def test_object_template_serde():
"""Test serde of an object template."""
length_template = PropertyTemplate("Length", bounds=RealBounds(2.0, 3.5, 'cm'))
sub_bounds = RealBounds(2.5, 3.0, 'cm')
color_template = PropertyTemplate("Color", bounds=CategoricalBounds(["red", "green", "blue"]))
# Properties are a mixture of property templates and [template, bounds], pairs
block_template = MaterialTemplate("Block", properties=[[length_template, sub_bounds],
color_template])
copy_template = MaterialTemplate.build(block_template.dump())
assert copy_template == block_template
# Tests below exercise similar code, but for measurement and process templates
pressure_template = ConditionTemplate("pressure", bounds=RealBounds(0.1, 0.11, 'MPa'))
index_template = ParameterTemplate("index", bounds=IntegerBounds(2, 10))
meas_template = MeasurementTemplate("A measurement of length", properties=[length_template],
conditions=[pressure_template], description="Description",
parameters=[index_template], tags=["foo"])
assert MeasurementTemplate.build(meas_template.dump()) == meas_template
proc_template = ProcessTemplate("Make an object", parameters=[index_template],
conditions=[pressure_template], allowed_labels=["Label"],
allowed_names=["first sample", "second sample"])
assert ProcessTemplate.build(proc_template.dump()) == proc_template
# Check that serde still works if the template is a LinkByUID
pressure_template.uids['id'] = '12345' # uids['id'] not populated by default
proc_template.conditions[0][0] = LinkByUID('id', pressure_template.uids['id'])
assert ProcessTemplate.build(proc_template.dump()) == proc_template
def _build_child_objects(cls, data: dict, session: Session = None):
"""
Build the condition and parameter templates and bounds.
Parameters
----------
data: dict
A serialized material template.
session: Session, optional
Citrine session used to connect to the database.
Returns
-------
None
The serialized process template is modified so that its conditions are now a list
of object pairs of the form [ConditionTemplate,
:py:class:`BaseBounds <taurus.entity.bounds.base_bounds.BaseBounds>`],
and the parameters are [ParameterTemplate,
:py:class:`BaseBounds <taurus.entity.bounds.base_bounds.BaseBounds>`].
"""
if 'conditions' in data and len(data['conditions']) != 0:
data['conditions'] = [[
ConditionTemplate.build(cond[0].as_dict()),
loads(dumps(cond[1]))
] for cond in data['conditions']]
if 'parameters' in data and len(data['parameters']) != 0:
data['parameters'] = [[
ParameterTemplate.build(param[0].as_dict()),
loads(dumps(param[1]))
] for param in data['parameters']]
def test_no_data_objects():
objs = [
PropertyTemplate("pt", bounds=CategoricalBounds()),
ConditionTemplate("ct", bounds=CategoricalBounds())
]
templates, data_objects = split_templates_from_objects(objs)
assert len(templates) == 2
assert len(data_objects) == 0
def test_both_present():
objs = [
ProcessSpec("ps"),
PropertyTemplate("pt", bounds=CategoricalBounds()),
MeasurementSpec("ms"),
ConditionTemplate("ct", bounds=CategoricalBounds())
]
templates, data_objects = split_templates_from_objects(objs)
assert len(templates) == 2
assert len(data_objects) == 2
def test_template_assignment():
"""Test that an object and its attributes can both be assigned templates."""
humidity_template = ConditionTemplate("Humidity",
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)
])
def test_flatten():
"""Test that gemd utility methods can be applied to citrine-python objects.
Citrine-python resources extend the gemd data model, so the gemd operations
should work on them.
