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run.py
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run.py
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# -*- coding: utf-8 -*-
"""Functions to call when running the function.
This module should contain a function called `run_module`, that is executed
when the module is run with `python -m MODULE_NAME`.
"""
import atexit
from datetime import datetime
from multiprocessing import cpu_count
import time
from typing import Dict, Any
from delphi_utils import (
add_prefix,
create_export_csv,
get_structured_logger
)
from delphi_utils.logger import pool_and_threadedlogger
from .constants import (END_FROM_TODAY_MINUS,
SMOOTHED_POSITIVE, RAW_POSITIVE,
SMOOTHED_TEST_PER_DEVICE, RAW_TEST_PER_DEVICE,
PARENT_GEO_RESOLUTIONS, SENSORS, SMOOTHERS, NONPARENT_GEO_RESOLUTIONS,
AGE_GROUPS)
from .generate_sensor import generate_sensor_for_parent_geo, generate_sensor_for_nonparent_geo
from .geo_maps import geo_map
from .pull import (pull_quidel_covidtest,
check_export_start_date,
check_export_end_date,
update_cache_file)
from .backfill import (store_backfill_file, merge_backfill_file)
def log_exit(start_time, stats, logger):
"""Log at program exit."""
elapsed_time_in_seconds = round(time.time() - start_time, 2)
min_max_date = stats and min(s[0] for s in stats)
csv_export_count = sum(s[-1] for s in stats)
max_lag_in_days = min_max_date and (datetime.now() - min_max_date).days
formatted_min_max_date = min_max_date and min_max_date.strftime("%Y-%m-%d")
logger.info("Completed indicator run",
elapsed_time_in_seconds = elapsed_time_in_seconds,
csv_export_count = csv_export_count,
max_lag_in_days = max_lag_in_days,
oldest_final_export_date = formatted_min_max_date)
def get_smooth_info(sensors, _SMOOTHERS):
"""Get smooth info from SMOOTHERS."""
smoothers = _SMOOTHERS.copy()
for sensor in sensors:
if sensor.endswith(SMOOTHED_POSITIVE):
smoothers[sensor] = smoothers.pop(SMOOTHED_POSITIVE)
elif sensor.endswith(RAW_POSITIVE):
smoothers[sensor] = smoothers.pop(RAW_POSITIVE)
elif sensor.endswith(SMOOTHED_TEST_PER_DEVICE):
smoothers[sensor] = smoothers.pop(SMOOTHED_TEST_PER_DEVICE)
else:
smoothers[sensor] = smoothers.pop(RAW_TEST_PER_DEVICE)
return smoothers
def generate_and_export_for_nonparent_geo(geo_groups, res_key, smooth, device,
first_date, last_date, suffix, # generate args
geo_res, sensor_name, export_dir,
export_start_date, export_end_date, # export args
threaded_logger): # logger args
"""Generate sensors, create export CSV then return stats."""
threaded_logger.info("Generating signal and exporting to CSV",
geo_res=geo_res,
sensor=sensor_name)
res_df = generate_sensor_for_nonparent_geo(geo_groups, res_key, smooth, device,
first_date, last_date, suffix)
dates = create_export_csv(res_df, geo_res=geo_res,
sensor=sensor_name, export_dir=export_dir,
start_date=export_start_date,
end_date=export_end_date)
return dates
def generate_and_export_for_parent_geo(geo_groups, geo_data, res_key, smooth, device,
first_date, last_date, suffix, # generate args
geo_res, sensor_name, export_dir,
export_start_date, export_end_date, # export args
threaded_logger): # logger args
"""Generate sensors, create export CSV then return stats."""
threaded_logger.info("Generating signal and exporting to CSV",
geo_res=geo_res,
sensor=sensor_name)
res_df = generate_sensor_for_parent_geo(geo_groups, geo_data, res_key, smooth, device,
first_date, last_date, suffix)
dates = create_export_csv(res_df, geo_res=geo_res,
sensor=sensor_name, export_dir=export_dir,
start_date=export_start_date,
end_date=export_end_date,
remove_null_samples=True) # for parent geo, remove null sample size
return dates
def run_module(params: Dict[str, Any]):
"""Run the quidel_covidtest indicator.
