delphi_epidata.py

"""
A module for DELPHI's Epidata API.

https://github.com/cmu-delphi/delphi-epidata

Notes:
 - Requires the `requests` module.
 - Compatible with Python 2 and 3.
"""

# External modules
import requests
import asyncio
from tenacity import retry, stop_after_attempt

from aiohttp import ClientSession, TCPConnector, BasicAuth
from pkg_resources import get_distribution, DistributionNotFound

# Obtain package version for the user-agent. Uses the installed version by
# preference, even if you've installed it and then use this script independently
# by accident.
try:
    _version = get_distribution("delphi-epidata").version
except DistributionNotFound:
    _version = "0.script"

_HEADERS = {"user-agent": "delphi_epidata/" + _version + " (Python)"}


class EpidataException(Exception):
    pass


class EpidataBadRequestException(EpidataException):
    pass


REGIONS_EPIWEEKS_REQUIRED = "`regions` and `epiweeks` are both required"
ISSUES_LAG_EXCLUSIVE = "`issues` and `lag` are mutually exclusive"
LOCATIONS_EPIWEEKS_REQUIRED = "`locations` and `epiweeks` are both required"

# Because the API is stateless, the Epidata class only contains static methods
class Epidata:
    """An interface to DELPHI's Epidata API."""

    # API base url
    BASE_URL = "https://api.delphi.cmu.edu/epidata"
    auth = None

    client_version = _version

    # Helper function to cast values and/or ranges to strings
    @staticmethod
    def _listitem(value):
        """Cast values and/or range to a string."""
        if isinstance(value, dict) and "from" in value and "to" in value:
            return str(value["from"]) + "-" + str(value["to"])
        else:
            return str(value)

    # Helper function to build a list of values and/or ranges
    @staticmethod
    def _list(values):
        """Turn a list/tuple of values/ranges into a comma-separated string."""
        if not isinstance(values, (list, tuple)):
            values = [values]
        return ",".join([Epidata._listitem(value) for value in values])

    @staticmethod
    @retry(reraise=True, stop=stop_after_attempt(2))
    def _request_with_retry(endpoint, params={}):
        """Make request with a retry if an exception is thrown."""
        request_url = f"{Epidata.BASE_URL}/{endpoint}"
        req = requests.get(request_url, params, auth=Epidata.auth, headers=_HEADERS)
        if req.status_code == 414:
            req = requests.post(request_url, params, auth=Epidata.auth, headers=_HEADERS)
        # handle 401 and 429
        req.raise_for_status()
        return req

    @staticmethod
    def _request(endpoint, params={}):
        """Request and parse epidata.

        We default to GET since it has better caching and logging
        capabilities, but fall back to POST if the request is too
        long and returns a 414.
        """
        try:
            result = Epidata._request_with_retry(endpoint, params)
        except Exception as e:
            return {"result": 0, "message": "error: " + str(e)}
        if params is not None and "format" in params and params["format"] == "csv":
            return result.text
        else:
            try:
                return result.json()
            except requests.exceptions.JSONDecodeError:
                return {"result": 0, "message": "error decoding json: " + result.text}

    # Raise an Exception on error, otherwise return epidata
    @staticmethod
    def check(resp):
        """Raise an Exception on error, otherwise return epidata."""
        if resp["result"] != 1:
            msg, code = resp["message"], resp["result"]
            raise EpidataException(f"Error fetching epidata: {msg}. (result={int(code)})")
        return resp["epidata"]

    # Build a `range` object (ex: dates/epiweeks)
    @staticmethod
    def range(from_, to_):
        """Build a `range` object (ex: dates/epiweeks)."""
        if to_ <= from_:
            from_, to_ = to_, from_
        return {"from": from_, "to": to_}

    # Fetch FluView data
    @staticmethod
    def fluview(regions, epiweeks, issues=None, lag=None, auth=None):
        """Fetch FluView data."""
        # Check parameters
        if regions is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(ISSUES_LAG_EXCLUSIVE)
        # Set up request
        params = {
            "regions": Epidata._list(regions),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        if auth is not None:
            params["auth"] = auth
        # Make the API call
        return Epidata._request("fluview", params)

