From 1a508568f6a5e438450e2f609aae38041b9e5d00 Mon Sep 17 00:00:00 2001 From: minhkhul Date: Tue, 28 May 2024 17:09:55 -0400 Subject: [PATCH 1/2] remove hhs_hosp dir --- hhs_hosp/.pylintrc | 22 - hhs_hosp/Makefile | 34 - hhs_hosp/README.md | 64 -- hhs_hosp/REVIEW.md | 39 -- hhs_hosp/cache/.gitignore | 1 - hhs_hosp/delphi_hhs/__init__.py | 16 - hhs_hosp/delphi_hhs/__main__.py | 11 - hhs_hosp/delphi_hhs/constants.py | 29 - hhs_hosp/delphi_hhs/run.py | 220 ------ hhs_hosp/params.json.template | 22 - hhs_hosp/receiving/.gitignore | 1 - hhs_hosp/setup.py | 31 - hhs_hosp/static/.gitignore | 0 hhs_hosp/tests/test_response.json | 1086 ----------------------------- hhs_hosp/tests/test_run.py | 232 ------ hhs_hosp/version.cfg | 1 - 16 files changed, 1809 deletions(-) delete mode 100644 hhs_hosp/.pylintrc delete mode 100644 hhs_hosp/Makefile delete mode 100644 hhs_hosp/README.md delete mode 100644 hhs_hosp/REVIEW.md delete mode 100644 hhs_hosp/cache/.gitignore delete mode 100644 hhs_hosp/delphi_hhs/__init__.py delete mode 100644 hhs_hosp/delphi_hhs/__main__.py delete mode 100644 hhs_hosp/delphi_hhs/constants.py delete mode 100644 hhs_hosp/delphi_hhs/run.py delete mode 100644 hhs_hosp/params.json.template delete mode 100644 hhs_hosp/receiving/.gitignore delete mode 100644 hhs_hosp/setup.py delete mode 100644 hhs_hosp/static/.gitignore delete mode 100644 hhs_hosp/tests/test_response.json delete mode 100644 hhs_hosp/tests/test_run.py delete mode 100644 hhs_hosp/version.cfg diff --git a/hhs_hosp/.pylintrc b/hhs_hosp/.pylintrc deleted file mode 100644 index 58c6edbba..000000000 --- a/hhs_hosp/.pylintrc +++ /dev/null @@ -1,22 +0,0 @@ - -[MESSAGES CONTROL] - -disable=logging-format-interpolation, - too-many-locals, - too-many-arguments, - # Allow pytest functions to be part of a class. - no-self-use, - # Allow pytest classes to have one test. - too-few-public-methods - -[BASIC] - -# Allow arbitrarily short-named variables. -variable-rgx=[a-z_][a-z0-9_]* -argument-rgx=[a-z_][a-z0-9_]* -attr-rgx=[a-z_][a-z0-9_]* - -[DESIGN] - -# Don't complain about pytest "unused" arguments. -ignored-argument-names=(_.*|run_as_module) diff --git a/hhs_hosp/Makefile b/hhs_hosp/Makefile deleted file mode 100644 index ea591dcb5..000000000 --- a/hhs_hosp/Makefile +++ /dev/null @@ -1,34 +0,0 @@ -.PHONY = venv, lint, test, clean - -dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1) -venv: - python3.8 -m venv env - -install: venv - . env/bin/activate; \ - pip install wheel ; \ - pip install -e ../_delphi_utils_python ;\ - pip install -e . - -install-ci: venv - . env/bin/activate; \ - pip install wheel ; \ - pip install ../_delphi_utils_python ;\ - pip install . - -lint: - . env/bin/activate; pylint $(dir) - . env/bin/activate; pydocstyle $(dir) - -test: - . env/bin/activate ;\ - (cd tests && ../env/bin/pytest --cov=$(dir) --cov-report=term-missing) - -clean: - rm -rf env - rm -f params.json - -run: - env/bin/python -m $(dir) - env/bin/python -m delphi_utils.validator --dry_run - env/bin/python -m delphi_utils.archive diff --git a/hhs_hosp/README.md b/hhs_hosp/README.md deleted file mode 100644 index ce68ee812..000000000 --- a/hhs_hosp/README.md +++ /dev/null @@ -1,64 +0,0 @@ -# HHS Hospitalizations - -This indicator computes the "ground truth" for official hospitalizations in the -US. It uses the Epidata API to fetch daily adult and pediatric hospital -admissions, sums them, and publishes the result as a COVIDcast signal. - -## Running the Indicator - -The indicator is run by directly executing the Python module contained in this -directory. The safest way to do this is to create a virtual environment, -installed the common DELPHI tools, and then install the module and its -dependencies. To do this, run the following command from this directory: - -``` -make install -``` - -This command will install the package in editable mode, so you can make changes that -will automatically propagate to the installed package. - -All of the user-changable parameters are stored in `params.json`. To execute -the module and produce the output datasets (by default, in `receiving`), run -the following: - -``` -env/bin/python -m delphi_hhs -``` - -If you want to enter the virtual environment in your shell, -you can run `source env/bin/activate`. Run `deactivate` to leave the virtual environment. - -Once you are finished, you can remove the virtual environment and -params file with the following: - -``` -make clean -``` - -## Testing the code - -To run static tests of the code style, run the following command: - -``` -make lint -``` - -Unit tests are also included in the module. To execute these, run the following -command from this directory: - -``` -make test -``` - -To run individual tests, run the following: - -``` -(cd tests && ../env/bin/pytest .py --cov=delphi_hhs --cov-report=term-missing) -``` - -The output will show the number of unit tests that passed and failed, along -with the percentage of code covered by the tests. - -None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and -should not include critical sub-routines. diff --git a/hhs_hosp/REVIEW.md b/hhs_hosp/REVIEW.md deleted file mode 100644 index 93a5a6579..000000000 --- a/hhs_hosp/REVIEW.md +++ /dev/null @@ -1,39 +0,0 @@ -## Code Review (Python) - -A code review of this module should include a careful look at the code and the -output. To assist in the process, but certainly not in replace of it, please -check the following items. - -**Documentation** - -- [ ] the README.md file template is filled out and currently accurate; it is -possible to load and test the code using only the instructions given -- [ ] minimal docstrings (one line describing what the function does) are -included for all functions; full docstrings describing the inputs and expected -outputs should be given for non-trivial functions - -**Structure** - -- [ ] code should use 4 spaces for indentation; other style decisions are -flexible, but be consistent within a module -- [ ] any required metadata files are checked into the repository and placed -within the directory `static` -- [ ] any intermediate files that are created and stored by the module should -be placed in the directory `cache` -- [ ] final expected output files to be uploaded to the API are placed in the -`receiving` directory; output files should not be committed to the respository -- [ ] all options and API keys are passed through the file `params.json` -- [ ] template parameter file (`params.json.template`) is checked into the -code; no personal (i.e., usernames) or private (i.e., API keys) information is -included in this template file - -**Testing** - -- [ ] module can be installed in a new virtual environment -- [ ] pylint with the default `.pylint` settings run over the module produces -minimal warnings; warnings that do exist have been confirmed as false positives -- [ ] reasonably high level of unit test coverage covering all of the main logic -of the code (e.g., missing coverage for raised errors that do not currently seem -possible to reach are okay; missing coverage for options that will be needed are -not) -- [ ] all unit tests run without errors diff --git a/hhs_hosp/cache/.gitignore b/hhs_hosp/cache/.gitignore deleted file mode 100644 index afed0735d..000000000 --- a/hhs_hosp/cache/.gitignore +++ /dev/null @@ -1 +0,0 @@ -*.csv diff --git a/hhs_hosp/delphi_hhs/__init__.py b/hhs_hosp/delphi_hhs/__init__.py deleted file mode 100644 index 5fc24f450..000000000 --- a/hhs_hosp/delphi_hhs/__init__.py +++ /dev/null @@ -1,16 +0,0 @@ -# -*- coding: utf-8 -*- -"""Module to pull and clean indicators from the Delphi Epidata covid_hosp endpoint. - -Epidata:covid_hosp contains HHS state-level hospitalization data. - -This file defines the functions that are made public by the module. As the -module is intended to be executed though the main method, these are primarily -for testing. - -""" - -from __future__ import absolute_import - -from . import run - -__version__ = "0.1.0" diff --git a/hhs_hosp/delphi_hhs/__main__.py b/hhs_hosp/delphi_hhs/__main__.py deleted file mode 100644 index 86ffe2c84..000000000 --- a/hhs_hosp/delphi_hhs/__main__.py +++ /dev/null @@ -1,11 +0,0 @@ -# -*- coding: utf-8 -*- -"""Call the function run_module when executed. - -This file indicates that calling the module (`python -m delphi_hhs`) will -call the function `run_module` found within the run.py file. There should be -no need to change this template. -""" -from delphi_utils import read_params -from .run import run_module # pragma: no cover - -run_module(read_params()) # pragma: no cover diff --git a/hhs_hosp/delphi_hhs/constants.py b/hhs_hosp/delphi_hhs/constants.py deleted file mode 100644 index 810c74eb7..000000000 --- a/hhs_hosp/delphi_hhs/constants.py +++ /dev/null @@ -1,29 +0,0 @@ -"""Registry for signal names.""" -from delphi_utils import Smoother - -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" - -SIGNALS = [ - CONFIRMED, - SUM_CONF_SUSP, - CONFIRMED_PROP, - SUM_CONF_SUSP_PROP, - CONFIRMED_FLU, - CONFIRMED_FLU_PROP -] - -GEOS = [ - "nation", - "hhs", - "state" -] - -SMOOTHERS = [ - (Smoother("identity", impute_method=None), ""), - (Smoother("moving_average", window_length=7), "_7dav"), -] diff --git a/hhs_hosp/delphi_hhs/run.py b/hhs_hosp/delphi_hhs/run.py deleted file mode 100644 index 22c259f30..000000000 --- a/hhs_hosp/delphi_hhs/run.py +++ /dev/null @@ -1,220 +0,0 @@ -# -*- 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 delphi_hhs`. -""" -from datetime import date, datetime, timedelta -from itertools import product - -import time -from delphi_epidata import Epidata -from delphi_utils.export import create_export_csv -from delphi_utils.geomap import GeoMapper -from delphi_utils import get_structured_logger -import numpy as np -import pandas as pd - -from .constants import SIGNALS, GEOS, SMOOTHERS, CONFIRMED, SUM_CONF_SUSP, CONFIRMED_FLU - -def _date_to_int(d): - """Return a date object as a yyyymmdd int.""" - return int(d.strftime("%Y%m%d")) - - -def int_date_to_previous_day_datetime(x): - """Convert integer dates to Python datetimes for the previous day. - - Epidata uses an integer date format. This needs to be converted to - a datetime so that the exporter can interpret it. - - The HHS columns we are interested in measure admissions for the - previous day. To accurately indicate the date of incidence, the - date must be shifted back by one day. - """ - return x.apply(lambda x: datetime.strptime(str(x), "%Y%m%d") - timedelta(days=1)) - - -def generate_date_ranges(start, end): - """ - Take a start and end date and convert to list of 30 day Epidata ranges. - - The final tuple may only be a few days depending of the modulo of the range and 30. - The ranges should partition the entire range, inclusive of both endpoints, and do not overlap, - i.e. they will be of the form (start, start+30), (start+31, start+61), (start+62, start+92), ... - - Parameters - ---------- - start: date - datetime.date object for first day. - end: datetime - datetime.date object for last day. - - Returns - ------- - Ordered list of dictionaries generated by Epidata.range specifying the partitioning intervals. - """ - curr_end = start + timedelta(30) - output = [] - while curr_end < end: - output.append(Epidata.range(_date_to_int(start), _date_to_int(curr_end))) - start += timedelta(31) - curr_end = start + timedelta(30) - output.append(Epidata.range(_date_to_int(start), _date_to_int(end))) - return output - - -def run_module(params): - """ - Generate ground truth HHS hospitalization data. - - Parameters - ---------- - params - Dictionary containing indicator configuration. Expected to have the following structure: - - "common": - - "export_dir": str, directory to write output - - "log_filename" (optional): str, name of file to write logs - - "epidata" (optional): dict, extra parameters to send to Epidata.covid_hosp - - "validation": - - "common": - - "api_credentials": str, api key to prevent hitting max number of query limit. - """ - if params.get("validation") and params["validation"].get("common") and \ - params["validation"]["common"].get("api_credentials"): - Epidata.auth = ('epidata', str(params["validation"]["common"]["api_credentials"])) - start_time = time.time() - logger = get_structured_logger( - __name__, filename=params["common"].get("log_filename"), - log_exceptions=params["common"].get("log_exceptions", True)) - mapper = GeoMapper() - request_all_states = ",".join(mapper.get_geo_values("state_id")) - end_day = date.today() - if "epidata" in params["common"] and \ - "as_of" in params["common"]["epidata"]: - end_day = min( - end_day, - datetime.strptime(str(params["common"]["epidata"]["as_of"]), "%Y%m%d").date() - ) - past_reference_day = date(year=2020, month=1, day=1) # first available date in DB - date_range = generate_date_ranges(past_reference_day, end_day) - dfs = [] - for r in date_range: - response = Epidata.covid_hosp(request_all_states, r, **params["common"].get("epidata", {})) - # The last date range might only have recent days that don't have any data, so don't error. - if response["result"] != 1 and r != date_range[-1]: - raise Exception(f"Bad result from Epidata for {r}: {response['message']}") - if response["result"] == -2 and r == date_range[-1]: # -2 code means no results - continue - dfs.append(pd.DataFrame(response['epidata'])) - all_columns = pd.concat(dfs) - geo_mapper = GeoMapper() - stats = [] - for sensor, smoother, geo in product(SIGNALS, SMOOTHERS, GEOS): - logger.info("Generating signal and exporting to CSV", - geo_res = geo, - sensor = sensor, - smoother = smoother) - df = make_signal(all_columns, sensor) - df = transform_signal(sensor, smoother, geo, df, geo_mapper) - if df.empty: - continue - sensor_name = sensor + smoother[1] - # don't export first 6 days for smoothed signals since they'll be nan. - start_date = min(df.timestamp) + timedelta(6) if smoother[1] else min(df.timestamp) - dates = create_export_csv(df, - params["common"]["export_dir"], - geo, - sensor_name, - start_date=start_date) - if len(dates) > 0: - stats.append((max(dates), len(dates))) - - 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 smooth_values(df, smoother): - """Smooth the value column in the dataframe.""" - df["val"] = df["val"].astype(float) - df["val"] = df[["geo_id", "val"]].groupby("geo_id")["val"].transform( - smoother.smooth - ) - return df - -def transform_signal(sensor, smoother, geo, df, geo_mapper): - """Transform base df into specified geo/smoothing/prop configuration.""" - df = geo_mapper.add_geocode(df, "state_id", "state_code", from_col="state") - # handling population: - # add population column - # sum admission counts *and* population counts during make_geo - # *then* divide counts by population to get the proportion - if sensor.endswith("_prop"): - df=geo_mapper.add_population_column(df, "state_code") - df = make_geo(df, geo, geo_mapper) - if sensor.endswith("_prop"): - df["val"]=round(df["val"]/df["population"]*100000, 7) - df.drop("population", axis=1, inplace=True) - df = smooth_values(df, smoother[0]) - # Fix N/A MA values, see issue #1360 - if geo == "state" and sensor.startswith(CONFIRMED_FLU): - ma_filter = df.val.isna() & (df.geo_id == "ma") & (df.timestamp > "08-01-2021") & \ - (df.timestamp.dt.day_name() == "Tuesday") - df = df[~ma_filter] - return df - -def make_geo(state, geo, geo_mapper): - """Transform incoming geo (state) to another geo.""" - if geo == "state": - exported = state.rename(columns={"state": "geo_id"}) - exported = exported.drop(columns="state_code") - else: - exported = geo_mapper.replace_geocode(state, "state_code", geo, new_col="geo_id") - exported["se"] = np.nan - exported["sample_size"] = np.nan - return exported - - -def make_signal(all_columns, sig): - """Generate column sums according to signal name.""" - assert sig in SIGNALS, f"Unexpected signal name '{sig}';" + \ - " familiar names are '{', '.join(SIGNALS)}'" - if sig.startswith(CONFIRMED): - df = pd.DataFrame({ - "state": all_columns.state.apply(str.lower), - "timestamp":int_date_to_previous_day_datetime(all_columns.date), - "val": \ - all_columns.previous_day_admission_adult_covid_confirmed + \ - all_columns.previous_day_admission_pediatric_covid_confirmed - }) - elif sig.startswith(SUM_CONF_SUSP): - df = pd.DataFrame({ - "state": all_columns.state.apply(str.lower), - "timestamp":int_date_to_previous_day_datetime(all_columns.date), - "val": \ - all_columns.previous_day_admission_adult_covid_confirmed + \ - all_columns.previous_day_admission_adult_covid_suspected + \ - all_columns.previous_day_admission_pediatric_covid_confirmed + \ - all_columns.previous_day_admission_pediatric_covid_suspected, - }) - elif sig.startswith(CONFIRMED_FLU): - df = pd.DataFrame({ - "state": all_columns.state.apply(str.lower), - "timestamp":int_date_to_previous_day_datetime(all_columns.date), - "val": \ - all_columns.previous_day_admission_influenza_confirmed - }) - else: - raise Exception( - "Bad programmer: signal '{sig}' in SIGNALS but not handled in make_signal" - ) - df["val"] = df.val.astype(float) - return df diff --git a/hhs_hosp/params.json.template b/hhs_hosp/params.json.template deleted file mode 100644 index c2004f935..000000000 --- a/hhs_hosp/params.json.template +++ /dev/null @@ -1,22 +0,0 @@ -{ - "common": { - "export_dir": "./receiving", - "log_filename": "./hhs_hosp.log" - }, - "validation": { - "common": { - "data_source": "hhs", - "span_length": 14, - "min_expected_lag": {"all": "8"}, - "max_expected_lag": {"all": "14"}, - "dry_run": true, - "suppressed_errors": [] - }, - "static": { - "minimum_sample_size": 0, - "missing_se_allowed": true, - "missing_sample_size_allowed": true - }, - "dynamic": {} - } -} diff --git a/hhs_hosp/receiving/.gitignore b/hhs_hosp/receiving/.gitignore deleted file mode 100644 index afed0735d..000000000 --- a/hhs_hosp/receiving/.gitignore +++ /dev/null @@ -1 +0,0 @@ -*.csv diff --git a/hhs_hosp/setup.py b/hhs_hosp/setup.py deleted file mode 100644 index b19bcbb42..000000000 --- a/hhs_hosp/setup.py +++ /dev/null @@ -1,31 +0,0 @@ -from setuptools import setup -from setuptools import find_packages - -required = [ - "freezegun", - "numpy", - "pandas", - "pydocstyle", - "pytest", - "pytest-cov", - "pylint==2.8.3", - "delphi-utils", - "covidcast", - "delphi-epidata" -] - -setup( - name="delphi_hhs", - version="0.1.0", - description="SHORT DESCRIPTION", - author="", - author_email="", - url="https://github.com/cmu-delphi/covidcast-indicators", - install_requires=required, - classifiers=[ - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Developers", - "Programming Language :: Python :: 3.8", - ], - packages=find_packages(), -) diff --git a/hhs_hosp/static/.gitignore b/hhs_hosp/static/.gitignore deleted file mode 100644 index e69de29bb..000000000 diff --git a/hhs_hosp/tests/test_response.json b/hhs_hosp/tests/test_response.json deleted file mode 100644 index cc13037ae..000000000 --- a/hhs_hosp/tests/test_response.json +++ /dev/null @@ -1,1086 +0,0 @@ -{ - "epidata": [ - { - "state": "PA", - "geocoded_state": null, - "issue": 20211025, - "date": 20210911, - "critical_staffing_shortage_today_yes": 27, - "critical_staffing_shortage_today_no": 195, - "critical_staffing_shortage_today_not_reported": 6, - "critical_staffing_shortage_anticipated_within_week_yes": 34, - "critical_staffing_shortage_anticipated_within_week_no": 188, - "critical_staffing_shortage_anticipated_within_week_not_reported": 6, - "hospital_onset_covid": 15, - "hospital_onset_covid_coverage": 222, - "inpatient_beds": 31406, - "inpatient_beds_coverage": 228, - "inpatient_beds_used": 25583, - "inpatient_beds_used_coverage": 228, - "inpatient_beds_used_covid": 2555, - "inpatient_beds_used_covid_coverage": 222, - "previous_day_admission_adult_covid_confirmed": 264, - "previous_day_admission_adult_covid_confirmed_coverage": 228, - "previous_day_admission_adult_covid_suspected": 379, - "previous_day_admission_adult_covid_suspected_coverage": 222, - "previous_day_admission_pediatric_covid_confirmed": 7, - "previous_day_admission_pediatric_covid_confirmed_coverage": 221, - "previous_day_admission_pediatric_covid_suspected": 25, - "previous_day_admission_pediatric_covid_suspected_coverage": 221, - "staffed_adult_icu_bed_occupancy": 2895, - "staffed_adult_icu_bed_occupancy_coverage": 228, - "staffed_icu_adult_patients_confirmed_suspected_covid": 546, - "staffed_icu_adult_patients_confirmed_suspected_covid_coverage": 222, - "staffed_icu_adult_patients_confirmed_covid": 538, - "staffed_icu_adult_patients_confirmed_covid_coverage": 228, - "total_adult_patients_hosp_confirmed_suspected_covid": 2470, - "total_adult_patients_hosp_confirmed_suspected_covid_coverage": 222, - "total_adult_patients_hosp_confirmed_covid": 2148, - "total_adult_patients_hosp_confirmed_covid_coverage": 228, - "total_pediatric_patients_hosp_confirmed_suspected_covid": 85, - "total_pediatric_patients_hosp_confirmed_suspected_covid_coverage": 222, - "total_pediatric_patients_hosp_confirmed_covid": 42, - "total_pediatric_patients_hosp_confirmed_covid_coverage": 222, - "total_staffed_adult_icu_beds": 3693, - "total_staffed_adult_icu_beds_coverage": 228, - "inpatient_beds_utilization_coverage": 228, - "inpatient_beds_utilization_numerator": 25583, - "inpatient_beds_utilization_denominator": 31406, - "percent_of_inpatients_with_covid_coverage": 222, - 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"previous_day_admission_adult_covid_confirmed_30_39": 31, - "previous_day_admission_adult_covid_confirmed_30_39_coverage": 222, - "previous_day_admission_adult_covid_confirmed_40_49": 37, - "previous_day_admission_adult_covid_confirmed_40_49_coverage": 222, - "previous_day_admission_adult_covid_confirmed_50_59": 41, - "previous_day_admission_adult_covid_confirmed_50_59_coverage": 222, - "previous_day_admission_adult_covid_confirmed_60_69": 62, - "previous_day_admission_adult_covid_confirmed_60_69_coverage": 222, - "previous_day_admission_adult_covid_confirmed_70_79": 52, - "previous_day_admission_adult_covid_confirmed_70_79_coverage": 221, - "previous_day_admission_adult_covid_confirmed_80plus": 38, - "previous_day_admission_adult_covid_confirmed_80plus_coverage": 222, - "previous_day_admission_adult_covid_confirmed_unknown": 12, - "previous_day_admission_adult_covid_confirmed_unknown_coverage": 221, - "previous_day_admission_adult_covid_suspected_18_19": 2, - "previous_day_admission_adult_covid_suspected_18_19_coverage": 218, - "previous_day_admission_adult_covid_suspected_20_29": 37, - "previous_day_admission_adult_covid_suspected_20_29_coverage": 217, - "previous_day_admission_adult_covid_suspected_30_39": 37, - "previous_day_admission_adult_covid_suspected_30_39_coverage": 216, - "previous_day_admission_adult_covid_suspected_40_49": 33, - "previous_day_admission_adult_covid_suspected_40_49_coverage": 217, - "previous_day_admission_adult_covid_suspected_50_59": 43, - "previous_day_admission_adult_covid_suspected_50_59_coverage": 217, - "previous_day_admission_adult_covid_suspected_60_69": 70, - "previous_day_admission_adult_covid_suspected_60_69_coverage": 215, - "previous_day_admission_adult_covid_suspected_70_79": 63, - "previous_day_admission_adult_covid_suspected_70_79_coverage": 217, - "previous_day_admission_adult_covid_suspected_80plus": 73, - "previous_day_admission_adult_covid_suspected_80plus_coverage": 217, - "previous_day_admission_adult_covid_suspected_unknown": 7, - "previous_day_admission_adult_covid_suspected_unknown_coverage": 215, - "previous_day_admission_influenza_confirmed": 2, - "previous_day_admission_influenza_confirmed_coverage": 214, - "previous_day_deaths_covid_and_influenza": 0, - "previous_day_deaths_covid_and_influenza_coverage": 214, - "previous_day_deaths_influenza": 0, - "previous_day_deaths_influenza_coverage": 214, - "previous_week_therapeutic_a_casirivimab_imdevimab_courses_used": 1160, - "previous_week_therapeutic_b_bamlanivimab_courses_used": 1, - "previous_week_therapeutic_c_bamlanivimab_etesevimab_courses_used": 99, - "total_patients_hospitalized_confirmed_influenza": 16, - "total_patients_hospitalized_confirmed_influenza_coverage": 214, - "total_patients_hospitalized_confirmed_influenza_covid": null, - "total_patients_hospitalized_confirmed_influenza_covid_coverage": null, - "inpatient_beds_utilization": 0.844695506630617, - "percent_of_inpatients_with_covid": 0.107118148973787, - "inpatient_bed_covid_utilization": 0.090805421608237, - "adult_icu_bed_covid_utilization": 0.17480577136515, - "adult_icu_bed_utilization": 0.802209646995419 - }, - { - "state": "PA", - "geocoded_state": null, - "issue": 20211025, - "date": 20210918, - "critical_staffing_shortage_today_yes": 28, - "critical_staffing_shortage_today_no": 194, - "critical_staffing_shortage_today_not_reported": 6, - "critical_staffing_shortage_anticipated_within_week_yes": 32, - "critical_staffing_shortage_anticipated_within_week_no": 190, - "critical_staffing_shortage_anticipated_within_week_not_reported": 6, - "hospital_onset_covid": 18, - "hospital_onset_covid_coverage": 222, - "inpatient_beds": 30806, - "inpatient_beds_coverage": 228, - "inpatient_beds_used": 25526, - "inpatient_beds_used_coverage": 228, - "inpatient_beds_used_covid": 2758, - "inpatient_beds_used_covid_coverage": 222, - "previous_day_admission_adult_covid_confirmed": 301, - "previous_day_admission_adult_covid_confirmed_coverage": 228, - "previous_day_admission_adult_covid_suspected": 349, - "previous_day_admission_adult_covid_suspected_coverage": 222, - "previous_day_admission_pediatric_covid_confirmed": 11, - "previous_day_admission_pediatric_covid_confirmed_coverage": 221, - "previous_day_admission_pediatric_covid_suspected": 19, - "previous_day_admission_pediatric_covid_suspected_coverage": 221, - "staffed_adult_icu_bed_occupancy": 2868, - "staffed_adult_icu_bed_occupancy_coverage": 228, - "staffed_icu_adult_patients_confirmed_suspected_covid": 624, - "staffed_icu_adult_patients_confirmed_suspected_covid_coverage": 222, - "staffed_icu_adult_patients_confirmed_covid": 603, - "staffed_icu_adult_patients_confirmed_covid_coverage": 228, - "total_adult_patients_hosp_confirmed_suspected_covid": 2667, - "total_adult_patients_hosp_confirmed_suspected_covid_coverage": 222, - "total_adult_patients_hosp_confirmed_covid": 2350, - "total_adult_patients_hosp_confirmed_covid_coverage": 228, - "total_pediatric_patients_hosp_confirmed_suspected_covid": 91, - "total_pediatric_patients_hosp_confirmed_suspected_covid_coverage": 222, - "total_pediatric_patients_hosp_confirmed_covid": 48, - "total_pediatric_patients_hosp_confirmed_covid_coverage": 222, - "total_staffed_adult_icu_beds": 3624, - "total_staffed_adult_icu_beds_coverage": 228, - "inpatient_beds_utilization_coverage": 228, - "inpatient_beds_utilization_numerator": 25526, - "inpatient_beds_utilization_denominator": 30806, - "percent_of_inpatients_with_covid_coverage": 222, - "percent_of_inpatients_with_covid_numerator": 2758, - "percent_of_inpatients_with_covid_denominator": 25312, - "inpatient_bed_covid_utilization_coverage": 222, - "inpatient_bed_covid_utilization_numerator": 2758, - "inpatient_bed_covid_utilization_denominator": 30432, - "adult_icu_bed_covid_utilization_coverage": 222, - "adult_icu_bed_covid_utilization_numerator": 624, - "adult_icu_bed_covid_utilization_denominator": 3521, - "adult_icu_bed_utilization_coverage": 228, - "adult_icu_bed_utilization_numerator": 2868, - "adult_icu_bed_utilization_denominator": 3624, - "deaths_covid": 28, - "deaths_covid_coverage": 222, - "icu_patients_confirmed_influenza": 2, - "icu_patients_confirmed_influenza_coverage": 214, - "on_hand_supply_therapeutic_a_casirivimab_imdevimab_courses": 4135, - "on_hand_supply_therapeutic_b_bamlanivimab_courses": 4745, - "on_hand_supply_therapeutic_c_bamlanivimab_etesevimab_courses": 3767, - "previous_day_admission_adult_covid_confirmed_18_19": 0, - "previous_day_admission_adult_covid_confirmed_18_19_coverage": 225, - "previous_day_admission_adult_covid_confirmed_20_29": 14, - "previous_day_admission_adult_covid_confirmed_20_29_coverage": 221, - "previous_day_admission_adult_covid_confirmed_30_39": 32, - "previous_day_admission_adult_covid_confirmed_30_39_coverage": 220, - "previous_day_admission_adult_covid_confirmed_40_49": 35, - "previous_day_admission_adult_covid_confirmed_40_49_coverage": 221, - "previous_day_admission_adult_covid_confirmed_50_59": 50, - "previous_day_admission_adult_covid_confirmed_50_59_coverage": 221, - "previous_day_admission_adult_covid_confirmed_60_69": 47, - "previous_day_admission_adult_covid_confirmed_60_69_coverage": 223, - "previous_day_admission_adult_covid_confirmed_70_79": 59, - "previous_day_admission_adult_covid_confirmed_70_79_coverage": 222, - "previous_day_admission_adult_covid_confirmed_80plus": 51, - "previous_day_admission_adult_covid_confirmed_80plus_coverage": 221, - "previous_day_admission_adult_covid_confirmed_unknown": 13, - "previous_day_admission_adult_covid_confirmed_unknown_coverage": 221, - "previous_day_admission_adult_covid_suspected_18_19": 2, - "previous_day_admission_adult_covid_suspected_18_19_coverage": 219, - "previous_day_admission_adult_covid_suspected_20_29": 32, - "previous_day_admission_adult_covid_suspected_20_29_coverage": 216, - "previous_day_admission_adult_covid_suspected_30_39": 35, - "previous_day_admission_adult_covid_suspected_30_39_coverage": 216, - "previous_day_admission_adult_covid_suspected_40_49": 32, - "previous_day_admission_adult_covid_suspected_40_49_coverage": 215, - "previous_day_admission_adult_covid_suspected_50_59": 42, - "previous_day_admission_adult_covid_suspected_50_59_coverage": 215, - "previous_day_admission_adult_covid_suspected_60_69": 58, - "previous_day_admission_adult_covid_suspected_60_69_coverage": 215, - "previous_day_admission_adult_covid_suspected_70_79": 70, - "previous_day_admission_adult_covid_suspected_70_79_coverage": 215, - "previous_day_admission_adult_covid_suspected_80plus": 72, - "previous_day_admission_adult_covid_suspected_80plus_coverage": 215, - "previous_day_admission_adult_covid_suspected_unknown": 7, - "previous_day_admission_adult_covid_suspected_unknown_coverage": 215, - "previous_day_admission_influenza_confirmed": 4, - "previous_day_admission_influenza_confirmed_coverage": 214, - "previous_day_deaths_covid_and_influenza": 0, - "previous_day_deaths_covid_and_influenza_coverage": 214, - "previous_day_deaths_influenza": 0, - "previous_day_deaths_influenza_coverage": 214, - "previous_week_therapeutic_a_casirivimab_imdevimab_courses_used": 1158, - "previous_week_therapeutic_b_bamlanivimab_courses_used": 1281, - "previous_week_therapeutic_c_bamlanivimab_etesevimab_courses_used": 102, - "total_patients_hospitalized_confirmed_influenza": 19, - "total_patients_hospitalized_confirmed_influenza_coverage": 214, - "total_patients_hospitalized_confirmed_influenza_covid": null, - "total_patients_hospitalized_confirmed_influenza_covid_coverage": null, - "inpatient_beds_utilization": 