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1620 lines (1451 loc) · 65.5 KB
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"""Test the project module."""
import copy
import re
import tempfile
import warnings
from pathlib import Path
from typing import Callable
import numpy as np
import pydantic
import pytest
from typing_extensions import get_args, get_origin
import ratapi
from ratapi.utils.enums import Calculations, LayerModels, TypeOptions
layer_params = {"thickness": "Test Thickness", "SLD": "Test SLD", "roughness": "Test Roughness"}
absorption_layer_params = {
"thickness": "Test Thickness",
"SLD_real": "Test SLD",
"SLD_imaginary": "Test SLD",
"roughness": "Test Roughness",
}
model_classes = {
"parameters": ratapi.models.Parameter,
"bulk_in": ratapi.models.Parameter,
"bulk_out": ratapi.models.Parameter,
"scalefactors": ratapi.models.Parameter,
"domain_ratios": ratapi.models.Parameter,
"background_parameters": ratapi.models.Parameter,
"resolution_parameters": ratapi.models.Parameter,
"backgrounds": ratapi.models.Background,
"resolutions": ratapi.models.Resolution,
"custom_files": ratapi.models.CustomFile,
"data": ratapi.models.Data,
"layers": ratapi.models.Layer,
"domain_contrasts": ratapi.models.DomainContrast,
"contrasts": ratapi.models.Contrast,
}
@pytest.fixture
def test_project():
"""Add parameters to the default project, so each ClassList can be tested properly."""
test_project = ratapi.Project(
data=ratapi.ClassList([ratapi.models.Data(name="Simulation", data=np.array([[1.0, 1.0, 1.0]]))]),
)
test_project.parameters.append(name="Test Thickness")
test_project.parameters.append(name="Test SLD")
test_project.parameters.append(name="Test Roughness")
test_project.custom_files.append(name="Test Custom File")
test_project.layers.append(
name="Test Layer",
thickness="Test Thickness",
SLD="Test SLD",
roughness="Test Roughness",
)
test_project.contrasts.append(
name="Test Contrast",
data="Simulation",
background="Background 1",
bulk_in="SLD Air",
bulk_out="SLD D2O",
scalefactor="Scalefactor 1",
resolution="Resolution 1",
model=["Test Layer"],
)
return test_project
@pytest.fixture
def default_project_str():
"""A string of the output of str() for a Project model with no parameters specified."""
return (
"Calculation: ---------------------------------------------------------------------------------------\n\n"
"normal\n\n"
"Model: ---------------------------------------------------------------------------------------------\n\n"
"standard layers\n\n"
"Geometry: ------------------------------------------------------------------------------------------\n\n"
"air/substrate\n\n"
"Parameters: ----------------------------------------------------------------------------------------\n\n"
"+-------+---------------------+-----+-------+-----+------+\n"
"| index | name | min | value | max | fit |\n"
"+-------+---------------------+-----+-------+-----+------+\n"
"| 0 | Substrate Roughness | 1.0 | 3.0 | 5.0 | True |\n"
"+-------+---------------------+-----+-------+-----+------+\n\n"
"Bulk In: -------------------------------------------------------------------------------------------\n\n"
"+-------+---------+-----+-------+-----+-------+\n"
"| index | name | min | value | max | fit |\n"
"+-------+---------+-----+-------+-----+-------+\n"
"| 0 | SLD Air | 0.0 | 0.0 | 0.0 | False |\n"
"+-------+---------+-----+-------+-----+-------+\n\n"
"Bulk Out: ------------------------------------------------------------------------------------------\n\n"
"+-------+---------+---------+----------+----------+-------+\n"
"| index | name | min | value | max | fit |\n"
"+-------+---------+---------+----------+----------+-------+\n"
"| 0 | SLD D2O | 6.2e-06 | 6.35e-06 | 6.35e-06 | False |\n"
"+-------+---------+---------+----------+----------+-------+\n\n"
"Scalefactors: --------------------------------------------------------------------------------------\n\n"
"+-------+---------------+------+-------+------+-------+\n"
"| index | name | min | value | max | fit |\n"
"+-------+---------------+------+-------+------+-------+\n"
"| 0 | Scalefactor 1 | 0.02 | 0.23 | 0.25 | False |\n"
"+-------+---------------+------+-------+------+-------+\n\n"
"Background Parameters: -----------------------------------------------------------------------------\n\n"
"+-------+--------------------+-------+-------+-------+-------+\n"
"| index | name | min | value | max | fit |\n"
"+-------+--------------------+-------+-------+-------+-------+\n"
"| 0 | Background Param 1 | 1e-07 | 1e-06 | 1e-05 | False |\n"
"+-------+--------------------+-------+-------+-------+-------+\n\n"
