def mi(asdr, cv, csmr, population, covariate_data, Demographics, settings):
m = MeasurementInputsFromSettings(settings=settings)
m.asdr = deepcopy(asdr)
m.csmr = deepcopy(csmr)
m.data = deepcopy(cv)
m.covariate_data = [deepcopy(covariate_data)]
m.population = deepcopy(population)
m.demographics = Demographics
m.configure_inputs_for_dismod(settings=settings, mortality_year_reduction=1)
return m
def test_location_drill_start_end(ihme):
these_settings = deepcopy(BASE_CASE)
model_settings = these_settings["model"]
tree = LocationDAG(these_settings['location_set_version_id'],
these_settings['gbd_round_id'])
region_ids = tree.parent_children(1)
parent_test_loc = choice(region_ids)
test_children = list(tree.parent_children(parent_test_loc))
num_test_children = randint(2, len(test_children))
children_test_locs = sample(test_children, num_test_children)
num_descendants = 0
for child in children_test_locs:
num_descendants += len(tree.descendants(child))
model_settings['drill_location_end'] = children_test_locs
model_settings['drill_location_start'] = parent_test_loc
these_settings['model'] = model_settings
s = load_settings(these_settings)
mi = MeasurementInputsFromSettings(settings=s)
# demographics.location_id shoul be set to all descendants of each
# location in drill_location_end, plus drill_location_end locations
# themselves, plus the drill_location_start location
assert len(mi.demographics.location_id) == (num_descendants +
len(children_test_locs) + 1)
assert len(mi.demographics.drill_locations) == (len(children_test_locs) +
1)
def main():
"""
Grabs the inputs for a specific model version ID, sets up the folder
structure, and pickles the inputs object plus writes the settings json
for use later on.
If you're doing a drill, then only get input data from locations
that will be used for the drilling for parent-children.
"""
args = get_args()
logging.basicConfig(level=LEVELS[args.loglevel])
LOG.info(
f"Configuring inputs for model version ID {args.model_version_id}.")
LOG.debug(f"Arguments: {args}.")
context = Context(model_version_id=args.model_version_id,
make=args.make,
configure_application=args.configure)
parameter_json = settings_json_from_model_version_id(
model_version_id=args.model_version_id,
conn_def=context.model_connection)
settings = load_settings(settings_json=parameter_json)
inputs = MeasurementInputsFromSettings(settings=settings)
inputs.get_raw_inputs()
inputs.configure_inputs_for_dismod(settings=settings)
context.write_inputs(inputs=inputs, settings=parameter_json)
def configure_inputs(model_version_id: int,
make: bool,
configure: bool,
midpoint: bool = False,
test_dir: Optional[str] = None,
json_file: Optional[str] = None) -> None:
"""
Grabs the inputs for a specific model version ID, sets up the folder
structure, and pickles the inputs object plus writes the settings json
for use later on. Also uploads CSMR to the database attached to the model version,
if applicable.
Optionally use a json file for settings instead of a model version ID's json file.
Parameters
----------
model_version_id
The model version ID to configure inputs for
make
Whether or not to make the directory structure for the model version ID
configure
Configure the application for the IHME cluster, otherwise will use the
test_dir for the directory tree instead.
test_dir
A test directory to use rather than the directory specified by the
model version context in the IHME file system.
json_file
An optional filepath pointing to a different json than is attached to the
model_version_id. Will use this instead for settings.
"""
LOG.info(f"Configuring inputs for model version ID {model_version_id}.")
context = Context(model_version_id=model_version_id,
make=make,
configure_application=configure,
root_directory=test_dir)
if json_file:
LOG.info(f"Reading settings from file: {json_file}")
with open(json_file, 'r') as json_file:
parameter_json = json.load(json_file)
else:
parameter_json = settings_json_from_model_version_id(
model_version_id=model_version_id,
conn_def=context.model_connection)
settings = load_settings(settings_json=parameter_json)
inputs = MeasurementInputsFromSettings(settings=settings)
inputs.get_raw_inputs()
inputs.configure_inputs_for_dismod(settings=settings, midpoint=midpoint)
if not inputs.csmr.raw.empty:
LOG.info("Uploading CSMR to t3 table.")
inputs.csmr.attach_to_model_version_in_db(
model_version_id=model_version_id,
conn_def=context.model_connection)
context.write_inputs(inputs=inputs, settings=parameter_json)
def test_no_drill(ihme):
these_settings = deepcopy(BASE_CASE)
model_settings = these_settings["model"]
tree = LocationDAG(these_settings['location_set_version_id'],
these_settings['gbd_round_id'])
num_descendants = len(tree.descendants(1))
model_settings.pop('drill_location_end')
model_settings.pop('drill_location_start')
these_settings['model'] = model_settings
s = load_settings(these_settings)
mi = MeasurementInputsFromSettings(settings=s)
# since we haven't set either drill_location_start or
# drill_location_end, demographics.location_id should be set
# to the entire hierarchy
assert len(mi.demographics.location_id) == num_descendants + 1
assert len(mi.demographics.drill_locations) == num_descendants + 1
def test_location_drill_start_only(ihme):
these_settings = deepcopy(BASE_CASE)
model_settings = these_settings["model"]
tree = LocationDAG(these_settings['location_set_version_id'],
these_settings['gbd_round_id'])
region_ids = tree.parent_children(1)
test_loc = choice(region_ids)
num_descendants = len(tree.descendants(test_loc))
num_mr_locs = len(tree.parent_children(test_loc))
model_settings.pop("drill_location_end")
model_settings['drill_location_start'] = test_loc
these_settings["model"] = model_settings
s = load_settings(these_settings)
mi = MeasurementInputsFromSettings(settings=s)
# with drill_location_end unset, demographics.location_id should
# be set to all descendants of the test loc, plus the test loc itself
assert len(mi.demographics.location_id) == num_descendants + 1
assert len(mi.demographics.drill_locations) == num_mr_locs