0.828604817243394, - "percent_of_inpatients_with_covid": 0.10896017699115, - "inpatient_bed_covid_utilization": 0.090628286014721, - "adult_icu_bed_covid_utilization": 0.17722238000568, - "adult_icu_bed_utilization": 0.791390728476821 - }, - { - "state": "PA", - "geocoded_state": null, - "issue": 20211025, - "date": 20210919, - "critical_staffing_shortage_today_yes": 28, - "critical_staffing_shortage_today_no": 194, - "critical_staffing_shortage_today_not_reported": 6, - "critical_staffing_shortage_anticipated_within_week_yes": 35, - "critical_staffing_shortage_anticipated_within_week_no": 187, - "critical_staffing_shortage_anticipated_within_week_not_reported": 6, - "hospital_onset_covid": 19, - "hospital_onset_covid_coverage": 222, - "inpatient_beds": 30820, - "inpatient_beds_coverage": 228, - "inpatient_beds_used": 24956, - "inpatient_beds_used_coverage": 228, - "inpatient_beds_used_covid": 2775, - "inpatient_beds_used_covid_coverage": 222, - "previous_day_admission_adult_covid_confirmed": 252, - "previous_day_admission_adult_covid_confirmed_coverage": 228, - "previous_day_admission_adult_covid_suspected": 380, - "previous_day_admission_adult_covid_suspected_coverage": 222, - "previous_day_admission_pediatric_covid_confirmed": 7, - "previous_day_admission_pediatric_covid_confirmed_coverage": 221, - "previous_day_admission_pediatric_covid_suspected": 17, - "previous_day_admission_pediatric_covid_suspected_coverage": 221, - "staffed_adult_icu_bed_occupancy": 2760, - "staffed_adult_icu_bed_occupancy_coverage": 228, - "staffed_icu_adult_patients_confirmed_suspected_covid": 637, - "staffed_icu_adult_patients_confirmed_suspected_covid_coverage": 222, - "staffed_icu_adult_patients_confirmed_covid": 611, - "staffed_icu_adult_patients_confirmed_covid_coverage": 228, - "total_adult_patients_hosp_confirmed_suspected_covid": 2693, - "total_adult_patients_hosp_confirmed_suspected_covid_coverage": 222, - "total_adult_patients_hosp_confirmed_covid": 2351, - "total_adult_patients_hosp_confirmed_covid_coverage": 228, - "total_pediatric_patients_hosp_confirmed_suspected_covid": 82, - "total_pediatric_patients_hosp_confirmed_suspected_covid_coverage": 222, - "total_pediatric_patients_hosp_confirmed_covid": 47, - "total_pediatric_patients_hosp_confirmed_covid_coverage": 222, - "total_staffed_adult_icu_beds": 3504, - "total_staffed_adult_icu_beds_coverage": 228, - "inpatient_beds_utilization_coverage": 228, - "inpatient_beds_utilization_numerator": 24956, - "inpatient_beds_utilization_denominator": 30820, - "percent_of_inpatients_with_covid_coverage": 222, - "percent_of_inpatients_with_covid_numerator": 2775, - "percent_of_inpatients_with_covid_denominator": 24757, - "inpatient_bed_covid_utilization_coverage": 222, - "inpatient_bed_covid_utilization_numerator": 2775, - "inpatient_bed_covid_utilization_denominator": 30450, - "adult_icu_bed_covid_utilization_coverage": 222, - "adult_icu_bed_covid_utilization_numerator": 637, - "adult_icu_bed_covid_utilization_denominator": 3400, - "adult_icu_bed_utilization_coverage": 228, - "adult_icu_bed_utilization_numerator": 2760, - "adult_icu_bed_utilization_denominator": 3504, - "deaths_covid": 32, - "deaths_covid_coverage": 222, - "icu_patients_confirmed_influenza": 2, - "icu_patients_confirmed_influenza_coverage": 216, - "on_hand_supply_therapeutic_a_casirivimab_imdevimab_courses": 4108, - "on_hand_supply_therapeutic_b_bamlanivimab_courses": 4734, - "on_hand_supply_therapeutic_c_bamlanivimab_etesevimab_courses": 3770, - "previous_day_admission_adult_covid_confirmed_18_19": 1, - "previous_day_admission_adult_covid_confirmed_18_19_coverage": 225, - "previous_day_admission_adult_covid_confirmed_20_29": 11, - "previous_day_admission_adult_covid_confirmed_20_29_coverage": 223, - "previous_day_admission_adult_covid_confirmed_30_39": 23, - "previous_day_admission_adult_covid_confirmed_30_39_coverage": 222, - "previous_day_admission_adult_covid_confirmed_40_49": 28, - "previous_day_admission_adult_covid_confirmed_40_49_coverage": 223, - "previous_day_admission_adult_covid_confirmed_50_59": 48, - "previous_day_admission_adult_covid_confirmed_50_59_coverage": 224, - "previous_day_admission_adult_covid_confirmed_60_69": 43, - "previous_day_admission_adult_covid_confirmed_60_69_coverage": 223, - "previous_day_admission_adult_covid_confirmed_70_79": 41, - "previous_day_admission_adult_covid_confirmed_70_79_coverage": 223, - "previous_day_admission_adult_covid_confirmed_80plus": 42, - "previous_day_admission_adult_covid_confirmed_80plus_coverage": 224, - "previous_day_admission_adult_covid_confirmed_unknown": 15, - "previous_day_admission_adult_covid_confirmed_unknown_coverage": 221, - "previous_day_admission_adult_covid_suspected_18_19": 3, - "previous_day_admission_adult_covid_suspected_18_19_coverage": 218, - "previous_day_admission_adult_covid_suspected_20_29": 28, - "previous_day_admission_adult_covid_suspected_20_29_coverage": 217, - "previous_day_admission_adult_covid_suspected_30_39": 36, - "previous_day_admission_adult_covid_suspected_30_39_coverage": 217, - "previous_day_admission_adult_covid_suspected_40_49": 38, - "previous_day_admission_adult_covid_suspected_40_49_coverage": 217, - "previous_day_admission_adult_covid_suspected_50_59": 57, - "previous_day_admission_adult_covid_suspected_50_59_coverage": 218, - "previous_day_admission_adult_covid_suspected_60_69": 75, - "previous_day_admission_adult_covid_suspected_60_69_coverage": 217, - "previous_day_admission_adult_covid_suspected_70_79": 73, - "previous_day_admission_adult_covid_suspected_70_79_coverage": 218, - "previous_day_admission_adult_covid_suspected_80plus": 62, - "previous_day_admission_adult_covid_suspected_80plus_coverage": 217, - "previous_day_admission_adult_covid_suspected_unknown": 10, - "previous_day_admission_adult_covid_suspected_unknown_coverage": 214, - "previous_day_admission_influenza_confirmed": 3, - "previous_day_admission_influenza_confirmed_coverage": 216, - "previous_day_deaths_covid_and_influenza": 0, - "previous_day_deaths_covid_and_influenza_coverage": 216, - "previous_day_deaths_influenza": 