"Backgrounds: ---------------------------------------------------------------------------------------\n\n"
"+-------+--------------+----------+--------------------+\n"
"| index | name | type | source |\n"
"+-------+--------------+----------+--------------------+\n"
"| 0 | Background 1 | constant | Background Param 1 |\n"
"+-------+--------------+----------+--------------------+\n\n"
"Resolution Parameters: -----------------------------------------------------------------------------\n\n"
"+-------+--------------------+------+-------+------+-------+\n"
"| index | name | min | value | max | fit |\n"
"+-------+--------------------+------+-------+------+-------+\n"
"| 0 | Resolution Param 1 | 0.01 | 0.03 | 0.05 | False |\n"
"+-------+--------------------+------+-------+------+-------+\n\n"
"Resolutions: ---------------------------------------------------------------------------------------\n\n"
"+-------+--------------+----------+--------------------+\n"
"| index | name | type | source |\n"
"+-------+--------------+----------+--------------------+\n"
"| 0 | Resolution 1 | constant | Resolution Param 1 |\n"
"+-------+--------------+----------+--------------------+\n\n"
"Data: ----------------------------------------------------------------------------------------------\n\n"
"+-------+------------+------+------------+------------------+\n"
"| index | name | data | data range | simulation range |\n"
"+-------+------------+------+------------+------------------+\n"
"| 0 | Simulation | [] | [] | [0.005, 0.7] |\n"
"+-------+------------+------+------------+------------------+\n\n"
)
def test_classlists(test_project) -> None:
"""The ClassLists in the "Project" model should contain instances of the models given by the dictionary
"model_in_classlist".
"""
for model in (fields := ratapi.Project.model_fields):
if get_origin(fields[model].annotation) == ratapi.ClassList:
class_list = getattr(test_project, model)
assert class_list._class_handle == get_args(fields[model].annotation)[0]
def test_classlists_specific_cases() -> None:
"""The ClassLists in the "Project" model should contain instances of specific models given various non-default
options.
"""
project = ratapi.Project(calculation=Calculations.Domains, absorption=True)
assert project.layers._class_handle.__name__ == "AbsorptionLayer"
assert project.contrasts._class_handle.__name__ == "ContrastWithRatio"
@pytest.mark.parametrize(
["input_model", "model_params"],
[
(ratapi.models.Background, {}),
(ratapi.models.Contrast, {}),
(ratapi.models.ContrastWithRatio, {}),
(ratapi.models.CustomFile, {}),
(ratapi.models.Data, {}),
(ratapi.models.DomainContrast, {}),
(ratapi.models.Layer, layer_params),
(ratapi.models.AbsorptionLayer, absorption_layer_params),
(ratapi.models.Resolution, {}),
],
)
def test_initialise_wrong_classes(input_model: Callable, model_params: dict) -> None:
"""If the "Project" model is initialised with incorrect classes, we should raise a ValidationError."""
with pytest.raises(
pydantic.ValidationError,
match="1 validation error for Project\nparameters\n "
"Value error, This ClassList only supports elements of type Parameter. In the input list:\n"
f" index 0 is of type {input_model.__name__}",
):
ratapi.Project(parameters=ratapi.ClassList(input_model(**model_params)))
@pytest.mark.parametrize(
["input_model", "model_params", "absorption", "actual_model_name"],
[
(ratapi.models.Layer, layer_params, True, "AbsorptionLayer"),
(ratapi.models.AbsorptionLayer, absorption_layer_params, False, "Layer"),
],
)
def test_initialise_wrong_layers(
input_model: Callable,
model_params: dict,
absorption: bool,
actual_model_name: str,
) -> None:
"""If the "Project" model is initialised with the incorrect layer model given the value of absorption, we should
raise a ValidationError.
"""
with pytest.raises(
pydantic.ValidationError,
match=f"1 validation error for Project\nlayers\n Value error, "
f'"The layers attribute contains {input_model.__name__}s, but the absorption parameter is '
f'{absorption}. The attribute should be a ClassList of {actual_model_name} instead."',
):
ratapi.Project(absorption=absorption, layers=ratapi.ClassList(input_model(**model_params)))
@pytest.mark.parametrize(
["input_model", "calculation", "actual_model_name"],
[
(ratapi.models.Contrast, Calculations.Domains, "ContrastWithRatio"),
(ratapi.models.ContrastWithRatio, Calculations.Normal, "Contrast"),
],
)
def test_initialise_wrong_contrasts(
input_model: ratapi.models.RATModel, calculation: Calculations, actual_model_name: str
) -> None:
"""If the "Project" model is initialised with the incorrect contrast model given the value of calculation, we
should raise a ValidationError.
