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_template_access():
"""A process run's template should be equal to its spec's template."""
template = ProcessTemplate("process template", uids={'id': str(uuid4())})
spec = ProcessSpec("A spec", uids={'id': str(uuid4())}, template=template)
proc = ProcessRun("A run", uids={'id': str(uuid4())}, spec=spec)
assert proc.template == template
proc.spec = LinkByUID.from_entity(spec)
assert proc.template is None
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_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 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_process_spec():
"""Tests that the Process Spec/Run connection persists when serializing."""
# Create the ProcessSpec
condition1 = Condition(name="a condition on the process in general")
spec = ProcessSpec(conditions=condition1)
# Create the ProcessRun with a link to the ProcessSpec from above
condition2 = Condition(name="a condition on this process run in particular")
process = ProcessRun(conditions=condition2, spec=spec)
copy_process = loads(dumps(process))
assert dumps(copy_process.spec) == dumps(spec), \
"Process spec should be preserved through serialization"
def __init__(self,
name: str,
*,
uids: Optional[Dict[str, str]] = None,
tags: Optional[List[str]] = None,
notes: Optional[str] = None,
conditions: Optional[List[Condition]] = None,
parameters: Optional[List[Parameter]] = None,
spec: Optional[GEMDProcessSpec] = None,
file_links: Optional[List[FileLink]] = None,
source: Optional[PerformedSource] = None):
if uids is None:
uids = dict()
DataConcepts.__init__(self, GEMDProcessRun.typ)
GEMDProcessRun.__init__(self,
name=name,
uids=uids,
tags=tags,
conditions=conditions,
parameters=parameters,
spec=spec,
file_links=file_links,
notes=notes,
source=source)
def test_invalid_assignment():
"""Invalid assignments to `spec` throw a TypeError."""
with pytest.raises(TypeError):
ProcessRun("name", spec=[ProcessSpec("spec")])
def test_serde():
"""Test that an object with a case-insensitive dict can be serialized properly."""
process = ProcessRun("A process", uids={'Foo': str(17)})
process_copy = loads(dumps(process))
assert process == process_copy
assert process_copy.uids['foo'] == process_copy.uids['Foo']