="A property",
origin="bad origin",
value=NominalReal(17, units=''))
# Create a MaterialSpec with a property
prop = Property(name="A property",
origin="specified",
value=NominalReal(17, units=''))
mat_spec = MaterialSpec(name="a specification for a material",
properties=PropertyAndConditions(prop),
notes="Funny lookin'")
# Make sure that when property is serialized, origin (an enumeration) is serialized as a string
copy_prop = json.loads(dumps(mat_spec))
copy_origin = copy_prop["context"][0]["properties"][0]['property'][
'origin']
assert isinstance(copy_origin, str)
# Create a MaterialRun, and make sure an inappropriate value for sample_type throws ValueError
with pytest.raises(ValueError):
mat = MaterialRun(spec=mat_spec, sample_type="imaginary")
mat = MaterialRun(spec=mat_spec, sample_type="virtual")
# ensure that serialization does not change the MaterialRun
copy = loads(dumps(mat))
assert dumps(copy) == dumps(mat), \
"Material run is modified by serialization or deserialization"
def test_simple_deserialization(valid_data):
"""Ensure that a deserialized Material Spec looks sane."""
material_spec: MaterialSpec = MaterialSpec.build(valid_data)
assert material_spec.uids == {'id': valid_data['uids']['id']}
assert material_spec.name == 'spec of material'
assert material_spec.tags == []
assert material_spec.notes is None
assert material_spec.process is None
assert material_spec.properties[0] == \
PropertyAndConditions(Property("color", origin='specified',
value=NominalCategorical("tan")),
conditions=[Condition('temperature', origin='specified',
value=NominalReal(300, units='kelvin'))])
assert material_spec.template is None
assert material_spec.file_links == []
assert material_spec.typ == 'material_spec'
def test_default_nested_serde():
"""Test that defaults work in nested dictionaries."""
good_obj = SampleClass("Can be serialized", NominalReal(17, ''))
data = good_obj.dump()
# If 'prop_string.string' is a non-string, that's an error
data['prop_string']['string'] = 0
with pytest.raises(ValueError):
SampleClass.build(data)
# If data['prop_string'] is an empty dictionary, then the default is used
data['prop_string'] = dict()
assert SampleClass.build(data).prop_string == 'default'
# If `data` does not even have a 'prop_string' key, then the default is used
del data['prop_string']
assert SampleClass.build(data).prop_string == 'default'
def test_recursive_foreach():
"""Test that recursive foreach will actually walk through a material history."""
mat_run = MaterialRun("foo")
process_run = ProcessRun("bar")
IngredientRun(process=process_run, material=mat_run)
output = MaterialRun("material", process=process_run)
# property templates are trickier than templates because they are referenced in attributes
template = PropertyTemplate("prop", bounds=RealBounds(0, 1, ""))
prop = Property("prop", value=NominalReal(1.0, ""), template=template)
MeasurementRun("check", material=output, properties=prop)
types = []
recursive_foreach(output, lambda x: types.append(x.typ))
expected = [
"ingredient_run", "material_run", "material_run", "process_run",
"measurement_run", "property_template"
]
assert sorted(types) == sorted(expected)
def make_flexural_test_measurement(my_id, deflection, extra_tags=frozenset()):
"""
Compute the stree, strain, and modulus.
According to https://en.wikipedia.org/wiki/Three-point_flexural_test
"""
stress = 3 * applied_force * span / (2 * thickness * thickness * width)
strain = 6 * deflection * thickness / (span * span)
modulus = stress / strain
measurement = MeasurementRun(
name="3 Point Bend",
uids={"my_id": my_id},
tags=["3_pt_bend", "mechanical", "flex"] + list(extra_tags),
properties=[
Property(
name="flexural stress",
value=NormalReal(stress, std=(0.01 * stress), units="MPa"),
origin=Origin.MEASURED
),
Property(
name="flexural strain",
value=NormalReal(strain, std=(0.01 * strain), units=""),
origin=Origin.MEASURED
),
Property(
name="flexural modulus",
value=NormalReal(modulus, std=(0.01 * modulus), units="MPa"),
origin=Origin.MEASURED
),
Property(
name="deflection",
value=NominalReal(deflection, units="mm"),
origin=Origin.MEASURED
)
]
)
return measurement
def test_validation_control(caplog):
"""Verify that when validation is requested, limits are enforced."""
with validation_level(WarningLevel.WARNING):
IngredientSpec(name="name", mass_fraction=NominalReal(0.5, ''))
assert len(caplog.records) == 0, "Warned on valid values with WARNING."
IngredientSpec(name="name", mass_fraction=NominalReal(5, ''))
assert len(
caplog.records) == 1, "Didn't warn on invalid values with WARNING."
IngredientSpec(name="name", mass_fraction=NominalReal(0.5, 'm'))
assert len(
caplog.records) == 2, "Didn't warn on invalid units with WARNING."
with validation_level(WarningLevel.FATAL):
# The following should not raise an exception
IngredientSpec(name="name", mass_fraction=NominalReal(0.5, ''))
with pytest.raises(ValueError):
IngredientSpec(name="name", mass_fraction=NominalReal(5, ''))
with pytest.raises(ValueError):
IngredientSpec(name="name", mass_fraction=NominalReal(0.5, 'm'))
def test_simple_deserialization(valid_data):
"""Ensure that a deserialized Process Run looks sane."""