"""
word = "without" if calculation == Calculations.Domains else "with"
with pytest.raises(
pydantic.ValidationError,
match=f"1 validation error for Project\ncontrasts\n"
f' Value error, "The contrasts attribute contains contrasts {word} ratio, '
f'but the calculation is {calculation}"',
):
ratapi.Project(calculation=calculation, contrasts=ratapi.ClassList(input_model()))
@pytest.mark.parametrize(
"calculation, model",
[(Calculations.Domains, ratapi.models.ContrastWithRatio), (Calculations.Normal, ratapi.models.Contrast)],
)
def test_initialise_ambiguous_contrasts(calculation: Calculations, model: ratapi.models.RATModel):
"""If a sequence of dictionaries is passed to 'contrasts', convert them to the correct model for the calculation."""
proj = ratapi.Project(calculation=calculation, contrasts=ratapi.ClassList([{"name": "Contrast 1"}]))
assert proj.contrasts._class_handle == model
def test_initialise_without_substrate_roughness() -> None:
"""If the "Project" model is initialised without "Substrate Roughness" as a parameter, add it as a protected
parameter to the front of the "parameters" ClassList.
"""
project = ratapi.Project(parameters=ratapi.ClassList(ratapi.models.Parameter(name="Test Parameter")))
assert project.parameters[0] == ratapi.models.ProtectedParameter(
name="Substrate Roughness",
min=1.0,
value=3.0,
max=5.0,
fit=True,
prior_type=ratapi.models.Priors.Uniform,
mu=0.0,
sigma=np.inf,
)
@pytest.mark.parametrize(
"input_parameter",
[
ratapi.models.Parameter(name="Substrate Roughness"),
ratapi.models.Parameter(name="SUBSTRATE ROUGHNESS"),
ratapi.models.Parameter(name="substrate roughness"),
],
)
def test_initialise_without_protected_substrate_roughness(input_parameter: ratapi.models.Parameter) -> None:
"""If the "Project" model is initialised without "Substrate Roughness" as a protected parameter, add it to the
front of the "parameters" ClassList.
"""
project = ratapi.Project(parameters=ratapi.ClassList(input_parameter))
assert project.parameters[0] == ratapi.models.ProtectedParameter(name=input_parameter.name)
def test_initialise_without_simulation() -> None:
"""If the "Project" model is initialised without "Simulation" in the "data" ClassList, add it to the front of the
"data" ClassList.
"""
project = ratapi.Project(parameters=ratapi.ClassList(ratapi.models.Parameter(name="Test Parameter")))
assert project.data[0] == ratapi.models.Data(name="Simulation", simulation_range=[0.005, 0.7])
@pytest.mark.parametrize(
["field", "model_type", "wrong_input_model", "model_params"],
[
("backgrounds", "Background", ratapi.models.Resolution, {}),
("contrasts", "Contrast", ratapi.models.Layer, layer_params),
("domain_contrasts", "DomainContrast", ratapi.models.Parameter, {}),
("custom_files", "CustomFile", ratapi.models.Data, {}),
("data", "Data", ratapi.models.Contrast, {}),
("layers", "Layer", ratapi.models.DomainContrast, {}),
("parameters", "Parameter", ratapi.models.CustomFile, {}),
("resolutions", "Resolution", ratapi.models.Background, {}),
],
)
def test_assign_wrong_classes(
test_project, field: str, model_type: str, wrong_input_model: Callable, model_params: dict
) -> None:
"""If we assign incorrect classes to the "Project" model, we should raise a ValidationError."""
if field == "contrasts":
field_name = "contrasts.no_ratio"
elif field == "layers":
field_name = "layers.no_abs"
else:
field_name = field
with pytest.raises(
pydantic.ValidationError,
match=(
f"1 validation error for Project\n{field_name}\n"
f" Value error, This ClassList only supports elements of type {model_type}. In the input list:\n"
f" index 0 is of type {wrong_input_model.__name__}"
),
):
setattr(test_project, field, ratapi.ClassList(wrong_input_model(**model_params)))
@pytest.mark.parametrize(
["wrong_input_model", "model_params", "absorption", "actual_model_name"],
[
(ratapi.models.Layer, layer_params, True, "AbsorptionLayer"),
(ratapi.models.AbsorptionLayer, absorption_layer_params, False, "Layer"),
],
)
def test_assign_wrong_layers(
wrong_input_model: Callable,
model_params: dict,
absorption: bool,
actual_model_name: str,
) -> None:
"""If we assign incorrect classes to the "Project" model, we should raise a ValidationError."""
