class CountryCovariate(Form):
country_covariate_id = IntField(display="Covariate")
measure_id = IntField(display="Measure")
mulcov_type = OptionField(["rate_value", "meas_value", "meas_std"],
display="Multiplier type")
transformation = IntField(display="Transformation")
age_time_specific = IntField(display="Age and Time specific")
age_grid = StringListField(constructor=float,
nullable=True,
display="Age grid")
time_grid = StringListField(constructor=float,
nullable=True,
display="Time grid")
default = SmoothingPriorGroup(display="Defaults")
mulstd = SmoothingPriorGroup(nullable=True, display="MulStd")
detail = FormList(SmoothingPrior, nullable=True, display="Detail")
custom_age_grid = Dummy()
custom_time_grid = Dummy()
class StudyCovariate(Form):
study_covariate_id: IntField = IntField(display="Covariate")
measure_id: StrField = StrField(display="Measure")
mulcov_type: OptionField = OptionField(
["rate_value", "meas_value", "meas_noise"], display="Multiplier type")
transformation: IntField = IntField(display="Transformation")
age_time_specific: IntField = IntField(display="Age and Time specific")
age_grid: StringListField = StringListField(constructor=float,
nullable=True,
display="Age grid")
time_grid: StringListField = StringListField(constructor=float,
nullable=True,
display="Time grid")
default: SmoothingPriorGroup = SmoothingPriorGroup(display="Defaults")
mulstd: SmoothingPriorGroup = SmoothingPriorGroup(nullable=True,
display="MulStd")
detail: FormList = FormList(SmoothingPrior,
nullable=True,
display="Detail")
custom_age_grid: Dummy = Dummy()
custom_time_grid: Dummy = Dummy()
class Model(Form):
modelable_entity_id = IntField()
decomp_step_id = IntField()
model_version_id = IntField(nullable=True)
random_seed = IntField()
minimum_meas_cv = FloatField(nullable=True, display="Data CV floor")
add_csmr_cause = IntField(nullable=True, display="CSMR cause")
title = StrField(nullable=True, display="Title")
description = StrField(nullable=True, display="Description")
crosswalk_version_id = IntField(nullable=False,
display="Crosswalk version ID")
bundle_id = IntField(nullable=True, display="Data bundle")
drill = OptionField(["cascade", "drill"], display="Drill")
drill_location = IntField(display="Drill location", nullable=True)
drill_location_start = IntField(display="Drill location start",
nullable=True)
drill_location_end = NativeListField(display="Drill location end",
nullable=True)
drill_sex = OptionField([1, 2],
constructor=int,
nullable=True,
display="Drill sex")
birth_prev = OptionField([0, 1],
constructor=int,
nullable=True,
default=0,
display="Prevalence at birth")
default_age_grid = StringListField(constructor=float,
display="(Cascade) Age grid")
default_time_grid = StringListField(constructor=float,
display="(Cascade) Time grid")
constrain_omega = OptionField([0, 1],
constructor=int,
nullable=False,
display="Constrain other cause mortality")
exclude_data_for_param = ListField(constructor=int,
nullable=True,
display="Exclude data for parameter")
ode_step_size = FloatField(display="ODE step size")
addl_ode_stpes = StringListField(constructor=float,
nullable=True,
display="Advanced additional ODE steps")
split_sex = OptionField(["most_detailed", "1", "2", "3", "4", "5"],
display="Split sex (Being used as Drill Start)")
quasi_fixed = OptionField([0, 1],
default=0,
constructor=int,
nullable=True)
zero_sum_random = ListField(nullable=True,
display="Zero-sum random effects")
bound_frac_fixed = FloatField(
default=1e-2,
nullable=True,
display="allowed modification to point to move it within bounds")
bound_random = FloatField(
nullable=True,
display="allowed modification to point to move it within bounds")
rate_case = StrField(nullable=False, display="The rate case")
data_density = StrField(nullable=True, display="Data density")
relabel_incidence = IntField(nullable=False, display="Relabel incidence")
def _full_form_validation(self, root):
errors = []
if self.drill == "drill":
if self.is_field_unset("drill_sex"):
errors.append("For a drill, please specify Drill sex.")
return errors
class Smoothing(Form):
rate = OptionField(["pini", "iota", "rho", "chi", "omega"], "Rate")
location = IntField(nullable=True)
age_grid = StringListField(constructor=float,
nullable=True,
display="Age grid")
time_grid = StringListField(constructor=float,
nullable=True,
display="Time grid")
default = SmoothingPriorGroup(display="Defaults")
mulstd = SmoothingPriorGroup(nullable=True, display="MulStd")
detail = FormList(SmoothingPrior, nullable=True, display="Detail")
age_time_specific = IntField(display="Age and Time specific",
nullable=True)
custom_age_grid = Dummy()
custom_time_grid = Dummy()
def _full_form_validation(self, root):
errors = []
if self.rate == "pini":
if not self.is_field_unset("age_grid") and len(self.age_grid) != 1:
errors.append("Pini must have exactly one age point")
else:
age_grid = self.age_grid or root.model.default_age_grid
if len(age_grid) > 1 and self.default.is_field_unset("dage"):
errors.append(
"You must supply a default age diff prior if the "
"smoothing has extent over age")
time_grid = self.time_grid or root.model.default_time_grid
if len(time_grid) > 1 and self.default.is_field_unset("dtime"):
errors.append(
"You must supply a default time diff prior if the smoothing "
"has extent over time")
if self._container._name == "rate":
# This validation only makes sense for Fixed Effects not
# Random Effects
# TODO This repeats validation logic in cascade.model.rates but I
# don't see a good way to bring that in here
is_negative = True
is_positive = True
for prior in (
[self.default.value] +
[p for p in self.detail or [] if p.prior_type == "value"]):
is_negative = is_negative and prior.min == 0 and prior.max == 0
is_positive = is_positive and prior.min > 0
if prior.min < 0:
errors.append(
"Rates must be constrained to be >= 0 at all points. "
"Add or correct the lower bound")
break
if self.rate in ["iota", "rho"]:
if not (is_negative or is_positive):
errors.append(
f"Rate {self.rate} must be either fully positive or "
f"constrained to zero")
return errors
class MyForm(Form):
ints_field = StringListField(separator=",", constructor=int)
class MyInnerSanctum(Form):
int_field = IntField()
float_list_field = StringListField(separator=" ", constructor=float)
further_in = FormList(EvenMoreInner)
class EvenMoreInner(Form):
int_list_field = StringListField(separator=" ", constructor=float)