Settings Configuration¶

Helper Functions¶

cascade_at.settings.settings.load_settings(settings_json)[source]¶

Loads settings from a settings_json.

Parameters: settings_json (Dict[str, Any]) – dictionary of settings

Examples

>>> from cascade_at.settings.base_case import BASE_CASE
>>> settings = load_settings(BASE_CASE)

Return type: SettingsConfig

cascade_at.settings.settings.settings_json_from_model_version_id(model_version_id, conn_def)[source]¶

Loads settings for a specific model version ID into a json.

Parameters

model_version_id (int) – the model version ID
conn_def (str) – the connection definition like ‘dismod-at-dev’

Return type

Dict[str, any]

cascade_at.settings.settings.settings_from_model_version_id(model_version_id, conn_def)[source]¶

Loads settings for a specific model version ID.

Parameters

model_version_id (int) – the model version ID
conn_def (str) – the connection definition like ‘dismod-at-dev’

Examples

>>> settings = settings_from_model_version_id(model_version_id=395837,
>>>                                           conn_def='dismod-at-dev')

Return type: SettingsConfig

Settings Configuration Form¶

All available options from EpiViz-AT.

class cascade_at.settings.settings_config.SettingsConfig(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

The root Form of the whole settings inputs tree. This collects all settings from EpiViz-AT and adds default values when they are missing.

A representation of the configuration form we expect to receive from EpiViz. The hope is that this form will do as much validation and precondition checking as is feasible within the constraint that it must be able to validate a full EpiViz parameter document in significantly less than one second. This is because it will be used as part of a web service which gates EpiViz submissions and must return in near real time.

The Configuration class is the root of the form.

Example

>>> import json
>>> input_data = json.loads(json_blob)
>>> form = SettingsConfig(input_data)
>>> errors = form.validate_and_normalize()

model: cascade_at.settings.settings_config.Model = None¶

policies: cascade_at.settings.settings_config.Policies = None¶

gbd_round_id: cascade_at.core.form.fields.IntField = None¶

random_effect: cascade_at.core.form.fields.FormList = None¶

rate: cascade_at.core.form.fields.FormList = None¶

country_covariate: cascade_at.core.form.fields.FormList = None¶

study_covariate: cascade_at.core.form.fields.FormList = None¶

eta: cascade_at.settings.settings_config.Eta = None¶

students_dof: cascade_at.settings.settings_config.StudentsDOF = None¶

log_students_dof: cascade_at.settings.settings_config.StudentsDOF = None¶

location_set_version_id: cascade_at.core.form.fields.IntField = None¶

csmr_cod_output_version_id: cascade_at.core.form.fields.IntField = None¶

csmr_mortality_output_version_id: cascade_at.core.form.fields.Dummy = NO_VALUE¶

min_cv: cascade_at.core.form.fields.FormList = None¶

min_cv_by_rate: cascade_at.core.form.fields.FormList = None¶

re_bound_location: cascade_at.core.form.fields.FormList = None¶

derivative_test: cascade_at.settings.settings_config.DerivativeTest = None¶

max_num_iter: cascade_at.settings.settings_config.FixedRandomInt = None¶

print_level: cascade_at.settings.settings_config.FixedRandomInt = None¶

accept_after_max_steps: cascade_at.settings.settings_config.FixedRandomInt = None¶

tolerance: cascade_at.settings.settings_config.FixedRandomFloat = None¶

data_cv_by_integrand: cascade_at.core.form.fields.FormList = None¶

data_eta_by_integrand: cascade_at.core.form.fields.FormList = None¶

data_density_by_integrand: cascade_at.core.form.fields.FormList = None¶

config_version: cascade_at.core.form.fields.StrField = None¶

class cascade_at.settings.settings_config.SmoothingPrior(*args, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

Priors for smoothing.