project = ratapi.Project(absorption=absorption)
with pytest.raises(
pydantic.ValidationError,
match=f"1 validation error for Project\nlayers\n Value error, "
f'"The layers attribute contains {wrong_input_model.__name__}s, but the absorption parameter is '
f'{absorption}. The attribute should be a ClassList of {actual_model_name} instead."',
):
project.layers = ratapi.ClassList(wrong_input_model(**model_params))
@pytest.mark.parametrize(
["wrong_input_model", "calculation", "actual_model_name"],
[
(ratapi.models.Contrast, Calculations.Domains, "ContrastWithRatio"),
(ratapi.models.ContrastWithRatio, Calculations.Normal, "Contrast"),
],
)
def test_assign_wrong_contrasts(wrong_input_model: Callable, calculation: Calculations, actual_model_name: str) -> None:
"""If we assign incorrect classes to the "Project" model, we should raise a ValidationError."""
project = ratapi.Project(calculation=calculation)
word = "without" if calculation == Calculations.Domains else "with"
with pytest.raises(
pydantic.ValidationError,
match=f"1 validation error for Project\ncontrasts\n"
f' Value error, "The contrasts attribute contains contrasts {word} ratio, but the calculation is '
f'{calculation}"',
):
project.contrasts = ratapi.ClassList(wrong_input_model())
@pytest.mark.parametrize(
["field", "model_params"],
[
("backgrounds", {}),
("contrasts", {}),
("custom_files", {}),
("data", {}),
("layers", layer_params),
("parameters", {}),
("resolutions", {}),
],
)
def test_assign_models(test_project, field: str, model_params: dict) -> None:
"""If the "Project" model is initialised with models rather than ClassLists, we should raise a ValidationError."""
input_model = model_classes[field]
with pytest.raises(
pydantic.ValidationError,
match=f"1 validation error for Project\n{field}\n Input should be an instance of ClassList",
):
setattr(test_project, field, input_model(**model_params))
def test_wrapped_routines(test_project) -> None:
"""When initialising a project, several ClassList routines should be wrapped."""
wrapped_methods = [
"_setitem",
"_delitem",
"_iadd",
"append",
"insert",
"pop",
"remove",
"clear",
"extend",
"set_fields",
]
for class_list in ratapi.project.class_lists:
attribute = getattr(test_project, class_list)
for methodName in wrapped_methods:
assert hasattr(getattr(attribute, methodName), "__wrapped__")
def test_set_domain_ratios(test_project) -> None:
"""If we are not running a domains calculation, the "domain_ratios" field of the model should always be empty."""
assert test_project.domain_ratios == []
test_project.domain_ratios.append(name="New Domain Ratio")
assert test_project.domain_ratios == []
@pytest.mark.parametrize(
"project_parameters",
[
({"calculation": Calculations.Normal, "model": LayerModels.StandardLayers}),
({"calculation": Calculations.Normal, "model": LayerModels.CustomLayers}),
({"calculation": Calculations.Normal, "model": LayerModels.CustomXY}),
({"calculation": Calculations.Domains, "model": LayerModels.CustomLayers}),
({"calculation": Calculations.Domains, "model": LayerModels.CustomXY}),
],
)
def test_set_domain_contrasts(project_parameters: dict) -> None:
"""If we are not running a domains calculation with standard layers, the "domain_contrasts" field of the model
should always be empty.
"""
project = ratapi.Project(**project_parameters)
assert project.domain_contrasts == []
project.domain_contrasts.append(name="New Domain Contrast")
assert project.domain_contrasts == []
@pytest.mark.parametrize(
"project_parameters",
[
({"model": LayerModels.CustomLayers}),
({"model": LayerModels.CustomXY}),
],
)
def test_set_layers(project_parameters: dict) -> None:
"""If we are not using a standard layers model, the "layers" field of the model should always be empty."""
project = ratapi.Project(**project_parameters)
assert project.layers == []
project.layers.append(name="New Layer", thickness="Test Thickness", SLD="Test SLD", roughness="Test Roughness")
assert project.layers == []
@pytest.mark.parametrize(
["input_calculation", "input_contrast", "new_calculation", "new_contrast_model", "num_domain_ratios"],
[
(Calculations.Normal, ratapi.models.Contrast, Calculations.Domains, "ContrastWithRatio", 1),
(Calculations.Domains, ratapi.models.ContrastWithRatio, Calculations.Normal, "Contrast", 0),
],
)
def test_set_calculation(
input_calculation: Calculations,
input_contrast: Callable,
new_calculation: Calculations,
new_contrast_model: str,
num_domain_ratios: int,
) -> None:
"""When changing the value of the calculation option, the "contrasts" ClassList should switch to using the
appropriate Contrast model.