process_run: ProcessRun = ProcessRun.build(valid_data)
assert process_run.uids == {
'id': valid_data['uids']['id'],
'my_id': 'process1-v1'
}
assert process_run.tags == ['baking::cakes', 'danger::low']
assert process_run.conditions[0] == Condition(name='oven temp',
value=NominalReal(203.0, ''),
origin='measured')
assert process_run.parameters == []
assert process_run.file_links == []
assert process_run.template is None
assert process_run.output_material is None
assert process_run.spec == \
ProcessSpec(name="Spec for proc 1",
uids={'id': valid_data['spec']['uids']['id']},
conditions=[Condition(name='oven temp', value=UniformReal(175, 225, ''),
origin='specified')]
)
assert process_run.name == 'Process 1'
assert process_run.notes == 'make sure to use oven mitts'
assert process_run.typ == 'process_run'
def test_bad_object_serde():
"""Test that a 'mystery' object cannot be serialized."""
bad_obj = SampleClass("Cannot be serialized", NominalReal(34, ''), UnserializableClass(1))
with pytest.raises(AttributeError):
bad_obj.dump()
def test_default_units():
"""An empty string should turn into the 'dimensionless' unit."""
assert NominalReal(2.7, "") == NominalReal(2.7, "dimensionless")
def test_units():
"""Make sure units can be set without error."""
NominalReal(2.7, "")
NominalReal(2.7, "cm")
NominalReal(2.7, "cm^2/joule")
NominalReal(2.7, "")
def test_contains():
"""Test that bounds know if a Value is contained within it."""
bounds = RealBounds(1, 3, 'm')
assert bounds.contains(NominalReal(200, 'cm')._to_bounds())
assert not bounds.contains(NominalReal(5, 'm')._to_bounds())
assert set(boiling.ingredients) == {oil, potatoes}
assert frying.ingredients == []
oil.process = frying
assert oil.process == frying
assert boiling.ingredients == [potatoes]
assert frying.ingredients == [oil]
potatoes.process = frying
assert potatoes.process == frying
assert boiling.ingredients == []
assert set(frying.ingredients) == {oil, potatoes}
VALID_QUANTITIES = [
NominalReal(14.0, ''),
UniformReal(0.5, 0.6, 'm'),
NormalReal(-0.3, 0.6, "kg")
]
INVALID_QUANTITIES = [
NominalCategorical("blue"),
NominalInteger(5),
EmpiricalFormula("CH4"), 0.33, "0.5"
]
@pytest.mark.parametrize("valid_quantity", VALID_QUANTITIES)
def test_valid_quantities(valid_quantity):
"""
Check that all quantities must be continuous values.
def test_gemd_object_serde():
"""Test that an unspecified gemd object can be serialized and deserialized."""
good_obj = SampleClass("Can be serialized", NominalReal(17, ''))
copy = SampleClass.build(good_obj.dump())
assert copy.prop_value == good_obj.prop_value
assert copy.prop_string == good_obj.prop_string
def make_data_island(density,
bulk_modulus,
firing_temperature,
binders,
powders,
tag=None):
"""Helper function to create a relatively involved data island."""
binder_specs = keymap(lambda x: MaterialSpec(name=x), binders)
powder_specs = keymap(lambda x: MaterialSpec(name=x), powders)
binder_runs = keymap(lambda x: MaterialRun(name=x.name, spec=x),
binder_specs)
powder_runs = keymap(lambda x: MaterialRun(name=x.name, spec=x),
powder_specs)
all_input_materials = keymap(lambda x: x.spec.name,
merge(binder_runs, powder_runs))
mixing_composition = Condition(
name="composition", value=NominalComposition(all_input_materials))
mixing_process = ProcessRun(name="Mixing",
tags=["mixing"],
conditions=[mixing_composition])
binder_ingredients = []
for run in binder_runs:
binder_ingredients.append(
IngredientRun(
material=run,
process=mixing_process,
mass_fraction=NominalReal(binders[run.spec.name], ''),
))
powder_ingredients = []
for run in powder_runs:
powder_ingredients.append(
IngredientRun(
material=run,
process=mixing_process,
mass_fraction=NominalReal(powders[run.spec.name], ''),
))
green_sample = MaterialRun("Green", process=mixing_process)
measured_firing_temperature = Condition(
name="Firing Temperature",
value=UniformReal(firing_temperature - 0.5, firing_temperature + 0.5,
'degC'),
template=firing_temperature_template)
specified_firing_setting = Parameter(name="Firing setting",
value=DiscreteCategorical("hot"))
firing_spec = ProcessSpec("Firing", template=firing_template)
firing_process = ProcessRun(name=firing_spec.name,
conditions=[measured_firing_temperature],
parameters=[specified_firing_setting],
spec=firing_spec)
IngredientRun(material=green_sample,
process=firing_process,
mass_fraction=NormalReal(1.0, 0.0, ''),
volume_fraction=NormalReal(1.0, 0.0, ''),
number_fraction=NormalReal(1.0, 0.0, ''))
measured_density = Property(name="Density",
value=NominalReal(density, ''),
template=density_template)
measured_modulus = Property(name="Bulk modulus",
value=NormalReal(bulk_modulus,
bulk_modulus / 100.0, ''))
measurement_spec = MeasurementSpec("Mechanical Properties",
template=measurement_template)
measurement = MeasurementRun(
measurement_spec.name,
properties=[measured_density, measured_modulus],
spec=measurement_spec)
tags = [tag] if tag else []
material_spec = MaterialSpec("Coupon", template=material_template)
material_run = MaterialRun(material_spec.name,
process=firing_process,
tags=tags,
spec=material_spec)
measurement.material = material_run
return material_run
def test_template_assignment():
"""Test that an object and its attributes can both be assigned templates."""
humidity_template = ConditionTemplate("Humidity", bounds=RealBounds(0.5, 0.75, ""))
template = ProcessTemplate("Dry", conditions=[[humidity_template, RealBounds(0.5, 0.65, "")]])
ProcessSpec("Dry a polymer", template=template, conditions=[
Condition("Humidity", value=NominalReal(0.6, ""), template=humidity_template)])
