def test_invalid_constructor():
"""Test types for constructor."""
with pytest.raises(ValueError):
CategoricalBounds(categories="foo")
with pytest.raises(ValueError):
CategoricalBounds(categories={1, 2})
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_categories():
"""Test categories setter."""
assert CategoricalBounds().categories == set()
assert CategoricalBounds(categories={"foo", "bar"}).categories == {
"foo", "bar"
}
assert CategoricalBounds(categories=["foo", "bar"]).categories == {
"foo", "bar"
}
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_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_numpy():
"""Test that ndarrays, Series work as well."""
assert len(array_like()) < 5 # In case we extend at some point
if len(array_like()) > 2: # Test numpy
import numpy as np
np_bounds = CategoricalBounds(np.array(["spam", "eggs"], dtype=object))
np_copy = loads(dumps(np_bounds))
assert np_copy == np_bounds
if len(array_like()) > 3: # Test numpy
import pandas as pd
pd_bounds = CategoricalBounds(pd.Series(["spam", "eggs"]))
pd_copy = loads(dumps(pd_bounds))
assert pd_copy == pd_bounds
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 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_flatten_bounds():
"""Test that flatten works when the objects contain other objects."""
bounds = CategoricalBounds(categories=["foo", "bar"])
template = ProcessTemplate(
"spam",
conditions=[(ConditionTemplate(name="eggs", bounds=bounds), bounds)]
)
spec = ProcessSpec(name="spec", template=template)
flat = flatten(spec, 'test-scope')
assert len(flat) == 2, "Expected 2 flattened objects"
def test_repeated_objects():
"""Test that objects aren't double counted."""
ct = ConditionTemplate(name="color",
bounds=CategoricalBounds(categories=["black", "white"]))
pt = ProcessTemplate(name="painting", conditions=[ct])
ps = ProcessSpec(name='painting',
template=pt,
conditions=Condition(name='Paint color',
value=NominalCategorical("black"),
template=ct
)
)
assert len(recursive_flatmap(ps, lambda x: [x])) == 3
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_fields_from_property():
"""Test that several fields of the attribute are derived from the property."""
prop_template = PropertyTemplate(name="cookie eating template", bounds=IntegerBounds(0, 1000))
cond_template = ConditionTemplate(name="Hunger template",
bounds=CategoricalBounds(["hungry", "full", "peckish"]))
prop = Property(name="number of cookies eaten",
template=prop_template,
origin='measured',
value=NominalInteger(27))
cond = Condition(name="hunger level",
template=cond_template,
origin='specified',
value=NominalCategorical("hungry"))
prop_and_conds = PropertyAndConditions(property=prop, conditions=[cond])
assert prop_and_conds.name == prop.name
assert prop_and_conds.template == prop.template
assert prop_and_conds.origin == prop.origin
assert prop_and_conds.value == prop.value
def make_templates(template_scope=DEMO_TEMPLATE_SCOPE):
"""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={template_scope: 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={template_scope: name},
tags=['citrine::demo::template::object'],
**kw_args)
return tmpl
def test_property_template():
"""Test creation and serde of condition templates."""
bounds = CategoricalBounds(['solid', 'liquid', 'gas'])
template = PropertyTemplate("State", bounds=bounds, uids={'my_id': '0'})
assert PropertyTemplate.build(template.dump()) == template
from gemd.entity.bounds.real_bounds import RealBounds
from gemd.entity.value.uniform_real import UniformReal
from gemd.entity.template.attribute_template import AttributeTemplate
from gemd.entity.template.property_template import PropertyTemplate
from gemd.entity.template.condition_template import ConditionTemplate
from gemd.entity.template.parameter_template import ParameterTemplate
from gemd.json import dumps, loads
class SampleAttributeTemplate(AttributeTemplate):
"""A class to flex the base attribute template."""
typ = "sample_attribute_template"
cat_bounds = CategoricalBounds(categories={"a", "b", "c"})
def test_name_is_a_string():
"""Test that name is a string."""
with pytest.raises(ValueError) as error:
SampleAttributeTemplate(name=42, bounds=cat_bounds)
assert "must be a string" in str(error.value)
def test_invalid_bounds():
"""Test that invalid bounds throw the appropriate error."""
with pytest.raises(ValueError):
SampleAttributeTemplate(name="name") # Must have a bounds
with pytest.raises(TypeError):
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 = {
"knob_2_setting": ParameterTemplate(
name="knob_2_setting",
bounds=CategoricalBounds(categories={"low", "medium", "high"})
)
}
def _parse_value(val):
"""Example field-parsing logic."""
# If the string is complicated, split it up and try to get uncertainty and/or units
if isinstance(val, str) and len(val.split()) > 1:
toks = val.split()
mean = float(toks[0])
std = -1
if toks[1] in {"+-", "+/-"}:
std = float(toks[2])
try:
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"})
from gemd.entity.value import NominalCategorical
assert bounds.contains(NominalCategorical("spam"))
assert not bounds.contains(NominalCategorical("foo"))
def test_json():
"""Test that serialization works (categories is encoded as a list)."""
bounds = CategoricalBounds(categories={"spam", "eggs"})
copy = loads(dumps(bounds))
assert copy == bounds