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_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_material_spec():
"""Test that Process/Material Spec link survives serialization."""
# Create a ProcessSpec
proc_spec = ProcessSpec(name="a process spec", tags=["tag1", "tag2"])
# Create MaterialSpec without a ProcessSpec
prop = Property(name="The material is a solid",
value=DiscreteCategorical(probabilities="solid"))
mat_spec = MaterialSpec(name="a material spec",
properties=PropertyAndConditions(prop))
assert mat_spec.process is None, \
"MaterialSpec should be initialized with no ProcessSpec, by default"
# Assign a ProcessSpec to mat_spec, first ensuring that the type is enforced
with pytest.raises(TypeError):
mat_spec.process = 17
mat_spec.process = proc_spec
# Assert circular links
assert dumps(proc_spec.output_material.process) == dumps(proc_spec), \
"ProcessSpec should link to MaterialSpec that links back to itself"
assert dumps(mat_spec.process.output_material) == dumps(mat_spec), \
"MaterialSpec should link to ProcessSpec that links back to itself"
# Make copies of both specs
mat_spec_copy = loads(dumps(mat_spec))
proc_spec_copy = loads(dumps(proc_spec))
assert proc_spec_copy.output_material == mat_spec, \
"Serialization should preserve link from ProcessSpec to MaterialSpec"
assert mat_spec_copy.process == proc_spec, \
"Serialization should preserve link from MaterialSpec to ProcessSpec"
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_json_serde():
"""Test that values can be ser/de using our custom json loads/dumps."""
# Enums are only used in the context of another class --
# it is not possible to deserialize to enum with the current
# serialization strategy (plain string) without this context.
original = Property(name="foo", origin=Origin.MEASURED)
copy = loads(dumps(original))
assert original == copy
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_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_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_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 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_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_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 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 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_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_strehlow_objects(table=None, template_scope=DEMO_TEMPLATE_SCOPE):
"""Make a table with Strehlow & Cook data."""
tmpl = make_templates(template_scope)
if table is None:
table = import_table()
# Specs
msr_spec = MeasurementSpec(name='Band gap',
template=tmpl["Band gap measurement"]
)
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
content_map = {
RealBounds: real_mapper,
CategoricalBounds: lambda prop: NominalCategorical(category=prop['scalars'][0]['value']),
type(None): lambda bnd: 'Label'
}
datapoints = []
compounds = dict()
for row in table:
formula = formula_clean(row['chemicalFormula'])
if formula not in compounds:
compounds[formula] = MaterialSpec(
name=formula_latex(formula),
template=tmpl["Chemical"],
process=ProcessSpec(name="Sample preparation",
template=tmpl["Sample preparation"]
))
spec = compounds[formula]
run = make_instance(spec)
datapoints.append(run)
if not spec.properties:
spec.properties.append(
PropertyAndConditions(
property=Property(name=spec.template.properties[0][0].name,
value=EmpiricalFormula(formula=formula),
template=spec.template.properties[0][0])
))
msr = make_instance(msr_spec)
msr.material = run
# 2 categories in the PIF need to be split to avoid repeat Attribute Templates in a Run
name_map = {
'Phase': 'Crystal system',
'Transition': 'Bands'
}
origin_map = {
'EXPERIMENTAL': Origin.MEASURED,
'COMPUTATIONAL': Origin.COMPUTED
}
seen = set() # Some conditions come in from multiple properties on the same object
for prop in row['properties']:
origin = origin_map.get(prop.get('dataType', None), Origin.UNKNOWN)
if 'method' in prop:
method = 'Method: ' + prop['method']['name']
else:
method = 'Method: unreported'
for attr in [prop] + prop.get('conditions', []):
if attr['name'] in seen:
# Early return if it's a repeat
continue
seen.add(attr['name'])
template = tmpl[attr['name']]
# Figure out if we need to split this column
if attr['name'] in name_map:
value = attr['scalars'][0]['value']
if value not in template.bounds.categories:
template = tmpl[name_map[attr['name']]]
# Move into GEMD structure
if type(template) == PropertyTemplate:
msr.properties.append(
Property(name=template.name,
template=template,
value=content_map[type(template.bounds)](attr),
origin=origin,
notes=method
))
elif type(template) == ConditionTemplate:
msr.conditions.append(
Condition(name=template.name,
template=template,
value=content_map[type(template.bounds)](attr),
origin=origin,
notes=method
))
return datapoints
def ingest_material_run(data, material_spec=None, process_run=None):
"""Ingest material run with data, a material spec, and an originating process run."""
if isinstance(data, list):
return [ingest_material_run(x, material_spec) for x in data]
if not isinstance(data, dict):
raise ValueError("This ingester operates on dict, but got {}".format(type(data)))
material = MaterialRun()
sample_id = data.get("sample_id")
if sample_id:
material.add_uid("given_sample_id", sample_id)
tags = data.get("tags")
if tags:
material.tags = tags
for experiment in data.get("experiments", []):
measurement = MeasurementRun()
for name in set(known_properties.keys()).intersection(experiment.keys()):
prop = Property(
name=name,
template=known_properties[name],
value=_parse_value(experiment[name])
)
measurement.properties.append(prop)
for name in set(known_conditions.keys()).intersection(experiment.keys()):
cond = Condition(
name=name,
template=known_conditions[name],
value=_parse_value(experiment[name])
)
measurement.conditions.append(cond)
for name in set(known_parameters.keys()).intersection(experiment.keys()):
param = Parameter(
name=name,
template=known_parameters[name],
value=_parse_value(experiment[name])
)
measurement.parameters.append(param)
scan_id = experiment.get("scan_id")
if scan_id:
measurement.add_uid("given_scan_id", scan_id)
tags = experiment.get("tags")
if tags:
measurement.tags = tags
measurement.material = material
if material_spec:
material.material_spec = material_spec
if process_run:
material.process = process_run
return material
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_get_object_id_from_base_attribute():
with pytest.raises(ValueError):
get_object_id(Property('some property'))
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