prior_type: cascade_at.core.form.fields.OptionField = None¶

age_lower: cascade_at.core.form.fields.FloatField = None¶

age_upper: cascade_at.core.form.fields.FloatField = None¶

time_lower: cascade_at.core.form.fields.FloatField = None¶

time_upper: cascade_at.core.form.fields.FloatField = None¶

born_lower: cascade_at.core.form.fields.FloatField = None¶

born_upper: cascade_at.core.form.fields.FloatField = None¶

density: cascade_at.core.form.fields.OptionField = None¶

min: cascade_at.core.form.fields.FloatField = None¶

mean: cascade_at.core.form.fields.FloatField = None¶

max: cascade_at.core.form.fields.FloatField = None¶

std: cascade_at.core.form.fields.FloatField = None¶

nu: cascade_at.core.form.fields.FloatField = None¶

eta: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.SmoothingPriorGroup(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

dage: cascade_at.settings.settings_config.SmoothingPrior = None¶

dtime: cascade_at.settings.settings_config.SmoothingPrior = None¶

value: cascade_at.settings.settings_config.SmoothingPrior = None¶

class cascade_at.settings.settings_config.Smoothing(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

rate: cascade_at.core.form.fields.OptionField = None¶

location: cascade_at.core.form.fields.IntField = None¶

age_grid: cascade_at.core.form.fields.StringListField = None¶

time_grid: cascade_at.core.form.fields.StringListField = None¶

default: cascade_at.settings.settings_config.SmoothingPriorGroup = None¶

mulstd: cascade_at.settings.settings_config.SmoothingPriorGroup = None¶

detail: cascade_at.core.form.fields.FormList = None¶

age_time_specific: cascade_at.core.form.fields.IntField = None¶

custom_age_grid: cascade_at.core.form.fields.Dummy = NO_VALUE¶

custom_time_grid: cascade_at.core.form.fields.Dummy = NO_VALUE¶

class cascade_at.settings.settings_config.StudyCovariate(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

study_covariate_id: cascade_at.core.form.fields.IntField = None¶

measure_id: cascade_at.core.form.fields.StrField = None¶

mulcov_type: cascade_at.core.form.fields.OptionField = None¶

transformation: cascade_at.core.form.fields.IntField = None¶

age_time_specific: cascade_at.core.form.fields.IntField = None¶

age_grid: cascade_at.core.form.fields.StringListField = None¶

time_grid: cascade_at.core.form.fields.StringListField = None¶

default: cascade_at.settings.settings_config.SmoothingPriorGroup = None¶

mulstd: cascade_at.settings.settings_config.SmoothingPriorGroup = None¶

detail: cascade_at.core.form.fields.FormList = None¶

custom_age_grid: cascade_at.core.form.fields.Dummy = NO_VALUE¶

custom_time_grid: cascade_at.core.form.fields.Dummy = NO_VALUE¶

class cascade_at.settings.settings_config.CountryCovariate(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

country_covariate_id: cascade_at.core.form.fields.IntField = None¶

measure_id: cascade_at.core.form.fields.StrField = None¶

mulcov_type: cascade_at.core.form.fields.OptionField = None¶

transformation: cascade_at.core.form.fields.IntField = None¶

age_time_specific: cascade_at.core.form.fields.IntField = None¶

age_grid: cascade_at.core.form.fields.StringListField = None¶

time_grid: cascade_at.core.form.fields.StringListField = None¶

default: cascade_at.settings.settings_config.SmoothingPriorGroup = None¶

mulstd: cascade_at.settings.settings_config.SmoothingPriorGroup = None¶

detail: cascade_at.settings.settings_config.SmoothingPrior = None¶

custom_age_grid: cascade_at.core.form.fields.Dummy = NO_VALUE¶

custom_time_grid: cascade_at.core.form.fields.Dummy = NO_VALUE¶

class cascade_at.settings.settings_config.Model(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