"""
project = ratapi.Project(calculation=input_calculation, contrasts=ratapi.ClassList(input_contrast()))
project.calculation = new_calculation
assert project.calculation is new_calculation
assert type(project.contrasts[0]).__name__ == new_contrast_model
assert project.contrasts._class_handle.__name__ == new_contrast_model
assert len(project.domain_ratios) == num_domain_ratios
@pytest.mark.parametrize(
["new_calc", "new_model", "expected_contrast_model"],
[
(Calculations.Normal, LayerModels.StandardLayers, ["Test Layer"]),
(Calculations.Normal, LayerModels.CustomLayers, []),
(Calculations.Normal, LayerModels.CustomXY, []),
(Calculations.Domains, LayerModels.StandardLayers, []),
(Calculations.Domains, LayerModels.CustomLayers, []),
(Calculations.Domains, LayerModels.CustomXY, []),
],
)
def test_set_contrast_model_field(
test_project,
new_calc: Calculations,
new_model: LayerModels,
expected_contrast_model: list[str],
) -> None:
"""If we change the calculation and model such that the values of the "model" field of the "contrasts" model come
from a different field of the project, we should clear the contrast "model" field.
"""
test_project.calculation = new_calc
test_project.model = new_model
assert test_project.contrasts[0].model == expected_contrast_model
@pytest.mark.parametrize(
["input_model", "test_contrast_model", "error_message"],
[
(
LayerModels.StandardLayers,
["Test Domain Ratio"],
'For a standard layers domains calculation the "model" field of "contrasts" must contain exactly two '
"values.",
),
(
LayerModels.StandardLayers,
["Test Domain Ratio", "Test Domain Ratio", "Test Domain Ratio"],
'For a standard layers domains calculation the "model" field of "contrasts" must contain exactly two '
"values.",
),
(
LayerModels.CustomLayers,
["Test Custom File", "Test Custom File"],
'For a custom model calculation the "model" field of "contrasts" cannot contain more than one value.',
),
],
)
def test_check_contrast_model_length(
test_project,
input_model: LayerModels,
test_contrast_model: list[str],
error_message: str,
) -> None:
"""If we are not running a domains calculation with standard layers, the "domain_contrasts" field of the model
should always be empty.
"""
test_domain_ratios = ratapi.ClassList(ratapi.models.Parameter(name="Test Domain Ratio"))
test_contrasts = ratapi.ClassList(ratapi.models.ContrastWithRatio(model=test_contrast_model))
with pytest.raises(
pydantic.ValidationError,
match=f"1 validation error for Project\n Value error, {error_message}",
):
ratapi.Project(
calculation=Calculations.Domains,
model=input_model,
domain_ratios=test_domain_ratios,
contrasts=test_contrasts,
)
@pytest.mark.parametrize(
["input_layer", "model_params", "input_absorption", "new_layer_model"],
[
(ratapi.models.Layer, layer_params, False, "AbsorptionLayer"),
(ratapi.models.AbsorptionLayer, absorption_layer_params, True, "Layer"),
],
)
def test_set_absorption(
input_layer: Callable,
model_params: dict,
input_absorption: bool,
new_layer_model: str,
) -> None:
"""When changing the value of the absorption option, the "layers" ClassList should switch to using the appropriate
Layer model.
"""
project = ratapi.Project(
absorption=input_absorption,
parameters=ratapi.ClassList(
[
ratapi.models.Parameter(name="Test Thickness"),
ratapi.models.Parameter(name="Test SLD"),
ratapi.models.Parameter(name="Test Roughness"),
],
),
layers=ratapi.ClassList(input_layer(**model_params)),
)
project.absorption = not input_absorption
assert project.absorption is not input_absorption
assert type(project.layers[0]).__name__ == new_layer_model
assert project.layers._class_handle.__name__ == new_layer_model
@pytest.mark.parametrize(
"delete_operation",
[
"project.parameters.__delitem__(0)",
"project.parameters.pop()",
'project.parameters.remove("Substrate Roughness")',
"project.parameters.clear()",
],
)
def test_check_protected_parameters(delete_operation) -> None:
"""If we try to remove a protected parameter, we should raise an error."""
