def test_contains_incompatible_units():
"""Make sure contains returns false when the units don't match."""
dim = RealBounds(lower_bound=0, upper_bound=100, default_units="m")
dim2 = RealBounds(lower_bound=0, upper_bound=100, default_units="kJ")
dim3 = RealBounds(lower_bound=0, upper_bound=100, default_units='')
assert not dim.contains(dim2)
assert not dim.contains(dim3)
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'
def test_object_template_serde():
"""Test serde of an object template."""
length_template = PropertyTemplate("Length", RealBounds(2.0, 3.5, 'cm'))
sub_bounds = RealBounds(2.5, 3.0, 'cm')
color_template = PropertyTemplate("Color", 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", RealBounds(0.1, 0.11, 'MPa'))
index_template = ParameterTemplate("index", 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
proc_template.conditions[0][0] = LinkByUID('id', pressure_template.uids['id'])
assert ProcessTemplate.build(proc_template.dump()) == proc_template
def test_bounds_mismatch():
"""Test that a mismatch between the attribute and given bounds throws a ValueError."""
attribute_bounds = RealBounds(0, 100, '')
object_bounds = RealBounds(200, 300, '')
cond_template = ConditionTemplate("a condition", bounds=attribute_bounds)
with pytest.raises(ValueError):
ProcessTemplate("a process template",
conditions=[[cond_template, object_bounds]])
def make_cake_templates():
"""Define all templates independently, as in the wild this will be an independent operation."""
tmpl = dict()
# Attributes
tmpl['Cooking time'] = ConditionTemplate(
name="Cooking time",
description="The time elapsed during a cooking process",
bounds=RealBounds(0, 7 * 24.0, "hr")
)
tmpl["Oven temperature setting"] = ParameterTemplate(
name="Oven temperature setting",
description="Where the knob points",
bounds=RealBounds(0, 2000.0, "K")
)
tmpl["Oven temperature"] = ConditionTemplate(
name="Oven temperature",
description="Actual temperature measured by the thermocouple",
bounds=RealBounds(0, 2000.0, "K")
)
tmpl["Tastiness"] = PropertyTemplate(
name="Tastiness",
description="Yumminess on a fairly arbitrary scale",
bounds=IntegerBounds(lower_bound=1, upper_bound=10)
)
# Objects
tmpl["Baking in an oven"] = ProcessTemplate(
name="Baking in an oven",
description='Using heat to promote chemical reactions in a material',
allowed_labels=['precursor'],
conditions=[(tmpl["Oven temperature"], RealBounds(0, 700, "degF"))],
parameters=[(tmpl["Oven temperature setting"], RealBounds(100, 550, "degF"))]
)
tmpl["Taste test"] = MeasurementTemplate(
name="Taste test",
properties=[tmpl["Tastiness"]]
)
tmpl["Dessert"] = MaterialTemplate(
name="Dessert",
properties=[tmpl["Tastiness"]]
)
tmpl["Generic Material"] = MaterialTemplate(name="Generic")
tmpl["Icing"] = ProcessTemplate(name="Icing",
description='Applying a coating to a substrate',
allowed_labels=['coating', 'substrate'])
tmpl["Mixing"] = ProcessTemplate(name="Mixing",
description='Physically combining ingredients',
allowed_labels=['wet', 'dry', 'leavening', 'seasoning',
'sweetener', 'shortening', 'flavoring'])
tmpl["Procurement"] = ProcessTemplate(name="Procurement",
description="Buyin' stuff")
return tmpl
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_constructor_error():
"""Test that invalid real bounds cannot be constructed."""
with pytest.raises(ValueError):
RealBounds()
with pytest.raises(ValueError):
RealBounds(0, float("inf"), "meter")
with pytest.raises(ValueError):
RealBounds(None, 10, '')
with pytest.raises(ValueError):
RealBounds(0, 100)
with pytest.raises(ValueError):
RealBounds(100, 0, "m")
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_contains():
"""Test basic contains logic."""