"""
bounds = CategoricalBounds(categories=["foo", "bar"])
template = ProcessTemplate(
"spam",
conditions=[(ConditionTemplate(name="eggs", bounds=bounds), bounds)]
)
spec = ProcessSpec(name="spec", template=template)
flat = flatten(spec, scope='testing')
assert len(flat) == 3, "Expected 3 flattened objects"
def test_condition_template():
"""Test creation and serde of condition templates."""
bounds = RealBounds(2.5, 10.0, default_units='cm')
template = ConditionTemplate("Chamber width", bounds=bounds, description="width of chamber")
assert template.uids is not None # uids should be added automatically
# Take template through a serde cycle and ensure that it is unchanged
assert ConditionTemplate.build(template.dump()) == template
# A more complicated cycle that goes through both gemd-python and citrine-python serde.
assert ConditionTemplate.build(loads(dumps(template.dump())).as_dict()) == template
def test_object_template_validation():
"""Test that attribute templates are validated against given bounds."""
length_template = PropertyTemplate("Length", bounds=RealBounds(2.0, 3.5, 'cm'))
dial_template = ConditionTemplate("dial", bounds=IntegerBounds(0, 5))
color_template = ParameterTemplate("Color", bounds=CategoricalBounds(["red", "green", "blue"]))
with pytest.raises(TypeError):
MaterialTemplate()
with pytest.raises(ValueError):
MaterialTemplate("Block", properties=[[length_template, RealBounds(3.0, 4.0, 'cm')]])
with pytest.raises(ValueError):
ProcessTemplate("a process", conditions=[[color_template, CategoricalBounds(["zz"])]])
with pytest.raises(ValueError):
MeasurementTemplate("A measurement", parameters=[[dial_template, IntegerBounds(-3, -1)]])
def test_register_data_concepts(dataset):
"""Check that register routes to the correct collections"""
expected = {
MaterialTemplateCollection:
MaterialTemplate("foo"),
MaterialSpecCollection:
MaterialSpec("foo"),
MaterialRunCollection:
MaterialRun("foo"),
ProcessTemplateCollection:
ProcessTemplate("foo"),
ProcessSpecCollection:
ProcessSpec("foo"),
ProcessRunCollection:
ProcessRun("foo"),
MeasurementTemplateCollection:
MeasurementTemplate("foo"),
MeasurementSpecCollection:
MeasurementSpec("foo"),
MeasurementRunCollection:
MeasurementRun("foo"),
IngredientSpecCollection:
IngredientSpec("foo"),
IngredientRunCollection:
IngredientRun(),
PropertyTemplateCollection:
PropertyTemplate("bar", bounds=IntegerBounds(0, 1)),
ParameterTemplateCollection:
ParameterTemplate("bar", bounds=IntegerBounds(0, 1)),
ConditionTemplateCollection:
ConditionTemplate("bar", bounds=IntegerBounds(0, 1))
}
for collection, obj in expected.items():
assert len(obj.uids) == 0
registered = dataset.register(obj)
assert len(obj.uids) == 1
assert len(registered.uids) == 1
assert basename(dataset.session.calls[-1].path) == basename(
collection._path_template)
for pair in obj.uids.items():
assert pair[1] == registered.uids[pair[0]]
def test_register_all_data_concepts(dataset):
"""Check that register_all registers everything and routes to all collections"""
bounds = IntegerBounds(0, 1)
property_template = PropertyTemplate("bar", bounds=bounds)
parameter_template = ParameterTemplate("bar", bounds=bounds)
condition_template = ConditionTemplate("bar", bounds=bounds)
foo_process_template = ProcessTemplate(
"foo",
conditions=[[condition_template, bounds]],
parameters=[[parameter_template, bounds]])
foo_process_spec = ProcessSpec("foo", template=foo_process_template)
foo_process_run = ProcessRun("foo", spec=foo_process_spec)
foo_material_template = MaterialTemplate(
"foo", properties=[[property_template, bounds]])
foo_material_spec = MaterialSpec("foo",
template=foo_material_template,
process=foo_process_spec)
foo_material_run = MaterialRun("foo",
spec=foo_material_spec,
process=foo_process_run)
baz_template = MaterialTemplate("baz")
foo_measurement_template = MeasurementTemplate(
"foo",
conditions=[[condition_template, bounds]],
parameters=[[parameter_template, bounds]],
properties=[[property_template, bounds]])
foo_measurement_spec = MeasurementSpec("foo",
template=foo_measurement_template)
foo_measurement_run = MeasurementRun("foo",
spec=foo_measurement_spec,
material=foo_material_run)