    # Fetch FluView metadata
    @staticmethod
    def fluview_meta():
        """Fetch FluView metadata."""
        return Epidata._request("fluview_meta")

    # Fetch FluView clinical data
    @staticmethod
    def fluview_clinical(regions, epiweeks, issues=None, lag=None):
        """Fetch FluView clinical data."""
        # Check parameters
        if regions is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "regions": Epidata._list(regions),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        # Make the API call
        return Epidata._request("fluview_clinical", params)

    # Fetch FluSurv data
    @staticmethod
    def flusurv(locations, epiweeks, issues=None, lag=None):
        """Fetch FluSurv data."""
        # Check parameters
        if locations is None or epiweeks is None:
            raise EpidataBadRequestException(LOCATIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        # Make the API call
        return Epidata._request("flusurv", params)

    # Fetch PAHO Dengue data
    @staticmethod
    def paho_dengue(regions, epiweeks, issues=None, lag=None):
        """Fetch PAHO Dengue data."""
        # Check parameters
        if regions is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "regions": Epidata._list(regions),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        # Make the API call
        return Epidata._request("paho_dengue", params)

    # Fetch ECDC ILI data
    @staticmethod
    def ecdc_ili(regions, epiweeks, issues=None, lag=None):
        """Fetch ECDC ILI data."""
        # Check parameters
        if regions is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "regions": Epidata._list(regions),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        # Make the API call
        return Epidata._request("ecdc_ili", params)

    # Fetch KCDC ILI data
    @staticmethod
    def kcdc_ili(regions, epiweeks, issues=None, lag=None):
        """Fetch KCDC ILI data."""
        # Check parameters
        if regions is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "regions": Epidata._list(regions),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        # Make the API call
        return Epidata._request("kcdc_ili", params)

    # Fetch Google Flu Trends data
    @staticmethod
    def gft(locations, epiweeks):
        """Fetch Google Flu Trends data."""
        # Check parameters
        if locations is None or epiweeks is None:
            raise EpidataBadRequestException(LOCATIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        # Make the API call
        return Epidata._request("gft", params)

    # Fetch Google Health Trends data
    @staticmethod
    def ght(auth, locations, epiweeks, query):
        """Fetch Google Health Trends data."""
        # Check parameters
        if auth is None or locations is None or epiweeks is None or query is None:
            raise EpidataBadRequestException(
                "`auth`, `locations`, `epiweeks`, and `query` are all required"
            )
        # Set up request
        params = {
            "auth": auth,
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
            "query": query,
        }
        # Make the API call
        return Epidata._request("ght", params)

    # Fetch HealthTweets data
    @staticmethod
    def twitter(auth, locations, dates=None, epiweeks=None):
        """Fetch HealthTweets data."""
        # Check parameters
        if auth is None or locations is None:
            raise EpidataBadRequestException("`auth` and `locations` are both required")
        if not ((dates is None) ^ (epiweeks is None)):
            raise EpidataBadRequestException("exactly one of `dates` and `epiweeks` is required")
        # Set up request
        params = {
            "auth": auth,
            "locations": Epidata._list(locations),
        }
        if dates is not None:
            params["dates"] = Epidata._list(dates)
        if epiweeks is not None:
            params["epiweeks"] = Epidata._list(epiweeks)
        # Make the API call
        return Epidata._request("twitter", params)

    # Fetch Wikipedia access data
    @staticmethod
    def wiki(articles, dates=None, epiweeks=None, hours=None, language="en"):
        """Fetch Wikipedia access data."""
        # Check parameters
        if articles is None:
            raise EpidataBadRequestException("`articles` is required")
        if not ((dates is None) ^ (epiweeks is None)):
            raise EpidataBadRequestException("exactly one of `dates` and `epiweeks` is required")
        # Set up request
        params = {
            "articles": Epidata._list(articles),
            "language": language,
        }
        if dates is not None:
            params["dates"] = Epidata._list(dates)
        if epiweeks is not None:
            params["epiweeks"] = Epidata._list(epiweeks)
        if hours is not None:
            params["hours"] = Epidata._list(hours)
        # Make the API call
        return Epidata._request("wiki", params)