0, - "previous_day_deaths_influenza_coverage": 216, - "previous_week_therapeutic_a_casirivimab_imdevimab_courses_used": 1168, - "previous_week_therapeutic_b_bamlanivimab_courses_used": 1, - "previous_week_therapeutic_c_bamlanivimab_etesevimab_courses_used": 104, - "total_patients_hospitalized_confirmed_influenza": 17, - "total_patients_hospitalized_confirmed_influenza_coverage": 216, - "total_patients_hospitalized_confirmed_influenza_covid": null, - "total_patients_hospitalized_confirmed_influenza_covid_coverage": null, - "inpatient_beds_utilization": 0.809733939000649, - "percent_of_inpatients_with_covid": 0.112089510037565, - "inpatient_bed_covid_utilization": 0.091133004926108, - "adult_icu_bed_covid_utilization": 0.187352941176471, - "adult_icu_bed_utilization": 0.787671232876712 - } - ], - "result": 1, - "message": "success" -} diff --git a/hhs_hosp/tests/test_run.py b/hhs_hosp/tests/test_run.py deleted file mode 100644 index 75ded437d..000000000 --- a/hhs_hosp/tests/test_run.py +++ /dev/null @@ -1,232 +0,0 @@ -from datetime import datetime, date -import json -from unittest.mock import patch -import tempfile -import os - -from delphi_hhs.run import _date_to_int, int_date_to_previous_day_datetime, generate_date_ranges, \ - make_signal, make_geo, run_module, transform_signal -from delphi_hhs.constants import SMOOTHERS, GEOS, SIGNALS, \ - CONFIRMED, SUM_CONF_SUSP, CONFIRMED_FLU, CONFIRMED_PROP, SUM_CONF_SUSP_PROP, CONFIRMED_FLU_PROP -from delphi_utils.geomap import GeoMapper -from freezegun import freeze_time -import numpy as np -import pandas as pd -import pytest - - -def test__date_to_int(): - """Check that dates are converted to the right int.""" - assert _date_to_int(date(2020, 5, 1)) == 20200501 - - -def test_date_conversion(): - """Check that we convert dates properly between Epidata and datetime format.""" - data = pd.DataFrame({"date": [20200101, 20201231]}) - result = int_date_to_previous_day_datetime(data.date) - expected_result = [ - datetime(year=2019, month=12, day=31), - datetime(year=2020, month=12, day=30) - ] - for got, expected in zip(result, expected_result): - assert isinstance(got, datetime), f"Bad type: {type(got)}\n{result}" - assert got == expected - - -def test_generate_date_ranges(): - """Check ranges generated partition the specified inputs.""" - assert generate_date_ranges(date(2020, 1, 1), date(2020, 1, 1)) == \ - [{'from': 20200101, 'to': 20200101}] - assert generate_date_ranges(date(2020, 1, 1), date(2020, 1, 31)) == \ - [{'from': 20200101, 'to': 20200131}] - assert generate_date_ranges(date(2020, 1, 1), date(2020, 2, 1)) == \ - [{'from': 20200101, 'to': 20200131}, - {'from': 20200201, 'to': 20200201}] - assert generate_date_ranges(date(2020, 1, 1), date(2020, 5, 12)) == \ - [{'from': 20200101, 'to': 20200131}, - {'from': 20200201, 'to': 20200302}, - {'from': 20200303, 'to': 20200402}, - {'from': 20200403, 'to': 20200503}, - {'from': 20200504, 'to': 20200512}] - - -def test_make_signal(): - """Check that constructed signals sum the correct columns.""" - data = pd.DataFrame({ - 'state': ['NA'], - 'date': [20200102], - 'previous_day_admission_adult_covid_confirmed': [1], - 'previous_day_admission_adult_covid_suspected': [2], - 'previous_day_admission_pediatric_covid_confirmed': [4], - 'previous_day_admission_pediatric_covid_suspected': [8], - 'previous_day_admission_influenza_confirmed': [16] - }) - - expected_confirmed = pd.DataFrame({ - 'state': ['na'], - 'timestamp': [datetime(year=2020, month=1, day=1)], - 'val': [5.], - }) - pd.testing.assert_frame_equal(expected_confirmed, make_signal(data, CONFIRMED)) - pd.testing.assert_frame_equal(expected_confirmed, make_signal(data, CONFIRMED_PROP)) - - expected_sum = pd.DataFrame({ - 'state': ['na'], - 'timestamp': [datetime(year=2020, month=1, day=1)], - 'val': [15.], - }) - pd.testing.assert_frame_equal(expected_sum, make_signal(data, SUM_CONF_SUSP)) - pd.testing.assert_frame_equal(expected_sum, make_signal(data, SUM_CONF_SUSP_PROP)) - - expected_flu = pd.DataFrame({ - 'state': ['na'], - 'timestamp': [datetime(year=2020, month=1, day=1)], - 'val': [16.], - }) - pd.testing.assert_frame_equal(expected_flu, make_signal(data, CONFIRMED_FLU)) - pd.testing.assert_frame_equal(expected_flu, make_signal(data, CONFIRMED_FLU_PROP)) - - with pytest.raises(Exception): - make_signal(data, "zig") - -def test_transform_signal_pop(): - geo_mapper = GeoMapper() - state_pop = geo_mapper.get_crosswalk("state_id", "pop") - identity_smoother = SMOOTHERS[0] - hundo_k = 100000 - - test_df = pd.DataFrame({ - 'state': ['pa', 'wv'], - 'timestamp': [datetime(year=2020, month=1, day=1)]*2, - 'val': [15., 150.],}) - - pa_pop = int(state_pop[state_pop.state_id == "pa"]["pop"].iloc[0]) - wv_pop = int(state_pop[state_pop.state_id == "wv"]["pop"].iloc[0]) - pd.testing.assert_frame_equal( - transform_signal( - CONFIRMED_PROP, - identity_smoother, - 'state', - test_df.copy(), - geo_mapper), - pd.DataFrame({ - 'geo_id': ['pa', 'wv'], - 'timestamp': [datetime(year=2020, month=1, day=1)]*2, - 'val': [15/pa_pop*hundo_k, 150/wv_pop*hundo_k], - 'se': [None]*2, - 'sample_size': [None]*2,}), - check_dtype=False, - check_like=True - ) - - pd.testing.assert_frame_equal( - transform_signal( - CONFIRMED_PROP, - identity_smoother, - 'nation', - test_df.copy(), - geo_mapper), - pd.DataFrame({ - 'geo_id': ['us'], - 'timestamp': [datetime(year=2020, month=1, day=1)], - 'val': [165/(pa_pop+wv_pop)*hundo_k], - 'se': [None], - 'sample_size': [None],}), - check_dtype=False, - check_like=True - ) - -def test_make_geo(): - """Check that geographies transform correctly.""" - test_timestamp = datetime(year=2020, month=1, day=1) - geo_mapper = GeoMapper() - - data = pd.DataFrame({ - 'state': ['PA', 'WV', 'OH'], - 'state_code': [42, 54, 39], - 'timestamp': [test_timestamp] * 3, - 'val': [1., 2., 4.], - }) - - template = { - 'se': np.nan, - 'sample_size': np.nan, - } - expecteds = { - "state": pd.DataFrame( - dict(template, - geo_id=data.state, - timestamp=data.timestamp, - val=data.val)), - "hhs": pd.DataFrame( - dict(template, - geo_id=['3', '5'], - timestamp=[test_timestamp] * 2, - val=[3., 4.])), - "nation": pd.DataFrame( - dict(template, - geo_id=['us'], - timestamp=[test_timestamp], - val=[7.])) - } - for