foo_ingredient_spec = IngredientSpec("foo",
material=foo_material_spec,
process=foo_process_spec)
foo_ingredient_run = IngredientRun(spec=foo_ingredient_spec,
material=foo_material_run,
process=foo_process_run)
baz_run = MeasurementRun("baz")
# worst order possible
expected = {
foo_ingredient_run: IngredientRunCollection,
foo_ingredient_spec: IngredientSpecCollection,
foo_measurement_run: MeasurementRunCollection,
foo_measurement_spec: MeasurementSpecCollection,
foo_measurement_template: MeasurementTemplateCollection,
foo_material_run: MaterialRunCollection,
foo_material_spec: MaterialSpecCollection,
foo_material_template: MaterialTemplateCollection,
foo_process_run: ProcessRunCollection,
foo_process_spec: ProcessSpecCollection,
foo_process_template: ProcessTemplateCollection,
baz_template: MaterialTemplateCollection,
baz_run: MeasurementRunCollection,
property_template: PropertyTemplateCollection,
parameter_template: ParameterTemplateCollection,
condition_template: ConditionTemplateCollection
}
for obj in expected:
assert len(obj.uids) == 0 # All should be without ids
registered = dataset.register_all(expected.keys())
assert len(registered) == len(expected)
seen_ids = set()
for obj in expected:
assert len(obj.uids) == 1 # All should now have exactly 1 id
for pair in obj.uids.items():
assert pair not in seen_ids # All ids are different
seen_ids.add(pair)
for obj in registered:
for pair in obj.uids.items():
assert pair in seen_ids # registered items have the same ids
call_basenames = [
call.path.split('/')[-2] for call in dataset.session.calls
]
collection_basenames = [
basename(collection._path_template)
for collection in expected.values()
]
assert set(call_basenames) == set(collection_basenames)
assert len(set(call_basenames)) == len(
call_basenames) # calls are batched internally
# spot check order. Does not check every constraint
assert call_basenames.index(
basename(
IngredientRunCollection._path_template)) > call_basenames.index(
basename(IngredientSpecCollection._path_template))
assert call_basenames.index(basename(
MaterialRunCollection._path_template)) > call_basenames.index(
basename(MaterialSpecCollection._path_template))
assert call_basenames.index(
basename(
MeasurementRunCollection._path_template)) > call_basenames.index(
basename(MeasurementSpecCollection._path_template))
assert call_basenames.index(basename(
ProcessRunCollection._path_template)) > call_basenames.index(
basename(ProcessSpecCollection._path_template))
assert call_basenames.index(basename(
MaterialSpecCollection._path_template)) > call_basenames.index(
basename(MaterialTemplateCollection._path_template))
assert call_basenames.index(
basename(
MeasurementSpecCollection._path_template)) > call_basenames.index(
basename(MeasurementTemplateCollection._path_template))
assert call_basenames.index(basename(
ProcessSpecCollection._path_template)) > call_basenames.index(
basename(ProcessTemplateCollection._path_template))
assert call_basenames.index(basename(
MaterialSpecCollection._path_template)) > call_basenames.index(
basename(ProcessSpecCollection._path_template))
assert call_basenames.index(basename(
MaterialSpecCollection._path_template)) > call_basenames.index(
basename(MeasurementSpecCollection._path_template))
assert call_basenames.index(
basename(MeasurementTemplateCollection._path_template)
) > call_basenames.index(
basename(ConditionTemplateCollection._path_template))
assert call_basenames.index(
basename(MeasurementTemplateCollection._path_template)
) > call_basenames.index(
basename(ParameterTemplateCollection._path_template))
assert call_basenames.index(
basename(
MaterialTemplateCollection._path_template)) > call_basenames.index(
basename(PropertyTemplateCollection._path_template))
def test_get_object_id_from_data_concepts_id_is_none():
template = ConditionTemplate(name='test', bounds=RealBounds(0.0, 1.0, ''))
template.uids = {'id': None}
with pytest.raises(ValueError):
get_object_id(template)
def test_get_object_id_from_data_concepts():
uid = str(uuid.uuid4())
template = ConditionTemplate(name='test',
bounds=RealBounds(0.0, 1.0, ''),
uids={'id': uid})
assert uid == get_object_id(template)