import pandas as pd
from cascade_at.executor.args.arg_utils import ArgumentList
from cascade_at.executor.args.args import ModelVersionID, BoolArg, ListArg, StrArg, LogLevel
from cascade_at.context.model_context import Context
from cascade_at.core.log import get_loggers, LEVELS
from cascade_at.dismod.api.dismod_io import DismodIO
LOG = get_loggers(__name__)
ARG_LIST = ArgumentList([
ModelVersionID(),
ListArg('--locations', help='The locations to pull mulcov statistics from', type=int, required=True),
ListArg('--sexes', help='The sexes to pull mulcov statistics from', type=int, required=True),
StrArg('--outfile-name', help='Filepath where mulcov statistics will be saved', required=False, default='mulcov_stats'),
BoolArg('--sample', help='If true, the results will be pulled from the sample table rather'
'than the fit_var table'),
BoolArg('--mean', help='Whether or not to compute the mean'),
BoolArg('--std', help='Whether or not to compute the standard deviation'),
ListArg('--quantile', help='Quantiles to compute', type=float),
LogLevel()
])
def common_covariate_names(dbs):
return set.intersection(
*map(set, [d.covariate.c_covariate_name.tolist() for d in dbs])
)
from cascade_at.dismod.api.dismod_io import DismodIO
from cascade_at.dismod.process.process_behavior import check_sample_asymptotic, SampleAsymptoticError
from cascade_at.dismod.api.multithreading import _DismodThread, dmdismod_in_parallel
from cascade_at.dismod.api.run_dismod import run_dismod_commands
from cascade_at.executor import ExecutorError
LOG = get_loggers(__name__)
ARG_LIST = ArgumentList([
ModelVersionID(),
ParentLocationID(),
SexID(),
NSim(),
NPool(),
StrArg('--fit-type',
help='what type of fit to simulate for, fit fixed or both',
default='both'),
BoolArg('--asymptotic',
help='whether or not to do asymptotic statistics or fit-refit'),
LogLevel()
])
class SampleError(ExecutorError):
"""Raised when there are issues with sample simulate."""
pass
def simulate(path: Union[str, Path], n_sim: int):
"""
Simulate from a database, within a database.
help='whether or not to fill the dismod database with data'),
BoolArg(
'--prior-samples',
help='whether or not the prior came from samples or just a mean fit'),
IntArg(
'--prior-parent',
help='the location ID of the parent database to grab the prior for'),
IntArg('--prior-sex',
help='the sex ID of the parent database to grab prior for'),
IntArg('--prior-mulcov',
help='the model version id where mulcov stats is passed in',
required=False),
BoolArg('--save-fit', help='whether or not to save the fit'),
BoolArg('--save-prior', help='whether or not to save the prior'),
LogLevel(),
StrArg('--test-dir',
help='if set, will save files to the directory specified')
])
class DismodDBError(CascadeATError):
"""Raised when there is an error with running the dismod_db script."""
pass
def get_prior(path: Union[str, Path],
location_id: int,
sex_id: int,
rates: List[str],
samples: bool = True) -> Dict[str, Dict[str, np.ndarray]]:
"""
Gets priors from a path to a database for a given location ID and sex ID.
def test_str_arg():
a = StrArg()
assert a._parser_kwargs['type'] == str
from cascade_at.executor.args.arg_utils import ArgumentList
from cascade_at.core.log import get_loggers, LEVELS
from cascade_at.executor.args.args import ModelVersionID, BoolArg, LogLevel, StrArg
LOG = get_loggers(__name__)
ARG_LIST = ArgumentList([
ModelVersionID(),
BoolArg('--make',
help='whether or not to make the file structure for the cascade'),
BoolArg('--configure',
help='whether or not to configure for the IHME cluster'),
LogLevel(),
StrArg('--json-file',
help='for testing, pass a json file directly by filepath'
'instead of referencing a model version ID.'),
StrArg('--test-dir',
help='if set, will save files to the directory specified.'
'Invalidated if --configure is set.')
])
class CovariateReference:
def __init__(self, inputs):
self.inputs = inputs
self.cov_ids = {
c.covariate_id: c.name
for c in inputs.covariate_specs.covariate_specs
if c.study_country == 'country'
}
from cascade_at.jobmon.workflow import jobmon_workflow_from_cascade_command
from cascade_at.settings.settings import settings_from_model_version_id
from cascade_at.inputs.locations import LocationDAG
LOG = get_loggers(__name__)
ARG_LIST = ArgumentList([
ModelVersionID(),
BoolArg('--jobmon',
help='whether or not to use jobmon to run the cascade'
'or just run as a sequence of command line tasks'),
BoolArg('--make',
help='whether or not to make the file structure for the cascade'),
NSim(),
StrArg('--addl-workflow-args',
help='additional info to append to workflow args, to re-do models',
required=False),
BoolArg('--skip-configure'),
LogLevel()
])
def run(model_version_id: int,
jobmon: bool = True,
make: bool = True,
n_sim: int = 10,
addl_workflow_args: Optional[str] = None,
skip_configure: bool = False) -> None:
"""
Runs the whole cascade or drill for a model version (which one is specified
in the model version settings).
import logging
import sys
from typing import List
from cascade_at.executor.args.arg_utils import ArgumentList
from cascade_at.executor.args.args import StrArg, DmCommands, LogLevel
from cascade_at.core.log import get_loggers, LEVELS
from cascade_at.dismod.api.run_dismod import run_dismod
LOG = get_loggers(__name__)
ARG_LIST = ArgumentList([
StrArg('--file', help='Which database file to execute commands on'),
DmCommands(),
LogLevel()
])
def run_dmdismod(file, dm_commands: List[str]) -> None:
"""
Runs commands on a dismod file.
Parameters
----------
file
Filepath to a database
dm_commands
List of commands that dismod_at understands
"""
for c in dm_commands:
process = run_dismod(dm_file=file, command=c)
from cascade_at.settings.settings import settings_from_model_version_id
from cascade_at.settings.settings import load_settings
LOG = get_loggers(__name__)
ARG_LIST = ArgumentList([
ModelVersionID(),
BoolArg('--jobmon',
help='whether or not to use jobmon to run the cascade'
'or just run as a sequence of command line tasks'),
BoolArg('--make',
help='whether or not to make the file structure for the cascade'),
NSim(),
NPool(),
StrArg('--addl-workflow-args',
help='additional info to append to workflow args, to re-do models',
required=False),
BoolArg('--skip-configure',
help='Disable building the inputs.p and settings.json files.'),
StrArg('--json-file',
help='for testing, pass a json file directly by filepath',
required=False),
StrArg('--test-dir',
help='if set, specifies where files directory is.',
required=False),
LogLevel()
])
def run(model_version_id: int,
jobmon: bool = True,