def __init__(self,
*,
uids: Optional[Dict[str, str]] = None,
tags: Optional[List[str]] = None,
notes: Optional[str] = None,
material: Optional[GEMDMaterialRun] = None,
process: Optional[GEMDProcessRun] = None,
mass_fraction: Optional[ContinuousValue] = None,
volume_fraction: Optional[ContinuousValue] = None,
number_fraction: Optional[ContinuousValue] = None,
absolute_quantity: Optional[ContinuousValue] = None,
spec: Optional[GEMDIngredientSpec] = None,
file_links: Optional[List[FileLink]] = None):
if uids is None:
uids = dict()
DataConcepts.__init__(self, GEMDIngredientRun.typ)
GEMDIngredientRun.__init__(self,
uids=uids,
tags=tags,
notes=notes,
material=material,
process=process,
mass_fraction=mass_fraction,
volume_fraction=volume_fraction,
number_fraction=number_fraction,
absolute_quantity=absolute_quantity,
spec=spec,
file_links=file_links)
def test_id_case_sensitivitiy():
"""Test that uids are case insensitive."""
with pytest.raises(ValueError):
IngredientRun(uids={'my_id': 'sample1', 'My_ID': 'sample2'})
ingredient = IngredientRun(uids={'my_id': 'sample1'})
assert ingredient.uids['my_id'] == 'sample1'
assert ingredient.uids['MY_id'] == 'sample1'
def test_invalid_assignment():
"""Invalid assignments to `process` or `material` throw a TypeError."""
with pytest.raises(TypeError):
IngredientRun(material=RealBounds(0, 5.0, ''))
with pytest.raises(TypeError):
IngredientRun(process="process")
with pytest.raises(TypeError):
IngredientRun(spec=5)
def test_link_by_uid():
"""Test that linking works."""
root = MaterialRun(name='root', process=ProcessRun(name='root proc'))
leaf = MaterialRun(name='leaf', process=ProcessRun(name='leaf proc'))
IngredientRun(process=root.process, material=leaf)
IngredientRun(process=root.process, material=LinkByUID.from_entity(leaf))
copy = loads(dumps(root))
assert copy.process.ingredients[0].material == copy.process.ingredients[
1].material
def crawler(spec):
from gemd.entity.object.measurement_spec import MeasurementSpec
from gemd.entity.object.measurement_run import MeasurementRun
from gemd.entity.object.material_spec import MaterialSpec
from gemd.entity.object.material_run import MaterialRun
from gemd.entity.object.ingredient_spec import IngredientSpec
from gemd.entity.object.ingredient_run import IngredientRun
from gemd.entity.object.process_spec import ProcessSpec
from gemd.entity.object.process_run import ProcessRun
if id(spec) in seen:
return seen[id(spec)]
if isinstance(spec, MeasurementSpec):
seen[id(spec)] = MeasurementRun(name=spec.name, spec=spec)
elif isinstance(spec, MaterialSpec):
seen[id(spec)] = MaterialRun(name=spec.name, spec=spec)
seen[id(spec)].process = crawler(
spec.process) if spec.process else None
elif isinstance(spec, IngredientSpec):
seen[id(spec)] = IngredientRun(spec=spec)
seen[id(spec)].material = crawler(
spec.material) if spec.material else None
elif isinstance(spec, ProcessSpec):
seen[id(spec)] = ProcessRun(name=spec.name, spec=spec)
for x in spec.ingredients:
crawler(x).process = seen[id(spec)]
else:
raise TypeError(
'Passed object is not a spec-like object({})'.format(
type(spec)))
# Should we assume that the same MaterialSpec in different parts of the tree
# yields the same MaterialRun?
return seen[id(spec)]
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_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_uid_deser():
"""Test that uids continue to be a CaseInsensitiveDict after deserialization."""
material = MaterialRun("Input material", tags="input", uids={'Sample ID': '500-B'})
ingredient = IngredientRun(material=material)
ingredient_copy = loads(dumps(ingredient))
assert isinstance(ingredient_copy.uids, CaseInsensitiveDict)
assert ingredient_copy.material == material
assert ingredient_copy.material.uids['sample id'] == material.uids['Sample ID']
def test_name_persistance():
"""Verify that a serialized IngredientRun doesn't lose its name."""
