diff --git a/nhsn/delphi_nhsn/constants.py b/nhsn/delphi_nhsn/constants.py index 5f3cf1f62..d0e1d466a 100644 --- a/nhsn/delphi_nhsn/constants.py +++ b/nhsn/delphi_nhsn/constants.py @@ -1,109 +1,22 @@ """Registry for signal names.""" -from delphi_utils import Smoother GEOS = [ - "nation", - "hhs", - "state" -] -# FROM HHS -CONFIRMED = "confirmed_admissions_covid_1d" -SUM_CONF_SUSP = "sum_confirmed_suspected_admissions_covid_1d" -CONFIRMED_PROP = "confirmed_admissions_covid_1d_prop" -SUM_CONF_SUSP_PROP = "sum_confirmed_suspected_admissions_covid_1d_prop" -CONFIRMED_FLU = "confirmed_admissions_influenza_1d" -CONFIRMED_FLU_PROP = CONFIRMED_FLU+"_prop" - -# FROM CDC/METADATA -CONFIRMED_COVID = "Weekly Total COVID-19 Admissions" -HOSPITAL_CONFIRMED_COVID = "Percent Hospitals Reporting Total COVID-19 Admissions" - -ADULT_CONFIRMED_COVID = "Weekly Total Adult COVID-19 Admissions" -PEDIATRIC_CONFIRMED_COVID = "Weekly Total Pediatric COVID-19 Admissions" - -CONFIRMED_COVID_ADULT_PERCENT = "Percent Adult COVID-19 Admissions" -HOSPITAL_CONFIRMED_COVID_ADULT_PERCENT = "Percent Hospitals Reporting Adult COVID-19 Admissions" - -CONFIRMED_COVID_PEDIATRIC_PERCENT = "Percent Pediatric COVID-19 Admissions" -HOSPITAL_COVID_CONFIRMED_PEDIATRIC_PERCENT = "Percent Hospitals Reporting Pediatric COVID-19 Admissions" - -CONFIRMED_FLU = "Weekly Total Influenza Admissions" -HOSPITAL_CONFIRMED_FLU = "Percent Hospitals Reporting Influenza Admissions" - -CONFIRMED_FLU_ADULT_PERCENT = "Percent Adult Influenza Admissions" -HOSPITAL_CONFIRMED_FLU_ADULT_PERCENT = "Percent Hospitals Reporting TotalPatients Hospitalized with Influenza" - -CONFIRMED_FLU_PEDIATRIC_PERCENT = "Percent Pediatric Influenza Admissions" -HOSPTIAL_CONFIRMED_FLU_PEDIATRIC_PERCENT = "Percent Hospitals Reporting Pediatric Influenza Admissions" - -AGE_GROUPS = [ - "0to4", - "5to17", - "18to49", - "50to64", - "65to74", - "75plus", - "unk" + "state", + "nation" ] # column name from socrata TOTAL_ADMISSION_COVID_API = "totalconfc19newadm" -ADULT_ADMISSION_COVID_API = "numconfc19newadmadult" -TOTAL_ADULT_ADMISSION_COVID_API = "totalconfc19newadmadult" -PEDIATRIC_ADMISSION_COVID_API = "numconfc19newadmped" -TOTAL_PEDIATRIC_ADMISSION_COVID_API = "totalconfc19newadmped" - -PERCENT_ADULT_ADMISSION_COVID_API = "pctconfrsvnewadmadult" -PERCENT_PEDIATRIC_ADMISSION_COVID_API = "pctconfrsvnewadmped" - TOTAL_ADMISSION_FLU_API = "totalconfflunewadm" -ADULT_ADMISSION_FLU_API = "numconffluhosppatsadult" -TOTAL_ADULT_ADMISSION_FLU_API = "numconfflunewadmadult" -PEDIATRIC_ADMISSION_FLU_API = "numconfflunewadmped" -TOTAL_PEDIATRIC_ADMISSION_FLU_API = "totalconfflunewadmped" - -TOTAL_ADMISSION_RSV_API = "totalconfrsvnewadm" -ADULT_ADMISSION_RSV_API = "numconfrsvnewadmadult" -TOTAL_ADULT_ADMISSION_RSV_API = "totalconfrsvnewadmadult" -PEDIATRIC_ADMISSION_RSV_API = "numconfrsvnewadmped" -TOTAL_PEDIATRIC_ADMISSION_RSV_API = "totalconfrsvnewadmped" - -PARTIAL_SIGNALS = [ - TOTAL_ADMISSION_COVID_API, - ADULT_ADMISSION_COVID_API, - TOTAL_ADULT_ADMISSION_COVID_API, - PEDIATRIC_ADMISSION_COVID_API, - TOTAL_PEDIATRIC_ADMISSION_COVID_API, - PERCENT_ADULT_ADMISSION_COVID_API, - PERCENT_PEDIATRIC_ADMISSION_COVID_API, - TOTAL_ADMISSION_FLU_API, - ADULT_ADMISSION_FLU_API, - TOTAL_ADULT_ADMISSION_FLU_API, - PEDIATRIC_ADMISSION_FLU_API, - TOTAL_PEDIATRIC_ADMISSION_FLU_API, - TOTAL_ADMISSION_RSV_API, - ADULT_ADMISSION_RSV_API, - TOTAL_ADULT_ADMISSION_RSV_API, - PEDIATRIC_ADMISSION_RSV_API, - TOTAL_PEDIATRIC_ADMISSION_RSV_API, -] SIGNALS_MAP = { - "confirmed_admissions_covid": [TOTAL_ADMISSION_COVID_API], - "confirmed_admissions_flu": [TOTAL_ADMISSION_FLU_API], - "confirmed_admissions_rsv": [TOTAL_ADMISSION_RSV_API], + "confirmed_admissions_covid": TOTAL_ADMISSION_COVID_API, + "confirmed_admissions_flu": TOTAL_ADMISSION_FLU_API, } TYPE_DICT = { "timestamp": "datetime64[ns]", - "jurisdiction": str, - } - -TYPE_DICT.update({key: float for key in PARTIAL_SIGNALS}) - - + "geo_id": str, +} -SMOOTHERS = [ - (Smoother("identity", impute_method=None), ""), - (Smoother("moving_average", window_length=7), "_7dav"), -] \ No newline at end of file +TYPE_DICT.update({signal: float for signal in SIGNALS_MAP.keys()}) diff --git a/nhsn/delphi_nhsn/pull.py b/nhsn/delphi_nhsn/pull.py index 6a07864f2..02aa6beef 100644 --- a/nhsn/delphi_nhsn/pull.py +++ b/nhsn/delphi_nhsn/pull.py @@ -1,20 +1,13 @@ # -*- coding: utf-8 -*- """Functions for pulling NSSP ER data.""" import logging -import textwrap from typing import Optional import pandas as pd -from delphi_utils import create_backup_csv +from delphi_utils import create_backup_csv, GeoMapper from sodapy import Socrata -from .constants import SIGNALS_MAP, TYPE_DICT, PARTIAL_SIGNALS - - -def process_signal_data(df): - for signal, signal_parts in SIGNALS_MAP.items(): - df[signal] = sum([df[col] for col in signal_parts]) - return df +from .constants import TYPE_DICT, SIGNALS_MAP def pull_nhsn_data(socrata_token: str, backup_dir: str, custom_run: bool, logger: Optional[logging.Logger] = None): @@ -52,13 +45,21 @@ def pull_nhsn_data(socrata_token: str, backup_dir: str, custom_run: bool, logger break # exit the loop if no more results results.extend(page) offset += limit + df = pd.DataFrame.from_records(results) + keep_columns = list(TYPE_DICT.keys()) - create_backup_csv(df, backup_dir, custom_run, logger=logger) + if not df.empty: + create_backup_csv(df, backup_dir, custom_run, logger=logger) - df = df.rename(columns={"weekendingdate": "timestamp"}) - df = df[TYPE_DICT.keys()] - df = df.astype(TYPE_DICT) - processed_df = process_signal_data(df) - processed_df = processed_df.drop(columns=PARTIAL_SIGNALS) - return processed_df + df = df.rename(columns={"weekendingdate": "timestamp", "jurisdiction": "geo_id"}) + + for signal, col_name in SIGNALS_MAP.items(): + df[signal] = df[col_name] + + df = df[keep_columns] + df = df.astype(TYPE_DICT) + else: + df = pd.DataFrame(columns=keep_columns) + + return df diff --git a/nhsn/delphi_nhsn/run.py b/nhsn/delphi_nhsn/run.py index f19491354..6c350372d 100644 --- a/nhsn/delphi_nhsn/run.py +++ b/nhsn/delphi_nhsn/run.py @@ -15,15 +15,16 @@ - Any other indicator-specific settings """ import time -from datetime import timedelta, datetime +from datetime import timedelta, datetime, date from itertools import product +import numpy as np import pandas as pd from delphi_utils import get_structured_logger from delphi_utils.export import create_export_csv from delphi_utils.geomap import GeoMapper -from .constants import GEOS, SMOOTHERS, SIGNALS_MAP +from .constants import GEOS, SIGNALS_MAP from .pull import pull_nhsn_data @@ -46,7 +47,51 @@ def run_module(params): backup_dir = params["common"]["backup_dir"] custom_run = params["common"].get("custom_run", False) socrata_token = params["indicator"]["socrata_token"] - geo_mapper = GeoMapper() + export_start_date = params["indicator"]["export_start_date"] + run_stats = [] + + if export_start_date == "latest": # Find the previous Saturday + export_start_date = date.today() - timedelta( + days=date.today().weekday() + 2) + export_start_date = export_start_date.strftime('%Y-%m-%d') df_pull = pull_nhsn_data(socrata_token, backup_dir, custom_run=custom_run, logger=logger) + + nation_df = df_pull[df_pull["geo_id"] == "USA"] + state_df = df_pull[df_pull["geo_id"] != "USA"] + + if not df_pull.empty: + for geo in GEOS: + if geo == "nation": + df = nation_df + else: + df = state_df + for signal in SIGNALS_MAP.keys(): + df["val"] = df[signal] + df["se"] = np.nan + df["sample_size"] = np.nan + dates = create_export_csv( + df, + geo_res=geo, + export_dir=export_dir, + start_date=datetime.strptime(export_start_date, "%Y-%m-%d"), + sensor=signal, + weekly_dates=True + ) + if len(dates) > 0: + run_stats.append((max(dates), len(dates))) + + elapsed_time_in_seconds = round(time.time() - start_time, 2) + min_max_date = run_stats and min(s[0] for s in run_stats) + csv_export_count = sum(s[-1] for s in run_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, + ) + diff --git a/nhsn/tests/backups/.gitignore b/nhsn/tests/backups/.gitignore new file mode 100644 index 000000000..e69de29bb diff --git a/nhsn/tests/conftest.py b/nhsn/tests/conftest.py new file mode 100644 index 000000000..5ea83cf92 --- /dev/null +++ b/nhsn/tests/conftest.py @@ -0,0 +1,63 @@ +import copy +import json +from unittest.mock import patch + +import pytest +from pathlib import Path + +from delphi_nhsn.run import run_module + +TEST_DIR = Path(__file__).parent + +# test data generated with following url with socrata: +# https://data.cdc.gov/resource/ua7e-t2fy.json?$where=weekendingdate%20between%20%272023-08-19T00:00:00.000%27%20and%20%272023-10-19T00:00:00.000%27%20and%20jurisdiction%20in(%27CO%27,%27USA%27) +# queries the nhsn data with timestamp (2021-08-19, 2021-10-19) with CO and USA data +TEST_DATA = [] +with open("test_data/page.json", "r") as f: + TEST_DATA = json.load(f) + +@pytest.fixture(scope="session") +def params(): + params = { + "common": { + "export_dir": f"{TEST_DIR}/receiving", + "log_filename": f"{TEST_DIR}/test.log", + "backup_dir": f"{TEST_DIR}/backups", + "custom_run": False + }, + "indicator": { + "wip_signal": True, + "export_start_date": "2020-08-01", + "static_file_dir": "./static", + "socrata_token": "test_token" + }, + "validation": { + "common": { + "span_length": 14, + "min_expected_lag": {"all": "3"}, + "max_expected_lag": {"all": "4"}, + } + } + } + return copy.deepcopy(params) + +@pytest.fixture +def params_w_patch(params): + params_copy = copy.deepcopy(params) + params_copy["patch"] = { + "start_issue": "2024-06-27", + "end_issue": "2024-06-29", + "patch_dir": "./patch_dir" + } + return params_copy +@pytest.fixture +def mock_get(request): + with patch('sodapy.Socrata.get') as mock_get: + mock_get.side_effect = [TEST_DATA,[]] + yield mock_get + +@pytest.fixture(scope="function") +def run_as_module(params, mock_get): + + run_module(params) + diff --git a/nhsn/tests/params.json.template b/nhsn/tests/params.json.template deleted file mode 100644 index 3d55211cd..000000000 --- a/nhsn/tests/params.json.template +++ /dev/null @@ -1,6 +0,0 @@ -{ - "static_file_dir": "../static", - "export_dir": "./receiving", - "cache_dir": "./cache", - "wip_signal": "" -} diff --git a/nhsn/tests/test_data/page.json b/nhsn/tests/test_data/page.json new file mode 100644 index 000000000..749147244 --- /dev/null +++ b/nhsn/tests/test_data/page.json @@ -0,0 +1,2126 @@ +[ + { + "weekendingdate": "2021-08-21T00:00:00.000", + "jurisdiction": "CO", + "numinptbeds": "10282.71", + "numinptbedsadult": "9090.29", + "numinptbedsped": "742.29", + "numinptbedsocc": "7004.43", + "numinptbedsoccadult": "6343.0", + "numinptbedsoccped": "247.71", + "numicubeds": "1868.0", + "numicubedsadult": "1336.71", + "numicubedsped": "366.71", + "numicubedsocc": "1253.14", + "numicubedsoccadult": "961.0", + "numicubedsoccped": "135.29", + "numconfc19hosppatsadult": "590.71", + "numconfc19hosppatsped": "9.43", + "totalconfc19hosppats": "600.14", + "totalconffluhosppats": "0.0", + "numconfc19icupatsadult": "232.43", + "totalconfc19icupats": "232.43", + "totalconffluicupats": "0.0", + "totalconfc19newadmped": "34.0", + "numconfc19newadmadult18to49": "291.0", + "totalconfc19newadmadult": "818.0", + "numconfc19newadmunk": "2.0", + "totalconfc19newadm": "852.0", + "totalconfflunewadm": "0.0", + "pctinptbedsocc": "0.6812", + "pctconfc19inptbeds": "0.0584", + "pctconffluinptbeds": "0.0", + "pcticubedsocc": "0.6708", + "pctconfc19icubeds": "0.1244", + "pctconffluicubeds": "0.0", + "pctconfc19newadmadult": "0.9601", + "pctconfc19newadmped": "0.0399", + "numinptbedshosprep": "92", + "numinptbedsocchosprep": "92", + "numicubedshosprep": "92", + "numicubedsocchosprep": "92", + "totalconfc19hosppatshosprep": "92", + "totalconffluhosppatshosprep": "78", + "totalconfrsvhosppatshosprep": "0", + "totalconfc19icupatshosprep": "92", + "totalconffluicupatshosprep": "78", + "totalconfrsvicupatshosprep": "0", + "totalconfc19newadmpedhosprep": "90", + "totalconfc19newadmadulthosprep": "92", + "totalconfc19newadmhosprep": "92", + "totalconfflunewadmpedhosprep": "0", + "totalconfflunewadmadulthosprep": "0", + "totalconfflunewadmhosprep": "78", + "totalconfrsvnewadmpedhosprep": "0", + "totalconfrsvnewadmadulthosprep": "0", + "totalconfrsvnewadmhosprep": "0", + "pctinptbedsocchosprep": "92", + "pcticubedsocchosprep": "92", + "pctconfc19inptbedshosprep": "92", + "pctconffluinptbedshosprep": "78", + "pctconfrsvinptbedshosprep": "0", + "pctconfc19icubedshosprep": "92", + "pctconffluicubedshosprep": "78", + "pctconfrsvicubedshosprep": "0", + "numinptbedsperchosprep": "0.9293", + "numinptbedsoccperchosprep": "0.9293", + "numicubedsperchosprep": "0.9293", + "numicubedsoccperchosprep": "0.9293", + "totalconfc19hosppatsperc": "0.9293", + "totalconffluhosppatsperc": "0.7879", + "totalconfrsvhosppatsperc": "0.0", + "totalconfc19icupatsperchosprep": "0.9293", + "totalconffluicupatsperchosprep": "0.7879", + "totalconfrsvicupatsperchosprep": "0.0", + "totalconfc19newadmpedper": "0.9091", + "totalconfc19newadmadultp": "0.9293", + "totalconfc19newadmperchosprep": "92.93", + "totalconfflunewadmpedper": "0.0", + "totalconfflunewadmadultp": "0.0", + "totalconfflunewadmperchosprep": "78.79", + "totalconfrsvnewadmpedper": "0.0", + "totalconfrsvnewadmadultp": "0.0", + "totalconfrsvnewadmperchosprep": "0.0", + "pctinptbedsoccperchosprep": "0.9293", + "pcticubedsoccperchosprep": "0.9293", + "pctconfc19inptbedsperchosprep": "0.9293", + "pctconffluinptbedsperchosprep": "0.7879", + "pctconfrsvinptbedsperchosprep": "0.0", + "pctconfc19icubedsperchosprep": "0.9293", + "pctconffluicubedsperchosprep": "0.7879", + "pctconfrsvicubedsperchosprep": "0.0", + "numinptbedsperchosprepabschg": "0.0", + "numinptbedsoccperchospre": "0.0", + "numicubedsperchosprepabschg": "0.0", + "numicubedsoccperchosprepabschg": "0.0", + "totalconfc19hosppatsperc_1": "0.0", + "totalconffluhosppatsperc_1": "0.0", + "totalconfrsvhosppatsperc_1": "0.0", + "totalconfc19icupatsperch": "0.0", + "totalconffluicupatsperch": "0.0", + "totalconfrsvicupatsperch": "0.0", + "totalconfc19newadmpedper_1": "0.0", + "totalconfc19newadmadultp_1": "0.0", + "totalconfc19newadmpercho": "0.0", + "totalconfflunewadmpedper_1": "0.0", + "totalconfflunewadmadultp_1": "0.0", + "totalconfflunewadmpercho": "0.0", + "totalconfrsvnewadmpedper_1": "0.0", + "totalconfrsvnewadmadultp_1": "0.0", + "totalconfrsvnewadmpercho": "0.0", + "pctinptbedsoccperchospre": "0.0", + "pcticubedsoccperchosprepabschg": "0.0", + "pctconfc19inptbedspercho": "0.0", + "pctconffluinptbedspercho": "0.0", + "pctconfrsvinptbedspercho": "0.0", + "pctconfc19icubedsperchos": "0.0", + "pctconffluicubedsperchos": "0.0", + "pctconfrsvicubedsperchos": "0.0" + }, + { + "weekendingdate": "2021-08-21T00:00:00.000", + "jurisdiction": "USA", + "numinptbeds": "750150.99", + "numinptbedsadult": "679540.51", + "numinptbedsped": "51335.02", + "numinptbedsocc": "572345.09", + "numinptbedsoccadult": "526399.17", + "numinptbedsoccped": "32810.36", + "numicubeds": "120768.79", + "numicubedsadult": "91030.4", + "numicubedsped": "21419.35", + "numicubedsocc": "89853.28", + "numicubedsoccadult": "70595.31", + "numicubedsoccped": "14112.02", + "numconfc19hosppatsadult": "92782.24", + "numconfc19hosppatsped": "1268.64", + "totalconfc19hosppats": "94050.88", + "totalconffluhosppats": "292.67", + "numconfc19icupatsadult": "24692.91", + "totalconfc19icupats": "24692.91", + "totalconffluicupats": "45.57", + "totalconfc19newadmped": "2170.0", + "numconfc19newadmadult18to49": "27365.0", + "totalconfc19newadmadult": "90776.0", + "numconfc19newadmunk": "4827.0", + "totalconfc19newadm": "92946.0", + "totalconfflunewadm": "280.0", + "pctinptbedsocc": "0.763", + "pctconfc19inptbeds": "0.1254", + "pctconffluinptbeds": "0.0004", + "pcticubedsocc": "0.744", + "pctconfc19icubeds": "0.2045", + "pctconffluicubeds": "0.0004", + "pctconfc19newadmadult": "0.9767", + "pctconfc19newadmped": "0.0233", + "numinptbedshosprep": "5396", + "numinptbedsocchosprep": "5396", + "numicubedshosprep": "5396", + "numicubedsocchosprep": "5396", + "totalconfc19hosppatshosprep": "5393", + "totalconffluhosppatshosprep": "4417", + "totalconfrsvhosppatshosprep": "0", + "totalconfc19icupatshosprep": "5393", + "totalconffluicupatshosprep": "4415", + "totalconfrsvicupatshosprep": "0", + "totalconfc19newadmpedhosprep": "5276", + "totalconfc19newadmadulthosprep": "5392", + "totalconfc19newadmhosprep": "5392", + "totalconfflunewadmpedhosprep": "0", + 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"totalconfflunewadmadultp_1": "0.0", + "totalconfflunewadmpercho": "-0.21", + "totalconfrsvnewadmpedper_1": "0.0", + "totalconfrsvnewadmadultp_1": "0.0", + "totalconfrsvnewadmpercho": "0.0", + "pctinptbedsoccperchospre": "0.0002", + "pcticubedsoccperchosprepabschg": "0.0002", + "pctconfc19inptbedspercho": "0.0002", + "pctconffluinptbedspercho": "-0.0018", + "pctconfrsvinptbedspercho": "0.0", + "pctconfc19icubedsperchos": "0.0002", + "pctconffluicubedsperchos": "-0.0025", + "pctconfrsvicubedsperchos": "0.0" + }, + { + "weekendingdate": "2021-10-16T00:00:00.000", + "jurisdiction": "CO", + "numinptbeds": "10426.29", + "numinptbedsadult": "9195.0", + "numinptbedsped": "664.14", + "numinptbedsocc": "7365.71", + "numinptbedsoccadult": "6590.86", + "numinptbedsoccped": "322.71", + "numicubeds": "1820.57", + "numicubedsadult": "1345.29", + "numicubedsped": "300.29", + "numicubedsocc": "1362.0", + "numicubedsoccadult": "1088.0", + "numicubedsoccped": "176.71", + "numconfc19hosppatsadult": "996.86", + "numconfc19hosppatsped": "19.57", + "totalconfc19hosppats": "1016.43", + "totalconffluhosppats": "0.86", + "numconfc19icupatsadult": "346.14", + "totalconfc19icupats": "346.14", + "totalconffluicupats": "0.0", + "totalconfc19newadmped": "38.0", + "numconfc19newadmadult18to49": "332.0", + "totalconfc19newadmadult": "1193.0", + "numconfc19newadmunk": "8.0", + "totalconfc19newadm": "1231.0", + "totalconfflunewadm": "0.0", + "pctinptbedsocc": "0.7065", + "pctconfc19inptbeds": "0.0975", + "pctconffluinptbeds": "0.0001", + "pcticubedsocc": "0.7481", + "pctconfc19icubeds": "0.1901", + "pctconffluicubeds": "0.0", + "pctconfc19newadmadult": "0.9691", + "pctconfc19newadmped": "0.0309", + "numinptbedshosprep": "92", + "numinptbedsocchosprep": "92", + "numicubedshosprep": "92", + "numicubedsocchosprep": "92", + "totalconfc19hosppatshosprep": "92", + "totalconffluhosppatshosprep": "78", + "totalconfrsvhosppatshosprep": "0", + "totalconfc19icupatshosprep": "92", + "totalconffluicupatshosprep": "78", + "totalconfrsvicupatshosprep": "0", + "totalconfc19newadmpedhosprep": "90", + "totalconfc19newadmadulthosprep": "92", + "totalconfc19newadmhosprep": "92", + "totalconfflunewadmpedhosprep": "0", + "totalconfflunewadmadulthosprep": "0", + "totalconfflunewadmhosprep": "78", + "totalconfrsvnewadmpedhosprep": "0", + "totalconfrsvnewadmadulthosprep": "0", + "totalconfrsvnewadmhosprep": "0", + "pctinptbedsocchosprep": "92", + "pcticubedsocchosprep": "92", + "pctconfc19inptbedshosprep": "92", + "pctconffluinptbedshosprep": "78", + "pctconfrsvinptbedshosprep": "0", + "pctconfc19icubedshosprep": "92", + "pctconffluicubedshosprep": "78", + "pctconfrsvicubedshosprep": "0", + "numinptbedsperchosprep": "0.9293", + "numinptbedsoccperchosprep": "0.9293", + "numicubedsperchosprep": "0.9293", + "numicubedsoccperchosprep": "0.9293", + "totalconfc19hosppatsperc": "0.9293", + "totalconffluhosppatsperc": "0.7879", + "totalconfrsvhosppatsperc": "0.0", + "totalconfc19icupatsperchosprep": "0.9293", + "totalconffluicupatsperchosprep": "0.7879", + "totalconfrsvicupatsperchosprep": "0.0", + "totalconfc19newadmpedper": "0.9091", + "totalconfc19newadmadultp": "0.9293", + "totalconfc19newadmperchosprep": "92.93", + "totalconfflunewadmpedper": "0.0", + "totalconfflunewadmadultp": "0.0", + "totalconfflunewadmperchosprep": "78.79", + "totalconfrsvnewadmpedper": "0.0", + "totalconfrsvnewadmadultp": "0.0", + "totalconfrsvnewadmperchosprep": "0.0", + "pctinptbedsoccperchosprep": "0.9293", + "pcticubedsoccperchosprep": "0.9293", + "pctconfc19inptbedsperchosprep": "0.9293", + "pctconffluinptbedsperchosprep": "0.7879", + "pctconfrsvinptbedsperchosprep": "0.0", + "pctconfc19icubedsperchosprep": "0.9293", + "pctconffluicubedsperchosprep": "0.7879", + "pctconfrsvicubedsperchosprep": "0.0", + "numinptbedsperchosprepabschg": "0.0", + "numinptbedsoccperchospre": "0.0", + "numicubedsperchosprepabschg": "0.0", + "numicubedsoccperchosprepabschg": "0.0", + "totalconfc19hosppatsperc_1": "0.0", + "totalconffluhosppatsperc_1": "0.0", + "totalconfrsvhosppatsperc_1": "0.0", + "totalconfc19icupatsperch": "0.0", + "totalconffluicupatsperch": "0.0", + "totalconfrsvicupatsperch": "0.0", + "totalconfc19newadmpedper_1": "0.0", + "totalconfc19newadmadultp_1": "0.0", + "totalconfc19newadmpercho": "0.0", + "totalconfflunewadmpedper_1": "0.0", + "totalconfflunewadmadultp_1": "0.0", + "totalconfflunewadmpercho": "0.0", + "totalconfrsvnewadmpedper_1": "0.0", + "totalconfrsvnewadmadultp_1": "0.0", + "totalconfrsvnewadmpercho": "0.0", + "pctinptbedsoccperchospre": "0.0", + "pcticubedsoccperchosprepabschg": "0.0", + "pctconfc19inptbedspercho": "0.0", + "pctconffluinptbedspercho": "0.0", + "pctconfrsvinptbedspercho": "0.0", + "pctconfc19icubedsperchos": "0.0", + "pctconffluicubedsperchos": "0.0", + "pctconfrsvicubedsperchos": "0.0" + }, + { + "weekendingdate": "2021-10-16T00:00:00.000", + "jurisdiction": "USA", + "numinptbeds": "729772.05", + "numinptbedsadult": "660758.41", + "numinptbedsped": "53387.68", + "numinptbedsocc": "556817.29", + "numinptbedsoccadult": "510524.46", + "numinptbedsoccped": "35679.97", + "numicubeds": "114471.4", + "numicubedsadult": "86925.11", + "numicubedsped": "21902.45", + "numicubedsocc": "85344.84", + "numicubedsoccadult": "66877.69", + "numicubedsoccped": "14657.22", + "numconfc19hosppatsadult": "55448.05", + "numconfc19hosppatsped": "847.15", + "totalconfc19hosppats": "56295.2", + "totalconffluhosppats": "259.85", + "numconfc19icupatsadult": "18104.6", + "totalconfc19icupats": "18104.6", + "totalconffluicupats": "39.33", + "totalconfc19newadmped": "1301.0", + "numconfc19newadmadult18to49": "11532.0", + "totalconfc19newadmadult": "44677.0", + "numconfc19newadmunk": "1982.0", + "totalconfc19newadm": "45978.0", + "totalconfflunewadm": "266.0", + "pctinptbedsocc": "0.763", + "pctconfc19inptbeds": "0.0771", + "pctconffluinptbeds": "0.0004", + "pcticubedsocc": "0.7456", + "pctconfc19icubeds": "0.1582", + "pctconffluicubeds": "0.0003", + "pctconfc19newadmadult": "0.9717", + "pctconfc19newadmped": "0.0283", + "numinptbedshosprep": "5396", + "numinptbedsocchosprep": "5396", + "numicubedshosprep": "5396", + "numicubedsocchosprep": "5396", + "totalconfc19hosppatshosprep": "5396", + "totalconffluhosppatshosprep": "4317", + "totalconfrsvhosppatshosprep": "0", + "totalconfc19icupatshosprep": "5396", + "totalconffluicupatshosprep": "4306", + "totalconfrsvicupatshosprep": "0", + "totalconfc19newadmpedhosprep": "5278", + "totalconfc19newadmadulthosprep": "5394", + "totalconfc19newadmhosprep": "5394", + "totalconfflunewadmpedhosprep": "0", + "totalconfflunewadmadulthosprep": "0", + "totalconfflunewadmhosprep": "4307", + "totalconfrsvnewadmpedhosprep": "0", + "totalconfrsvnewadmadulthosprep": "0", + "totalconfrsvnewadmhosprep": "0", + "pctinptbedsocchosprep": "5396", + "pcticubedsocchosprep": "5396", + "pctconfc19inptbedshosprep": "5396", + "pctconffluinptbedshosprep": "4317", + "pctconfrsvinptbedshosprep": "0", + "pctconfc19icubedshosprep": "5396", + "pctconffluicubedshosprep": "4306", + "pctconfrsvicubedshosprep": "0", + "numinptbedsperchosprep": "0.9492", + "numinptbedsoccperchosprep": "0.9492", + "numicubedsperchosprep": "0.9492", + "numicubedsoccperchosprep": "0.9492", + "totalconfc19hosppatsperc": "0.9492", + "totalconffluhosppatsperc": "0.7594", + "totalconfrsvhosppatsperc": "0.0", + "totalconfc19icupatsperchosprep": "0.9492", + "totalconffluicupatsperchosprep": "0.7574", + "totalconfrsvicupatsperchosprep": "0.0", + "totalconfc19newadmpedper": "0.9284", + "totalconfc19newadmadultp": "0.9488", + "totalconfc19newadmperchosprep": "94.88", + "totalconfflunewadmpedper": "0.0", + "totalconfflunewadmadultp": "0.0", + "totalconfflunewadmperchosprep": "75.76", + "totalconfrsvnewadmpedper": "0.0", + "totalconfrsvnewadmadultp": "0.0", + "totalconfrsvnewadmperchosprep": "0.0", + "pctinptbedsoccperchosprep": "0.9492", + "pcticubedsoccperchosprep": "0.9492", + "pctconfc19inptbedsperchosprep": "0.9492", + "pctconffluinptbedsperchosprep": "0.7594", + "pctconfrsvinptbedsperchosprep": "0.0", + "pctconfc19icubedsperchosprep": "0.9492", + "pctconffluicubedsperchosprep": "0.7574", + "pctconfrsvicubedsperchosprep": "0.0", + "numinptbedsperchosprepabschg": "-0.07", + "numinptbedsoccperchospre": "-0.07", + "numicubedsperchosprepabschg": "-0.07", + "numicubedsoccperchosprepabschg": "-0.07", + "totalconfc19hosppatsperc_1": "-0.02", + "totalconffluhosppatsperc_1": "-1.23", + "totalconfrsvhosppatsperc_1": "0.0", + "totalconfc19icupatsperch": "-0.02", + "totalconffluicupatsperch": "-1.2", + "totalconfrsvicupatsperch": "0.0", + "totalconfc19newadmpedper_1": "-0.04", + "totalconfc19newadmadultp_1": "-0.04", + "totalconfc19newadmpercho": "-0.04", + "totalconfflunewadmpedper_1": "0.0", + "totalconfflunewadmadultp_1": "0.0", + "totalconfflunewadmpercho": "-1.27", + "totalconfrsvnewadmpedper_1": "0.0", + "totalconfrsvnewadmadultp_1": "0.0", + "totalconfrsvnewadmpercho": "0.0", + "pctinptbedsoccperchospre": "-0.0007", + "pcticubedsoccperchosprepabschg": "-0.0007", + "pctconfc19inptbedspercho": "-0.0002", + "pctconffluinptbedspercho": "-0.0123", + "pctconfrsvinptbedspercho": "0.0", + "pctconfc19icubedsperchos": "-0.0002", + "pctconffluicubedsperchos": "-0.012", + "pctconfrsvicubedsperchos": "0.0" + } +] \ No newline at end of file diff --git a/nhsn/tests/test_pull.py b/nhsn/tests/test_pull.py new file mode 100644 index 000000000..231f7a8ac --- /dev/null +++ b/nhsn/tests/test_pull.py @@ -0,0 +1,86 @@ +import glob +import json +from unittest.mock import patch, MagicMock +import os +import pytest + +import pandas as pd + +from delphi_nhsn.pull import ( + pull_nhsn_data, +) +from delphi_nhsn.constants import SIGNALS_MAP + +from delphi_utils import get_structured_logger + +class TestPullNHSNData: + @patch("delphi_nhsn.pull.Socrata") + def test_socrata_call(self, mock_socrata, params): + backup_dir = params["common"]["backup_dir"] + test_token = params["indicator"]["socrata_token"] + custom_run = True + logger = get_structured_logger() + + # Mock Socrata client and its get method + mock_client = MagicMock() + mock_socrata.return_value = mock_client + mock_client.get.side_effect = [[]] + + pull_nhsn_data(test_token, backup_dir, custom_run, logger) + + # Check that Socrata client was initialized with correct arguments + mock_socrata.assert_called_once_with("data.cdc.gov", test_token) + + # Check that get method was called with correct arguments + mock_client.get.assert_any_call("ua7e-t2fy", limit=50000, offset=0) + + def test_pull_nhsn_data_output(self, caplog, mock_get, params): + backup_dir = params["common"]["backup_dir"] + test_token = params["indicator"]["socrata_token"] + custom_run = True + + logger = get_structured_logger() + + result = pull_nhsn_data(test_token, backup_dir, custom_run, logger) + + # Check result + assert result["timestamp"].notnull().all(), "timestamp has rogue NaN" + assert result["geo_id"].notnull().all(), "geography has rogue NaN" + + # Check for each signal in SIGNALS + for signal in SIGNALS_MAP.keys(): + assert result[signal].notnull().all(), f"{signal} has rogue NaN" + def test_pull_nhsn_data_backup(self, mock_get, caplog, params): + today = pd.Timestamp.today().strftime("%Y%m%d") + backup_dir = params["common"]["backup_dir"] + custom_run = params["common"]["custom_run"] + test_token = params["indicator"]["socrata_token"] + + # Load test data + expected_data = pd.DataFrame() + with open("test_data/page.json", "r") as f: + test_data = json.load(f) + expected_data = pd.DataFrame(test_data) + + logger = get_structured_logger() + # Call function with test token + pull_nhsn_data(test_token, backup_dir, custom_run, logger) + + # Check logger used: + assert "Backup file created" in caplog.text + + # Check that backup file was created + backup_files = glob.glob(f"{backup_dir}/{today}*") + assert len(backup_files) == 2, "Backup file was not created" + + for backup_file in backup_files: + if backup_file.endswith(".csv.gz"): + dtypes = expected_data.dtypes.to_dict() + actual_data = pd.read_csv(backup_file, dtype=dtypes) + else: + actual_data = pd.read_parquet(backup_file) + pd.testing.assert_frame_equal(expected_data, actual_data) + + # clean up + for file in backup_files: + os.remove(file) \ No newline at end of file diff --git a/nhsn/tests/test_run.py b/nhsn/tests/test_run.py new file mode 100644 index 000000000..0b41e5f3b --- /dev/null +++ b/nhsn/tests/test_run.py @@ -0,0 +1,61 @@ +from os import listdir +import pytest + + +class TestRun: + # the 14th was a Monday + @pytest.mark.parametrize("date", ["2020-09-14", "2020-09-17", "2020-09-18"]) + def test_output_files_exist(self, params, run_as_module, date): + for output_folder in folders: + csv_files = listdir(output_folder) + + geos = ["nation", "state"] + dates = [ + "202030", + "202031", + "202032", + "202033", + "202034", + "202035", + "202036", + ] + metrics = ['deaths_covid_incidence', + 'deaths_allcause_incidence', + 'deaths_percent_of_expected', + 'deaths_pneumonia_notflu_incidence', + 'deaths_covid_and_pneumonia_notflu_incidence', + 'deaths_flu_incidence', + 'deaths_pneumonia_or_flu_or_covid_incidence'] + sensors = ["num", "prop"] + + expected_files = [] + for geo in geos: + for d in dates: + for metric in metrics: + if metric == "deaths_percent_of_expected": + expected_files += [f"weekly_{d}_{geo}_{metric}.csv"] + else: + for sensor in sensors: + expected_files += [f"weekly_{d}_{geo}_{metric}_{sensor}.csv"] + assert set(expected_files).issubset(set(csv_files)) + + # the 14th was a Monday + @pytest.mark.parametrize("date", ["2020-09-14", "2020-09-17", "2020-09-18"]) + def test_output_file_format(self, run_as_module, date): + is_mon_or_thurs = dt.datetime.strptime(date, "%Y-%m-%d").weekday() == (0 or 3) + + folders = ["daily_cache"] + if is_mon_or_thurs: + folders.append("receiving") + + geos = ["nation", "state"] + for geo in geos: + for output_folder in folders: + df = pd.read_csv( + join(output_folder, f"weekly_202026_{geo}_deaths_covid_incidence_prop.csv") + ) + expected_columns = [ + "geo_id", "val", "se", "sample_size", + "missing_val", "missing_se", "missing_sample_size" + ] + assert (df.columns.values == expected_columns).all()