cause_id = args.cause_id
return cause_id
if __name__ == '__main__':
# Get command line arguments
cause_id = parse_args()
# Set paths
parent_dir = 'FILEPATH'
log_dir = r'FILEPATH'
# Start logging
l.setup_logging(log_dir, 'generate_imported_cases', str(cause_id))
try:
# Get restricted locations
logging.info("Get restricted locations")
restricted_locations = get_restricted_locations_for_cause(cause_id)
# Get CoD data for cause
logging.info("Get CoD data for cause")
if cause_id == 361:
fetch_cause_id = 360
elif cause_id == 348:
fetch_cause_id = 347
else:
fetch_cause_id = cause_id
data = get_cod_data_for_cause_location(fetch_cause_id,
def pretty_now():
return datetime.now().strftime("[%m/%d/%Y %H:%M:%S]")
if __name__ == '__main__':
# Unpack arguments
version_id, cause_id, decomp_step, gbd_round_id, output_dir = parse_args()
# Set directories
outdir = os.path.join(output_dir, '{}'.format(cause_id))
if not os.path.exists(outdir):
os.makedirs(outdir)
logdir = 'FILEPATH'
log_utils.setup_logging(logdir,
'generate_imported_cases_{}'.format(cause_id))
try:
logging.info("{} Special cause considerations".format(pretty_now()))
logging.info("{} Get restricted locations".format(pretty_now()))
if cause_id == 562:
locations = get_data_rich_locations(4)
age_groups = list(range(2, 8))
else:
locations = get_cause_specific_locations(cause_id, gbd_round_id)
age_groups = list(range(2, 21)) + [30, 31, 32, 235]
logging.info("{} Get CoD data for cause".format(pretty_now()))
data = get_cod_data(cause_id,
age_group_id=age_groups,
job_project,
slots=job_slots,
resume=resume,
retry_attempts=1), job_dependencies)
return task_list
if __name__ == '__main__':
# Set some core variables
code_directory = 'FILEPATH'
output_directory = 'FILEPATH'
# Parse arguments
log_dir = r'FILEPATH'
l.setup_logging(log_dir, 'launch_imported_cases',
time.strftime("%m_%d_%Y_%H"))
resume = parse_args()
# Get list of current space-time restricted causes
spacetime_cause_ids = get_data_rich_spacetime_restricted_causes()
for cause_id in [298, 299, 300, 741, 347, 360]:
if cause_id in spacetime_cause_ids:
spacetime_cause_ids.remove(cause_id)
# Set up folders
parent_dir = set_up_folders(output_directory, spacetime_cause_ids)
# Generate Imported Cases jobs
job_list = TaskList()
job_list = generate_imported_cases_jobs(job_list,
code_directory,
os.makedirs(directory)
return outdir
if __name__ == '__main__':
# Manual creation of version for now.
version_id = 5
decomp_step = "step4"
gbd_round_id = GBD.GBD_ROUND_ID
# Directories
code_dir = 'FILEPATH'
outdir = 'FILEPATH'
logdir = os.path.join(outdir, 'logs')
log_utils.setup_logging(logdir, 'launch_imported_cases',
time.strftime('%m_%d_%Y_%H'))
logging.info("{} Starting Imported Cases Generator: "
"params-- version_id: {}, decomp_step: {} "
"gbd_round_id: {}"
.format(pretty_now(), version_id, decomp_step, gbd_round_id))
# Get a list of imported cases cause ids:
# spacetime-restricted causes + age-restricted causes
try:
logging.info("{} Getting cause ids to process".format(pretty_now()))
st_cause_ids = get_spacetime_restrictions(
GBD.GBD_ROUND
).cause_id.unique().tolist()
restricted_causes = st_cause_ids + list(ADDITIONAL_RESTRICTIONS.keys())