    # Fetch CDC page hits
    @staticmethod
    def cdc(auth, epiweeks, locations):
        """Fetch CDC page hits."""
        # Check parameters
        if auth is None or epiweeks is None or locations is None:
            raise EpidataBadRequestException("`auth`, `epiweeks`, and `locations` are all required")
        # Set up request
        params = {
            "auth": auth,
            "epiweeks": Epidata._list(epiweeks),
            "locations": Epidata._list(locations),
        }
        # Make the API call
        return Epidata._request("cdc", params)

    # Fetch Quidel data
    @staticmethod
    def quidel(auth, epiweeks, locations):
        """Fetch Quidel data."""
        # Check parameters
        if auth is None or epiweeks is None or locations is None:
            raise EpidataBadRequestException("`auth`, `epiweeks`, and `locations` are all required")
        # Set up request
        params = {
            "auth": auth,
            "epiweeks": Epidata._list(epiweeks),
            "locations": Epidata._list(locations),
        }
        # Make the API call
        return Epidata._request("quidel", params)

    # Fetch NoroSTAT data (point data, no min/max)
    @staticmethod
    def norostat(auth, location, epiweeks):
        """Fetch NoroSTAT data (point data, no min/max)."""
        # Check parameters
        if auth is None or location is None or epiweeks is None:
            raise EpidataBadRequestException("`auth`, `location`, and `epiweeks` are all required")
        # Set up request
        params = {
            "auth": auth,
            "location": location,
            "epiweeks": Epidata._list(epiweeks),
        }
        # Make the API call
        return Epidata._request("norostat", params)

    # Fetch NoroSTAT metadata
    @staticmethod
    def meta_norostat(auth):
        """Fetch NoroSTAT metadata."""
        # Check parameters
        if auth is None:
            raise EpidataBadRequestException("`auth` is required")
        # Set up request
        params = {
            "auth": auth,
        }
        # Make the API call
        return Epidata._request("meta_norostat", params)

    # Fetch NIDSS flu data
    @staticmethod
    def nidss_flu(regions, epiweeks, issues=None, lag=None):
        """Fetch NIDSS flu data."""
        # Check parameters
        if regions is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "regions": Epidata._list(regions),
            "epiweeks": Epidata._list(epiweeks),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag
        # Make the API call
        return Epidata._request("nidss_flu", params)

    # Fetch NIDSS dengue data
    @staticmethod
    def nidss_dengue(locations, epiweeks):
        """Fetch NIDSS dengue data."""
        # Check parameters
        if locations is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        # Make the API call
        return Epidata._request("nidss_dengue", params)

    # Fetch Delphi's forecast
    @staticmethod
    def delphi(system, epiweek):
        """Fetch Delphi's forecast."""
        # Check parameters
        if system is None or epiweek is None:
            raise EpidataBadRequestException("`system` and `epiweek` are both required")
        # Set up request
        params = {
            "system": system,
            "epiweek": epiweek,
        }
        # Make the API call
        return Epidata._request("delphi", params)

    # Fetch Delphi's digital surveillance sensors
    @staticmethod
    def sensors(auth, names, locations, epiweeks):
        """Fetch Delphi's digital surveillance sensors."""
        # Check parameters
        if names is None or locations is None or epiweeks is None:
            raise EpidataBadRequestException(
                "`names`, `locations`, and `epiweeks` are all required"
            )
        # Set up request
        params = {
            "names": Epidata._list(names),
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        if auth is not None:
            params["auth"] = auth
        # Make the API call
        return Epidata._request("sensors", params)

    # Fetch Delphi's dengue digital surveillance sensors
    @staticmethod
    def dengue_sensors(auth, names, locations, epiweeks):
        """Fetch Delphi's digital surveillance sensors."""
        # Check parameters
        if auth is None or names is None or locations is None or epiweeks is None:
            raise EpidataBadRequestException(
                "`auth`, `names`, `locations`, and `epiweeks` are all required"
            )
        # Set up request
        params = {
            "auth": auth,
            "names": Epidata._list(names),
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        # Make the API call
        return Epidata._request("dengue_sensors", params)