modelable_entity_id: cascade_at.core.form.fields.IntField = None¶

decomp_step_id: cascade_at.core.form.fields.IntField = None¶

model_version_id: cascade_at.core.form.fields.IntField = None¶

random_seed: cascade_at.core.form.fields.IntField = None¶

minimum_meas_cv: cascade_at.core.form.fields.FloatField = None¶

add_csmr_cause: cascade_at.core.form.fields.IntField = None¶

title: cascade_at.core.form.fields.StrField = None¶

description: cascade_at.core.form.fields.StrField = None¶

crosswalk_version_id: cascade_at.core.form.fields.IntField = None¶

bundle_id: cascade_at.core.form.fields.IntField = None¶

drill: cascade_at.core.form.fields.OptionField = None¶

drill_location: cascade_at.core.form.fields.IntField = None¶

drill_location_start: cascade_at.core.form.fields.IntField = None¶

drill_location_end: cascade_at.core.form.fields.NativeListField = None¶

drill_sex: cascade_at.core.form.fields.OptionField = None¶

birth_prev: cascade_at.core.form.fields.OptionField = None¶

default_age_grid: cascade_at.core.form.fields.StringListField = None¶

default_time_grid: cascade_at.core.form.fields.StringListField = None¶

constrain_omega: cascade_at.core.form.fields.OptionField = None¶

exclude_data_for_param: cascade_at.core.form.fields.ListField = None¶

ode_step_size: cascade_at.core.form.fields.FloatField = None¶

addl_ode_stpes: cascade_at.core.form.fields.StringListField = None¶

split_sex: cascade_at.core.form.fields.OptionField = None¶

quasi_fixed: cascade_at.core.form.fields.OptionField = None¶

zero_sum_random: cascade_at.core.form.fields.ListField = None¶

bound_frac_fixed: cascade_at.core.form.fields.FloatField = None¶

bound_random: cascade_at.core.form.fields.FloatField = None¶

rate_case: cascade_at.core.form.fields.StrField = None¶

data_density: cascade_at.core.form.fields.StrField = None¶

relabel_incidence: cascade_at.core.form.fields.IntField = None¶

midpoint_approximation: cascade_at.core.form.fields.NativeListField = None¶

class cascade_at.settings.settings_config.Eta(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

priors: cascade_at.core.form.fields.FloatField = None¶

data: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.DataCV(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

integrand_measure_id: cascade_at.core.form.fields.IntField = None¶

value: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.MinCV(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

cascade_level_id: cascade_at.core.form.fields.StrField = None¶

value: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.MinCVRate(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

cascade_level_id: cascade_at.core.form.fields.StrField = None¶

rate_measure_id: cascade_at.core.form.fields.StrField = None¶

value: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.DataEta(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

integrand_measure_id: cascade_at.core.form.fields.IntField = None¶

value: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.DataDensity(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

value: cascade_at.core.form.fields.StrField = None¶

integrand_measure_id: cascade_at.core.form.fields.IntField = None¶

class cascade_at.settings.settings_config.StudentsDOF(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

priors: cascade_at.core.form.fields.FloatField = None¶

data: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.DerivativeTest(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

fixed: cascade_at.core.form.fields.OptionField = None¶

random: cascade_at.core.form.fields.OptionField = None¶

class cascade_at.settings.settings_config.FixedRandomInt(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

fixed: cascade_at.core.form.fields.IntField = None¶

random: cascade_at.core.form.fields.IntField = None¶

class cascade_at.settings.settings_config.FixedRandomFloat(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

fixed: cascade_at.core.form.fields.FloatField = None¶

random: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.RandomEffectBound(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

location: cascade_at.core.form.fields.IntField = None¶

value: cascade_at.core.form.fields.FloatField = None¶

class cascade_at.settings.settings_config.Policies(source=None, name_field=None, nullable=False, display=None, **kwargs)[source]¶

Bases: cascade_at.core.form.abstract_form.Form

estimate_emr_from_prevalence: cascade_at.core.form.fields.OptionField = None¶

use_weighted_age_group_midpoints: cascade_at.core.form.fields.OptionField = None¶

number_of_fixed_effect_samples: cascade_at.core.form.fields.IntField = None¶

with_hiv: cascade_at.core.form.fields.BoolField = None¶

age_group_set_id: cascade_at.core.form.fields.IntField = None¶

exclude_relative_risk: cascade_at.core.form.fields.OptionField = None¶

meas_noise_effect: cascade_at.core.form.fields.OptionField = None¶

limited_memory_max_history_fixed: cascade_at.core.form.fields.IntField = None¶

gbd_round_id: cascade_at.core.form.fields.IntField = None¶