geo, expected in expecteds.items(): - result = make_geo(data, geo, geo_mapper) - for series in ["geo_id", "timestamp", "val", "se", "sample_size"]: - pd.testing.assert_series_equal(expected[series], result[series], obj=f"{geo}:{series}") - - -@freeze_time("2020-01-01") -@patch("delphi_epidata.Epidata.covid_hosp") -def test_output_files(mock_covid_hosp): - with open("test_response.json", "r") as f: - test_response = json.load(f) - mock_covid_hosp.return_value = test_response - with tempfile.TemporaryDirectory() as tmpdir: - params = { - "common": { - "export_dir": tmpdir - }, - "validation": { - "common": { - "data_source": "hhs", - "api_credentials": "fakecred" - } - } - } - run_module(params) - # 9 days in test data, so should be 9 days of unsmoothed and 3 days for smoothed - expected_num_files = len(GEOS) * len(SIGNALS) * 9 + len(GEOS) * len(SIGNALS) * 3 - assert len(os.listdir(tmpdir)) == expected_num_files - - -@freeze_time("2020-02-03") -@patch("delphi_hhs.run.create_export_csv") -@patch("delphi_epidata.Epidata.covid_hosp") -def test_ignore_last_range_no_results(mock_covid_hosp, mock_export): - mock_covid_hosp.side_effect = [ - {"result": 1, - "epidata": - {"state": ["placeholder"], - "date": ["20200101"], - "previous_day_admission_adult_covid_confirmed": [0], - "previous_day_admission_adult_covid_suspected": [0], - "previous_day_admission_pediatric_covid_confirmed": [0], - "previous_day_admission_pediatric_covid_suspected": [0], - "previous_day_admission_influenza_confirmed": [0] - } - }, - {"result": -2, "message": "no results"} - ] - mock_export.return_value = None - params = { - "common": { - "export_dir": "./receiving" - }, - "validation": { - "common": { - "data_source": "hhs", - "api_credentials": "fakecred" - } - } - } - assert not run_module(params) # function should not raise value error and has no return value diff --git a/hhs_hosp/version.cfg b/hhs_hosp/version.cfg deleted file mode 100644 index d3d61ed12..000000000 --- a/hhs_hosp/version.cfg +++ /dev/null @@ -1 +0,0 @@ -current_version = 0.3.54 From d404dc4be241a7a5fa18fd8e3ce015cfa3b34f35 Mon Sep 17 00:00:00 2001 From: minhkhul Date: Tue, 28 May 2024 23:16:18 -0400 Subject: [PATCH 2/2] remove ci --- .github/workflows/create-release.yml | 2 +- .github/workflows/python-ci.yml | 1 - Jenkinsfile | 2 +- .../templates/hhs_hosp-params-prod.json.j2 | 32 ------------------- ansible/templates/staging-api-match-list.j2 | 3 +- sir_complainsalot/params.json.template | 4 --- 6 files changed, 3 insertions(+), 41 deletions(-) delete mode 100644 ansible/templates/hhs_hosp-params-prod.json.j2 diff --git a/.github/workflows/create-release.yml b/.github/workflows/create-release.yml index a8cb6c3bb..c1fd326be 100644 --- a/.github/workflows/create-release.yml +++ b/.github/workflows/create-release.yml @@ -61,7 +61,7 @@ jobs: bump2version --list ${{ github.event.inputs.versionName }} | grep ^new_version | sed -r s,"^.*=",, - name: Copy version to indicator directory run: | - indicator_list=("changehc" "claims_hosp" "doctor_visits" "google_symptoms" "hhs_hosp" "nchs_mortality" "quidel_covidtest" "sir_complainsalot") + indicator_list=("changehc" "claims_hosp" "doctor_visits" "google_symptoms" "nchs_mortality" "quidel_covidtest" "sir_complainsalot") for path in ${indicator_list[@]}; do echo "current_version = ${{ steps.indicators.outputs.version }}" > $path/version.cfg done diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 0534cbce2..2dd88fce4 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -23,7 +23,6 @@ jobs: claims_hosp, doctor_visits, google_symptoms, - hhs_hosp, nchs_mortality, nwss_wastewater, quidel_covidtest, diff --git a/Jenkinsfile b/Jenkinsfile index 0052fd215..0c2801b28 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -10,7 +10,7 @@ - TODO: #527 Get this list automatically from python-ci.yml at runtime. */ -def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "nchs_mortality", "quidel_covidtest", "sir_complainsalot", "doctor_visits", "nwss_wastewater"] +def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "nchs_mortality", "quidel_covidtest", "sir_complainsalot", "doctor_visits", "nwss_wastewater"] def build_package_main = [:] def build_package_prod = [:] def deploy_staging = [:] diff --git a/ansible/templates/hhs_hosp-params-prod.json.j2 b/ansible/templates/hhs_hosp-params-prod.json.j2 deleted file mode 100644 index a4dfdf265..000000000 --- a/ansible/templates/hhs_hosp-params-prod.json.j2 +++ /dev/null @@ -1,32 +0,0 @@ -{ - "common": { - "export_dir": "/common/covidcast/receiving/hhs", - "log_filename": "/var/log/indicators/hhs_hosp.log" - }, - "validation": { - "common": { - "data_source": "hhs", - "api_credentials": "{{ validation_api_key }}", - "span_length": 14, - "min_expected_lag": {"all": "8"}, - "max_expected_lag": {"all": "14"}, - "dry_run": true, - "suppressed_errors": [] - }, - "static": { - "minimum_sample_size": 0, - "missing_se_allowed": true, - "missing_sample_size_allowed": true - }, - "dynamic": {} - }, - "archive": { - "aws_credentials": { - "aws_access_key_id": "{{ archive_differ_bucket_user_access_key_id }}", - "aws_secret_access_key": "{{ archive_differ_bucket_user_secret_access_key }}" - }, - "bucket_name": "{{ archive_differ_bucket_name }}", - "cache_dir": "./cache", - "indicator_prefix": "delphi_hhs_hosp" - } -} diff --git a/ansible/templates/staging-api-match-list.j2 b/ansible/templates/staging-api-match-list.j2 index 4a4609d2f..5938e59f9 100644 --- a/ansible/templates/staging-api-match-list.j2 +++ b/ansible/templates/staging-api-match-list.j2 @@ -1,5 +1,4 @@ data_source=quidel-staging&signal=covid_ag_ data_source=chng data_source=safegraph -data_source=google-symptoms -data_source=hhs \ No newline at end of file +data_source=google-symptoms \ No newline at end of file diff --git a/sir_complainsalot/params.json.template b/sir_complainsalot/params.json.template index b07b197a4..df0cddc4c 100644 --- a/sir_complainsalot/params.json.template +++ b/sir_complainsalot/params.json.template @@ -46,10 +46,6 @@ "nchs-mortality": { "max_age":19, "maintainers": [] - }, - "hhs": { - "max_age":15, - "maintainers": [] } } }