bounds = CompositionBounds(components={"spam", "eggs"})
assert bounds.contains(CompositionBounds(components={"spam"}))
assert not bounds.contains(CompositionBounds(components={"foo"}))
assert not bounds.contains(RealBounds(0.0, 2.0, ''))
assert not bounds.contains(None)
with pytest.raises(TypeError):
bounds.contains({"spam"})
def test_contains():
"""Test basic contains logic."""
bounds = CategoricalBounds(categories={"spam", "eggs"})
assert bounds.contains(CategoricalBounds(categories={"spam"}))
assert not bounds.contains(CategoricalBounds(categories={"spam", "foo"}))
assert not bounds.contains(RealBounds(0.0, 2.0, ''))
assert not bounds.contains(None)
with pytest.raises(TypeError):
bounds.contains({"spam", "eggs"})
def test_type_mismatch():
"""Test that incompatible types cannot be matched against RealBounds."""
bounds = RealBounds(0, 1, default_units="meters")
assert not bounds.contains(IntegerBounds(0, 1))
assert not bounds.contains(None)
with pytest.raises(TypeError):
bounds.contains([.33, .66])
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 taurus and citrine-python serde.
assert ConditionTemplate.build(loads(dumps(
template.dump())).as_dict()) == template
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_object_template_validation():
"""Test that attribute templates are validated against given bounds."""
length_template = PropertyTemplate("Length", RealBounds(2.0, 3.5, 'cm'))
dial_template = ConditionTemplate("dial", IntegerBounds(0, 5))
color_template = ParameterTemplate(
"Color", CategoricalBounds(["red", "green", "blue"]))
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_simple_deserialization(valid_data, attribute_list):
for (key, Attribute, AttributeTemplate) in attribute_list:
valid_data['type'] = key
valid_data['template']['type'] = key + '_template'
attribute: Attribute = Attribute.build(valid_data)
assert attribute.name == 'mass'
assert attribute.notes == 'This is a note'
assert attribute.value == NominalReal(5.0, units='gram')
assert attribute.template == \
AttributeTemplate('mass', uids={'id': valid_data['template']['uids']['id']},
description='mass of object', bounds=RealBounds(0.0, 20.0, 'gram')
)
assert attribute.origin == 'measured'
assert attribute.file_links == []
assert attribute.typ == key
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 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(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)
}, "<Material spec 'foo'>"),
(MaterialTemplate, {
'name': 'foo'
}, "<Material template 'foo'>"),
(MeasurementRun, {
'name': 'foo'
}, "<Measurement run 'foo'>"),
(MeasurementSpec, {
'name': 'foo'
}, "<Measurement spec 'foo'>"),
(MeasurementTemplate, {
'name': 'foo'
}, "<Measurement template 'foo'>"),
(ParameterTemplate, {
'name': 'foo',
'bounds': RealBounds(0, 1, '')
}, "<Parameter template 'foo'>"),
(ProcessRun, {
'name': 'foo'
}, "<Process run 'foo'>"),
(ProcessSpec, {
'name': 'foo'
}, "<Process spec 'foo'>"),
(ProcessTemplate, {
'name': 'foo'
}, "<Process template 'foo'>"),
(PropertyTemplate, {
'name': 'foo',
'bounds': RealBounds(0, 1, '')
}, "<Property template 'foo'>"),
(ConditionTemplate, {
def make_templates():
"""Build all templates needed for the table."""