The `params` argument is expected to have the following structure:
- "common":
- "export_dir": str, directory to write output
- "log_exceptions" (optional): bool, whether to log exceptions to file
- "log_filename" (optional): str, name of file to write logs
- indicator":
- "static_file_dir": str, directory name with population information
- "input_cache_dir": str, directory in which to cache input data
- "backfill_dir": str, directory in which to store the backfill files
- "export_start_date": str, YYYY-MM-DD format of earliest date to create output
- "export_end_date": str, YYYY-MM-DD format of latest date to create output or "" to create
through the present
- "pull_start_date": str, YYYY-MM-DD format of earliest date to pull input
- "pull_end_date": str, YYYY-MM-DD format of latest date to create output or "" to create
through the present
- "aws_credentials": Dict[str, str], authentication parameters for AWS S3; see S3
documentation
- "bucket_name": str, name of AWS bucket in which to find data
- "wip_signal": List[str], list of signal names that are works in progress
- "test_mode": bool, whether we are running in test mode
"""
start_time = time.time()
logger = get_structured_logger(
__name__, filename=params["common"].get("log_filename"),
log_exceptions=params["common"].get("log_exceptions", True))
stats = []
atexit.register(log_exit, start_time, stats, logger)
cache_dir = params["indicator"]["input_cache_dir"]
export_dir = params["common"]["export_dir"]
export_start_date = params["indicator"]["export_start_date"]
export_end_date = params["indicator"]["export_end_date"]
export_day_range = params["indicator"]["export_day_range"]
# Pull data and update export date
df, _end_date = pull_quidel_covidtest(params["indicator"], logger)
# Allow user to turn backfill file generation on or off. Defaults to True
# (generate files).
if params["indicator"].get("generate_backfill_files", True):
backfill_dir = params["indicator"]["backfill_dir"]
backfill_merge_day = params["indicator"]["backfill_merge_day"]
# Merge 4 weeks' data into one file to save runtime
# Notice that here we don't check the _end_date(receive date)
# since we always want such merging happens on a certain day of a week
merge_backfill_file(backfill_dir, backfill_merge_day, datetime.today())
if _end_date is None:
logger.info("The data is up-to-date. Currently, no new data to be ingested.")
return
# Store the backfill intermediate file
store_backfill_file(df, _end_date, backfill_dir)
export_end_date = check_export_end_date(
export_end_date, _end_date, END_FROM_TODAY_MINUS)
export_start_date = check_export_start_date(
export_start_date, export_end_date, export_day_range)
first_date, last_date = df["timestamp"].min(), df["timestamp"].max()
data = df.copy()
# Add prefix, if required
sensors = add_prefix(SENSORS,
wip_signal=params["indicator"]["wip_signal"],
prefix="wip_")
smoothers = get_smooth_info(sensors, SMOOTHERS)
n_cpu = min(8, cpu_count()) # for parallelization
with pool_and_threadedlogger(logger, n_cpu) as (pool, threaded_logger):
# for using loggers in multiple threads
logger.info("Parallelizing sensor generation", n_cpu=n_cpu)
pool_results = []
for geo_res in NONPARENT_GEO_RESOLUTIONS:
geo_data, res_key = geo_map(geo_res, data)
geo_groups = geo_data.groupby(res_key)
for agegroup in AGE_GROUPS:
for sensor in sensors:
if agegroup == "total":
sensor_name = sensor
else:
sensor_name = "_".join([sensor, agegroup])
pool_results.append(
pool.apply_async(
generate_and_export_for_nonparent_geo,
args=(
# generate_sensors_for_parent_geo
geo_groups, res_key,
smoothers[sensor][1], smoothers[sensor][0],
first_date, last_date, agegroup,
# create_export_csv
geo_res, sensor_name, export_dir,
export_start_date, export_end_date,
# logger
threaded_logger
)
)
)
assert geo_res == "state" # Make sure geo_groups is for state level
# County/HRR/MSA level
for geo_res in PARENT_GEO_RESOLUTIONS:
geo_data, res_key = geo_map(geo_res, data) # using the last geo_groups
for agegroup in AGE_GROUPS:
for sensor in sensors:
if agegroup == "total":
sensor_name = sensor
else:
sensor_name = "_".join([sensor, agegroup])
pool_results.append(
pool.apply_async(
generate_and_export_for_parent_geo,
args=(
# generate_sensors_for_parent_geo
geo_groups, geo_data, res_key,
smoothers[sensor][1], smoothers[sensor][0],
first_date, last_date, agegroup,
# create_export_csv
geo_res, sensor_name, export_dir,
export_start_date, export_end_date,
# logger
threaded_logger
)
)
)
pool_results = [proc.get() for proc in pool_results]
for dates in pool_results:
if len(dates) > 0:
stats.append((max(dates), len(dates)))
# Export the cache file if the pipeline runs successfully.
# Otherwise, don't update the cache file
update_cache_file(df, _end_date, cache_dir)