project = ratapi.Project()
with pytest.raises(
pydantic.ValidationError,
match="1 validation error for Project\n Value error, "
"Can't delete the protected parameters: Substrate Roughness",
):
eval(delete_operation)
# Ensure model was not deleted
assert project.parameters[0].name == "Substrate Roughness"
@pytest.mark.parametrize(
["model", "fields"],
[
("background_parameters", ["source"]),
("resolution_parameters", ["source"]),
("parameters", ["roughness"]),
("data", ["data", "source"]),
("custom_files", ["source", "source"]),
("backgrounds", ["background"]),
("bulk_in", ["bulk_in"]),
("bulk_out", ["bulk_out"]),
("scalefactors", ["scalefactor"]),
("resolutions", ["resolution"]),
],
)
def test_rename_models(test_project, model: str, fields: list[str]) -> None:
"""When renaming a model in the project, the new name should be recorded when that model is referred to elsewhere
in the project.
"""
if model == "data":
test_project.backgrounds[0] = ratapi.models.Background(type="data", source="Simulation")
if model == "custom_files":
test_project.backgrounds[0] = ratapi.models.Background(type="function", source="Test Custom File")
# workaround until function resolutions are added
# test_project.resolutions[0] = ratapi.models.Resolution(type="function", source="Test Custom File")
test_project.resolution_parameters.append(ratapi.models.Parameter(name="New Name"))
test_project.resolutions[0] = ratapi.models.Resolution(type="constant", source="New Name")
getattr(test_project, model).set_fields(-1, name="New Name")
model_name_lists = ratapi.project.model_names_used_in[model]
for model_name_list, field in zip(model_name_lists, fields):
attribute = model_name_list.attribute
assert getattr(getattr(test_project, attribute)[-1], field) == "New Name"
@pytest.mark.parametrize(
"background_type, expected_field",
[
[TypeOptions.Constant, "background_parameters"],
[TypeOptions.Data, "data"],
[TypeOptions.Function, "custom_files"],
],
)
def test_allowed_backgrounds(background_type, expected_field) -> None:
"""
If the source field of the Background model is set to a value that is not specified in the appropriate ClassList,
we should raise a ValidationError.
"""
test_background = ratapi.models.Background(type=background_type, source="undefined")
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f'1 validation error for Project\n Value error, The value "undefined" used in the "source" field of '
f'backgrounds[0] must be defined in "{expected_field}". Please add "undefined" to "{expected_field}" '
f'before including it in "backgrounds".'
),
):
ratapi.Project(backgrounds=ratapi.ClassList(test_background))
@pytest.mark.parametrize(
"field",
[
"thickness",
"SLD",
"roughness",
],
)
def test_allowed_layers(field: str) -> None:
"""If the "thickness", "SLD", or "roughness" fields of the Layer model are set to values that are not specified in
the parameters, we should raise a ValidationError.
"""
test_layer = ratapi.models.Layer(**{**layer_params, field: "undefined"})
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f'1 validation error for Project\n Value error, The value "undefined" used in the "{field}" '
f'field of layers[0] must be defined in "parameters". Please add "undefined" to "parameters" '
f'before including it in "layers".'
),
):
ratapi.Project(
absorption=False,
parameters=ratapi.ClassList(
[
ratapi.models.Parameter(name="Test Thickness"),
ratapi.models.Parameter(name="Test SLD"),
ratapi.models.Parameter(name="Test Roughness"),
],
),
layers=ratapi.ClassList(test_layer),
)
@pytest.mark.parametrize(
"field",
[
"thickness",
"SLD_real",
"SLD_imaginary",
"roughness",
],
)
def test_allowed_absorption_layers(field: str) -> None:
"""If the "thickness", "SLD_real", "SLD_imaginary", or "roughness" fields of the AbsorptionLayer model are set to
values that are not specified in the parameters, we should raise a ValidationError.
"""
test_layer = ratapi.models.AbsorptionLayer(**{**absorption_layer_params, field: "undefined"})
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f'1 validation error for Project\n Value error, The value "undefined" used in the "{field}" field of '
f'layers[0] must be defined in "parameters". Please add "undefined" to "parameters" before including it '
f'in "layers".'
),
):
ratapi.Project(
absorption=True,
parameters=ratapi.ClassList(
[
ratapi.models.Parameter(name="Test Thickness"),
ratapi.models.Parameter(name="Test SLD"),
ratapi.models.Parameter(name="Test Roughness"),
],
),
layers=ratapi.ClassList(test_layer),
)
@pytest.mark.parametrize(
"resolution_type, expected_field",
[
[TypeOptions.Constant, "resolution_parameters"],
# uncomment when function resolutions are added!
# [TypeOptions.Function, "custom_files"],
],
)
def test_allowed_resolutions(resolution_type, expected_field) -> None:
"""If the "value" fields of the Resolution model are set to values that are not specified in the resolution
parameters, we should raise a ValidationError.