tmpl = dict()
# Attribute Templates
attribute_feed = {
"Formula": [
PropertyTemplate,
CompositionBounds(components=EmpiricalFormula.all_elements())
],
"Crystallinity": [
ConditionTemplate,
CategoricalBounds(
['Amorphous', 'Polycrystalline', 'Single crystalline'])
],
"Color": [
PropertyTemplate,
CategoricalBounds([
'Amber', 'Black', 'Blue', 'Bluish', 'Bronze', 'Brown',
'Brown-Black', 'Copper-Red', 'Dark Brown', 'Dark Gray',
'Dark Green', 'Dark Red', 'Gray', 'Light Gray', 'Ocher',
'Orange', 'Orange-Red', 'Pale Yellow', 'Red', 'Red-Yellow',
'Violet', 'White', 'Yellow', 'Yellow-Orange', 'Yellow-White'
])
],
"Band gap": [
PropertyTemplate,
RealBounds(lower_bound=0.001, upper_bound=100, default_units='eV')
],
"Temperature": [
ConditionTemplate,
RealBounds(lower_bound=1, upper_bound=1000, default_units='K')
],
"Temperature derivative of band gap": [
PropertyTemplate,
RealBounds(lower_bound=-0.01,
upper_bound=0.01,
default_units='eV/K')
],
"Lasing": [PropertyTemplate,
CategoricalBounds(['True', 'False'])],
"Cathodoluminescence":
[PropertyTemplate,
CategoricalBounds(['True', 'False'])],
"Mechanical luminescence":
[PropertyTemplate,
CategoricalBounds(['True', 'False'])],
"Photoluminescence":
[PropertyTemplate,
CategoricalBounds(['True', 'False'])],
"Electroluminescence":
[PropertyTemplate,
CategoricalBounds(['True', 'False'])],
"Thermoluminescence":
[PropertyTemplate,
CategoricalBounds(['True', 'False'])],
"Morphology":
[ConditionTemplate,
CategoricalBounds(['Thin film', 'Bulk'])],
"Electric field polarization": [
ConditionTemplate,
CategoricalBounds([
'Parallel to A axis', 'Parallel to B axis',
'Parallel to C axis', 'Perpendicular to B axis',
'Perpendicular to C axis'
])
],
"Phase": [
ConditionTemplate,
CategoricalBounds([
'A', 'B', 'B1', 'B2', 'Fused quartz', 'Natural diamond',
'Rutile', 'Sapphire', 'Synthetic quartz'
])
],
"Crystal system": [
ConditionTemplate,
CategoricalBounds([
'Cubic', 'Hexagonal', 'Orthorhombic', 'Tetragonal', 'Trigonal'
])
],
"Transition": [
ConditionTemplate,
CategoricalBounds(['Direct', 'Excitonic', 'Indirect'])
],
"Bands": [
ConditionTemplate,
CategoricalBounds([
'G1 to X1', 'G15 to G1', 'G15 to X1', 'G25 to G1',
'G25 to G12', 'G25 to G15', 'G6 to G8', 'G8 to G6+',
'L6+ to L6-'
])
]
}
for (name, (typ, bounds)) in attribute_feed.items():
assert name not in tmpl
tmpl[name] = typ(name=name,
bounds=bounds,
uids={DEMO_SCOPE + '-template': name},
tags=['citrine::demo::template::attribute'])
# Object Templates
object_feed = {
"Sample preparation": [ProcessTemplate, dict()],
"Chemical": [MaterialTemplate, {
"properties": [tmpl["Formula"]]
}],
"Band gap measurement": [
MeasurementTemplate, {
"properties": [
tmpl["Band gap"],
tmpl["Temperature derivative of band gap"], tmpl["Color"],
tmpl["Lasing"], tmpl["Cathodoluminescence"],
tmpl["Mechanical luminescence"], tmpl["Photoluminescence"],
tmpl["Electroluminescence"], tmpl["Thermoluminescence"]
],
"conditions": [
tmpl["Temperature"], tmpl["Crystallinity"],
tmpl["Morphology"], tmpl["Electric field polarization"],
tmpl["Phase"], tmpl["Crystal system"], tmpl["Transition"],
tmpl["Bands"]
]
}
],
}
for (name, (typ, kw_args)) in object_feed.items():
assert name not in tmpl
tmpl[name] = typ(name=name,
uids={DEMO_SCOPE + '-template': name},
tags=['citrine::demo::template::object'],
**kw_args)
return tmpl
"""For entities that hve quantities."""
from taurus.entity.bounds.real_bounds import RealBounds
from taurus.entity.value.continuous_value import ContinuousValue
fraction_bounds = RealBounds(lower_bound=0.0, upper_bound=1.0, default_units='')
class HasQuantities(object):
"""Mixin-trait that includes the mass, volume, number fraction, and absolute quantity."""
