def test_simple_deserialization(valid_data):
"""Ensure that a deserialized Process Spec looks sane."""
process_spec: ProcessSpec = ProcessSpec.build(valid_data)
assert process_spec.uids == {'id': valid_data['uids']['id']}
assert process_spec.tags == ['baking::cakes', 'danger::low']
assert process_spec.parameters[0] == Parameter(name='oven temp',
value=UniformReal(
195, 205, ''),
origin='specified')
assert process_spec.conditions == []
assert process_spec.template == \
ProcessTemplate('the template', uids={'id': valid_data['template']['uids']['id']},
parameters=[
[ParameterTemplate('oven temp template',
bounds=RealBounds(175, 225, ''),
uids={'id': valid_data['template']['parameters'][0][0]['uids']['id']}),
RealBounds(175, 225, '')]
],
description='a long description',
allowed_labels=['a', 'b'],
allowed_names=['a name'])
assert process_spec.name == 'Process 1'
assert process_spec.notes == 'make sure to use oven mitts'
assert process_spec.file_links == [
FileLink('cake_recipe.txt', 'www.baking.com')
]
assert process_spec.typ == 'process_spec'
assert process_spec.audit_info == AuditInfo(**valid_data['audit_info'])
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_complex_substitutions():
"""Make sure accounting works for realistic objects."""
root = MaterialRun("root",
process=ProcessRun("root", spec=ProcessSpec("root")),
spec=MaterialSpec("root"))
root.spec.process = root.process.spec
input = MaterialRun("input",
process=ProcessRun("input", spec=ProcessSpec("input")),
spec=MaterialSpec("input"))
input.spec.process = input.process.spec
IngredientRun(process=root.process,
material=input,
spec=IngredientSpec("ingredient",
process=root.process.spec,
material=input.spec))
param = ParameterTemplate("Param", bounds=RealBounds(-1, 1, "m"))
root.process.spec.template = ProcessTemplate("Proc", parameters=[param])
root.process.parameters.append(
Parameter("Param", value=NormalReal(0, 1, 'm'), template=param))
links = flatten(root, scope="test-scope")
index = make_index(links)
rebuild = substitute_objects(links, index, inplace=True)
rebuilt_root = next(x for x in rebuild
if x.name == root.name and x.typ == root.typ)
all_objs = recursive_flatmap(rebuilt_root,
func=lambda x: [x],
unidirectional=False)
unique = [x for i, x in enumerate(all_objs) if i == all_objs.index(x)]
assert not any(isinstance(x, LinkByUID) for x in unique), "All are objects"
assert len(links) == len(unique), "Objects are missing"
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_recursive_foreach():
"""Test that recursive_foreach() applies a method to every object."""
new_tag = "Extra tag"
def func(base_ent):
"""Adds a specific tag to the object."""
base_ent.tags.extend([new_tag])
return
param_template = ParameterTemplate("a param template", bounds=RealBounds(0, 100, ''))
meas_template = MeasurementTemplate("Measurement template", parameters=[param_template])
parameter = Parameter(name="A parameter", value=NormalReal(mean=17, std=1, units=''))
measurement = MeasurementSpec(name="name", parameters=parameter, template=meas_template)
test_dict = {"foo": measurement}
recursive_foreach(test_dict, func, apply_first=True)
for ent in [param_template, meas_template, measurement]:
assert new_tag in ent.tags
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 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