from gemd.entity.object import IngredientSpec
from gemd.entity.link_by_uid import LinkByUID
from gemd.json import GEMDJson
je = GEMDJson()
ms_link = LinkByUID(scope='local', id='mat_spec')
mr_link = LinkByUID(scope='local', id='mat_run')
ps_link = LinkByUID(scope='local', id='pro_spec')
pr_link = LinkByUID(scope='local', id='pro_run')
spec = IngredientSpec(name='Ingred',
labels=['some', 'words'],
process=ps_link,
material=ms_link)
run = IngredientRun(spec=spec, process=pr_link, material=mr_link)
assert run.name == spec.name
assert run.labels == spec.labels
# Try changing them and make sure they change
spec.name = 'Frank'
spec.labels = ['other', 'words']
assert run.name == spec.name
assert run.labels == spec.labels
run.spec = LinkByUID(scope='local', id='ing_spec')
# Name and labels are now stashed but not stored
assert run == je.copy(run)
assert run.name == spec.name
assert run.labels == spec.labels
# Test that serialization doesn't get confused after a deser and set
spec_too = IngredientSpec(name='Jorge',
labels=[],
process=ps_link,
material=ms_link)
run.spec = spec_too
assert run == je.copy(run)
assert run.name == spec_too.name
assert run.labels == spec_too.labels
def test_to_link():
"""Test that to_link behaves as expected."""
obj = IngredientRun(uids={"Scope": "UID", "Second": "option"})
assert isinstance(obj.to_link(), LinkByUID), "Returns a useful LinkByUID"
assert LinkByUID(scope="Scope", id="UID") == obj.to_link("Scope"), "Correct choice of UID"
with pytest.raises(ValueError):
IngredientRun().to_link(), "to_link on an object w/o IDs is fatal"
with pytest.raises(ValueError):
obj.to_link("Third"), "to_link with a scope that an object lacks is fatal"
assert obj.to_link(scope="Third", allow_fallback=True).scope in obj.uids, \
"... unless allow_fallback is set"
def test_ingredient_run():
"""Tests that a process can house an ingredient, and that pairing survives serialization."""
# Create a ProcessSpec
proc_run = ProcessRun(name="a process spec", tags=["tag1", "tag2"])
ingred_run = IngredientRun(material=MaterialRun(name='Raw'), process=proc_run)
# Make copies of both specs
proc_run_copy = loads(dumps(proc_run))
assert proc_run_copy == proc_run, "Full structure wasn't preserved across serialization"
assert 'process' in repr(ingred_run)
assert 'ingredients' in repr(proc_run)
def test_many_ingredients():
"""Test that ingredients remain connected to processes when round-robined through json."""
proc = ProcessRun("foo", spec=ProcessSpec("sfoo"))
expected = []
for i in range(10):
mat = MaterialRun(name=str(i), spec=MaterialSpec("s{}".format(i)))
i_spec = IngredientSpec(name="i{}".format(i), material=mat.spec, process=proc.spec)
IngredientRun(process=proc, material=mat, spec=i_spec)
expected.append("i{}".format(i))
reloaded = loads(dumps(proc))
assert len(list(reloaded.ingredients)) == 10
names = [x.name for x in reloaded.ingredients]
assert sorted(names) == sorted(expected)
def test_implicit_fields():
"""These test that users can't directly set names and labels."""
name = 'name'
labels = ['label', 'also']
with pytest.raises(TypeError):
IngredientRun(name=name)
with pytest.raises(TypeError):
IngredientRun(labels=labels)
run = IngredientRun()
with pytest.raises(AttributeError):
run.name = name
with pytest.raises(AttributeError):
run.labels = labels
def test_ingredient_reassignment():
"""Check that an ingredient run can be re-assigned to a new process run."""
boiling = ProcessRun("Boil potatoes")
frying = ProcessRun("Fry potatoes")
oil = IngredientRun(process=boiling)
potatoes = IngredientRun(process=boiling)
assert oil.process == boiling
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}
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