"""
test_resolution = ratapi.models.Resolution(type=resolution_type, source="undefined")
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f'1 validation error for Project\n Value error, The value "undefined" used in the "source" field of '
f'resolutions[0] must be defined in "{expected_field}". Please add "undefined" to "{expected_field}" '
f'before including it in "resolutions".'
),
):
ratapi.Project(resolutions=ratapi.ClassList(test_resolution))
@pytest.mark.parametrize(
["field", "model_name"],
[
("data", "data"),
("background", "backgrounds"),
("bulk_in", "bulk_in"),
("bulk_out", "bulk_out"),
("scalefactor", "scalefactors"),
("resolution", "resolutions"),
],
)
def test_allowed_contrasts(field: str, model_name: str) -> None:
"""If the fields of the Contrast model are set to values not specified in the other respective models of the
project, we should raise a ValidationError.
"""
test_contrast = ratapi.models.Contrast(**{field: "undefined"})
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f'1 validation error for Project\n Value error, The value "undefined" used in the "{field}" field of '
f'contrasts[0] must be defined in "{model_name}". Please add "undefined" to "{model_name}" before '
f'including it in "contrasts".'
),
):
ratapi.Project(calculation=Calculations.Normal, contrasts=ratapi.ClassList(test_contrast))
@pytest.mark.parametrize(
["field", "model_name"],
[
("data", "data"),
("background", "backgrounds"),
("bulk_in", "bulk_in"),
("bulk_out", "bulk_out"),
("scalefactor", "scalefactors"),
("resolution", "resolutions"),
("domain_ratio", "domain_ratios"),
],
)
def test_allowed_contrasts_with_ratio(field: str, model_name: str) -> None:
"""If the fields of the ContrastWithRatio model are set to values not specified in the other respective models of
the project, we should raise a ValidationError.
"""
test_contrast = ratapi.models.ContrastWithRatio(**{field: "undefined"})
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f'1 validation error for Project\n Value error, The value "undefined" used in the "{field}" field of '
f'contrasts[0] must be defined in "{model_name}". Please add "undefined" to "{model_name}" before '
f'including it in "contrasts".'
),
):
ratapi.Project(calculation=Calculations.Domains, contrasts=ratapi.ClassList(test_contrast))
@pytest.mark.parametrize(
["input_calc", "input_model", "test_contrast", "field_name"],
[
(
Calculations.Domains,
LayerModels.StandardLayers,
ratapi.models.ContrastWithRatio(name="Test Contrast", model=["undefined", "undefined"]),
"domain_contrasts",
),
(
Calculations.Domains,
LayerModels.CustomLayers,
ratapi.models.ContrastWithRatio(name="Test Contrast", model=["undefined"]),
"custom_files",
),
(
Calculations.Domains,
LayerModels.CustomXY,
ratapi.models.ContrastWithRatio(name="Test Contrast", model=["undefined"]),
"custom_files",
),
(
Calculations.Normal,
LayerModels.StandardLayers,
ratapi.models.Contrast(name="Test Contrast", model=["undefined", "undefined", "undefined"]),
"layers",
),
(
Calculations.Normal,
LayerModels.CustomLayers,
ratapi.models.Contrast(name="Test Contrast", model=["undefined"]),
"custom_files",
),
(
Calculations.Normal,
LayerModels.CustomXY,
ratapi.models.Contrast(name="Test Contrast", model=["undefined"]),
"custom_files",
),
],
)
def test_allowed_contrast_models(
input_calc: Calculations,
input_model: LayerModels,
test_contrast: "ratapi.models",
field_name: str,
) -> None:
"""If any value in the model field of the contrasts is set to a value not specified in the appropriate part of the
project, we should raise a ValidationError.
"""
missing_values = list(set(test_contrast.model))
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
f"1 validation error for Project\n Value error, The value{'s' if len(missing_values) > 1 else ''}: "
f'"{", ".join(missing_values)}" used in the "model" field of contrasts[0] must be defined in '
f'"{field_name}". Please add all required values to "{field_name}" before including them in "contrasts".'
),
):
ratapi.Project(calculation=input_calc, model=input_model, contrasts=ratapi.ClassList(test_contrast))
def test_allowed_domain_contrast_models() -> None:
"""If any value in the model field of the domain_contrasts is set to a value not specified in the "layers" field of
the project, we should raise a ValidationError.