def __init__(self, mass_fraction=None, volume_fraction=None, number_fraction=None,
absolute_quantity=None):
self._mass_fraction = None
self.mass_fraction = mass_fraction
self._volume_fraction = None
self.volume_fraction = volume_fraction
self._number_fraction = None
self.number_fraction = number_fraction
self._absolute_quantity = None
self.absolute_quantity = absolute_quantity
@property
def mass_fraction(self):
"""Get mass fraction."""
return self._mass_fraction
@mass_fraction.setter
def test_json():
"""Test that json serialization round robins to the identity."""
template = PropertyTemplate(name="foo", bounds=RealBounds(0, 1, ""))
copy = loads(dumps(template))
assert copy == template
from taurus.entity.object import MeasurementRun, MaterialRun, ProcessRun, ProcessSpec,\
MeasurementSpec, MaterialSpec
from taurus.entity.template.condition_template import ConditionTemplate
from taurus.entity.template.material_template import MaterialTemplate
from taurus.entity.template.measurement_template import MeasurementTemplate
from taurus.entity.template.process_template import ProcessTemplate
from taurus.entity.template.property_template import PropertyTemplate
from taurus.entity.value.discrete_categorical import DiscreteCategorical
from taurus.entity.value.nominal_composition import NominalComposition
from taurus.entity.value.nominal_real import NominalReal
from taurus.entity.value.normal_real import NormalReal
from taurus.entity.value.uniform_real import UniformReal
density_template = PropertyTemplate(
name="Density",
bounds=RealBounds(lower_bound=0, upper_bound=1.0e9, default_units='')
)
firing_temperature_template = ConditionTemplate(
name="Firing Temperature",
bounds=RealBounds(lower_bound=0, upper_bound=1.0e9, default_units='degC')
)
measurement_template = MeasurementTemplate(properties=density_template)
firing_template = ProcessTemplate(
name="Firing in a kiln",
conditions=(firing_temperature_template, RealBounds(lower_bound=500, upper_bound=1000,
default_units='degC'))
)
material_template = MaterialTemplate(
name="Some ceramic thing",
properties=density_template
def test_incompatible_types():
"""Make sure that incompatible types aren't contained or validated."""
int_bounds = IntegerBounds(0, 1)
assert not int_bounds.contains(RealBounds(0.0, 1.0, ''))
from taurus.entity.attribute.parameter import Parameter
from taurus.entity.attribute.property import Property
from taurus.entity.bounds.categorical_bounds import CategoricalBounds
from taurus.entity.bounds.real_bounds import RealBounds
from taurus.entity.object import MaterialRun, MeasurementRun
from taurus.entity.template.condition_template import ConditionTemplate
from taurus.entity.template.parameter_template import ParameterTemplate
from taurus.entity.template.property_template import PropertyTemplate
from taurus.entity.value.discrete_categorical import DiscreteCategorical
from taurus.entity.value.nominal_real import NominalReal
from taurus.entity.value.normal_real import NormalReal
known_properties = {
"density": PropertyTemplate(
name="density",
bounds=RealBounds(lower_bound=0.0, upper_bound=1000.0, default_units='g / cm^3')
),
"kinematic viscosity": PropertyTemplate(
name="kinematic viscosity",
bounds=RealBounds(lower_bound=0.0, upper_bound=10.0**40, default_units="m^2 / s")
)
}
known_conditions = {
"temperature": ConditionTemplate(
name="temperature",
bounds=RealBounds(lower_bound=0.0, upper_bound=1000.0, default_units='K')
)
}
known_parameters = {
def test_contains_no_units():
"""Make sure contains handles boundsless values."""
dim = RealBounds(lower_bound=0, upper_bound=100, default_units="")
dim2 = RealBounds(lower_bound=0, upper_bound=100, default_units="")
assert dim.contains(dim2)
def test_contains():
"""Make sure unit conversions are applied to bounds for contains."""
dim = RealBounds(lower_bound=0, upper_bound=100, default_units="degC")
dim2 = RealBounds(lower_bound=33, upper_bound=200, default_units="degF")
assert dim.contains(dim2)