"""
test_contrast = ratapi.models.DomainContrast(name="Test Domain Contrast", model=["undefined"])
with pytest.raises(
pydantic.ValidationError,
match=re.escape(
'1 validation error for Project\n Value error, The value: "undefined" used in the "model" field of '
'domain_contrasts[0] must be defined in "layers". Please add all required values to "layers" before '
'including them in "domain_contrasts".'
),
):
ratapi.Project(calculation=Calculations.Domains, domain_contrasts=ratapi.ClassList(test_contrast))
def test_str(default_project_str: str) -> None:
"""We should be able to print the "Project" model as a formatted list of the fields."""
assert str(ratapi.Project()) == default_project_str
def test_get_all_names(test_project) -> None:
"""We should be able to get the names of all the models defined in the project."""
assert test_project.get_all_names() == {
"parameters": ["Substrate Roughness", "Test Thickness", "Test SLD", "Test Roughness"],
"bulk_in": ["SLD Air"],
"bulk_out": ["SLD D2O"],
"scalefactors": ["Scalefactor 1"],
"domain_ratios": [],
"background_parameters": ["Background Param 1"],
"backgrounds": ["Background 1"],
"resolution_parameters": ["Resolution Param 1"],
"resolutions": ["Resolution 1"],
"custom_files": ["Test Custom File"],
"data": ["Simulation"],
"layers": ["Test Layer"],
"domain_contrasts": [],
"contrasts": ["Test Contrast"],
}
def test_get_all_protected_parameters(test_project) -> None:
"""We should be able to get the names of all the protected parameters defined in the project."""
assert test_project.get_all_protected_parameters() == {
"parameters": ["Substrate Roughness"],
"bulk_in": [],
"bulk_out": [],
"scalefactors": [],
"domain_ratios": [],
"background_parameters": [],
"resolution_parameters": [],
}
@pytest.mark.parametrize(
"test_value",
[
"",
"Substrate Roughness",
],
)
def test_check_allowed_values(test_value: str) -> None:
"""We should not raise an error if string values are defined and on the list of allowed values."""
allowed_values = ["Substrate Roughness"]
project = ratapi.Project.model_construct(
layers=ratapi.ClassList(ratapi.models.Layer(**dict(layer_params, roughness=test_value)))
)
assert project.check_allowed_values("layers", ["roughness"], allowed_values, allowed_values) is None
@pytest.mark.parametrize(
"test_value",
[
"Undefined Param",
],
)
def test_check_allowed_values_not_on_list(test_value: str) -> None:
"""If string values are defined and are not included on the list of allowed values we should raise a ValueError."""
project = ratapi.Project.model_construct(
layers=ratapi.ClassList(ratapi.models.Layer(**dict(layer_params, roughness=test_value)))
)
allowed_values = ["Substrate Roughness"]
with pytest.raises(
ValueError,
match=re.escape(
f'The value "{test_value}" used in the "roughness" field of layers[0] must be defined in "parameters". '
f'Please add "{test_value}" to "parameters" before including it in "layers".'
),
):
project.check_allowed_values("layers", ["roughness"], allowed_values, allowed_values)
@pytest.mark.parametrize(
"test_value",
[
"",
"Background Param 1",
],
)
def test_check_allowed_background_resolution_values_constant(test_value: str) -> None:
"""We should not raise an error if string values are defined and on the appropriate list of allowed values."""
project = ratapi.Project.model_construct(
background_parameters=ratapi.ClassList(ratapi.models.Parameter(name="Background Param 1")),
backgrounds=ratapi.ClassList(ratapi.models.Background(type=TypeOptions.Constant, source=test_value)),
)
assert project.check_allowed_source("backgrounds") is None
@pytest.mark.parametrize(
"test_value",
[
"",
"Simulation",
],
)
def test_check_allowed_background_resolution_values_data(test_value: str) -> None:
"""We should not raise an error if string values are defined and on the appropriate list of allowed values."""
project = ratapi.Project.model_construct(
backgrounds=ratapi.ClassList(ratapi.models.Background(type=TypeOptions.Data, source=test_value))
)
assert project.check_allowed_source("backgrounds") is None
@pytest.mark.parametrize(
"test_value",
["Undefined Param", "Simulation"],
)
def test_check_allowed_background_resolution_values_not_on_constant_list(test_value: str) -> None:
"""If string values are defined and are not included on the correct list of allowed values we should raise a
You can’t perform that action at this time.