    # Fetch Delphi's wILI nowcast
    @staticmethod
    def nowcast(locations, epiweeks):
        """Fetch Delphi's wILI nowcast."""
        # Check parameters
        if locations is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        # Make the API call
        return Epidata._request("nowcast", params)

    # Fetch Delphi's dengue nowcast
    @staticmethod
    def dengue_nowcast(locations, epiweeks):
        """Fetch Delphi's dengue nowcast."""
        # Check parameters
        if locations is None or epiweeks is None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "locations": Epidata._list(locations),
            "epiweeks": Epidata._list(epiweeks),
        }
        # Make the API call
        return Epidata._request("dengue_nowcast", params)

    # Fetch API metadata
    @staticmethod
    def meta():
        """Fetch API metadata."""
        return Epidata._request("meta")

    # Fetch Delphi's COVID-19 Surveillance Streams
    @staticmethod
    def covidcast(
        data_source,
        signals,
        time_type,
        geo_type,
        time_values,
        geo_value,
        as_of=None,
        issues=None,
        lag=None,
        **kwargs,
    ):
        """Fetch Delphi's COVID-19 Surveillance Streams"""
        # also support old parameter name
        if signals is None and "signal" in kwargs:
            signals = kwargs["signal"]
        # Check parameters
        if None in (data_source, signals, time_type, geo_type, time_values, geo_value):
            raise EpidataBadRequestException(
                "`data_source`, `signals`, `time_type`, `geo_type`, "
                "`time_values`, and `geo_value` are all required"
            )
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "data_source": data_source,
            "signals": Epidata._list(signals),
            "time_type": time_type,
            "geo_type": geo_type,
            "time_values": Epidata._list(time_values),
        }

        if isinstance(geo_value, (list, tuple)):
            params["geo_values"] = ",".join(geo_value)
        else:
            params["geo_value"] = geo_value
        if as_of is not None:
            params["as_of"] = as_of
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag

        if "format" in kwargs:
            params["format"] = kwargs["format"]

        if "fields" in kwargs:
            params["fields"] = kwargs["fields"]

        # Make the API call
        return Epidata._request("covidcast", params)

    # Fetch Delphi's COVID-19 Surveillance Streams metadata
    @staticmethod
    def covidcast_meta():
        """Fetch Delphi's COVID-19 Surveillance Streams metadata"""
        return Epidata._request("covidcast_meta")

    # Fetch COVID hospitalization data
    @staticmethod
    def covid_hosp(states, dates, issues=None, as_of=None):
        """Fetch COVID hospitalization data."""
        # Check parameters
        if states is None or dates is None:
            raise EpidataBadRequestException("`states` and `dates` are both required")
        # Set up request
        params = {
            "states": Epidata._list(states),
            "dates": Epidata._list(dates),
        }
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if as_of is not None:
            params["as_of"] = as_of
        # Make the API call
        return Epidata._request("covid_hosp_state_timeseries", params)

    # Fetch COVID hospitalization data for specific facilities
    @staticmethod
    def covid_hosp_facility(hospital_pks, collection_weeks, publication_dates=None):
        """Fetch COVID hospitalization data for specific facilities."""
        # Check parameters
        if hospital_pks is None or collection_weeks is None:
            raise EpidataBadRequestException(
                "`hospital_pks` and `collection_weeks` are both required"
            )
        # Set up request
        params = {
            "hospital_pks": Epidata._list(hospital_pks),
            "collection_weeks": Epidata._list(collection_weeks),
        }
        if publication_dates is not None:
            params["publication_dates"] = Epidata._list(publication_dates)
        # Make the API call
        return Epidata._request("covid_hosp_facility", params)

    # Lookup COVID hospitalization facility identifiers
    @staticmethod
    def covid_hosp_facility_lookup(state=None, ccn=None, city=None, zip=None, fips_code=None):
        """Lookup COVID hospitalization facility identifiers."""
        # Set up request
        params = {}
        if state is not None:
            params["state"] = state
        elif ccn is not None:
            params["ccn"] = ccn
        elif city is not None:
            params["city"] = city
        elif zip is not None:
            params["zip"] = zip
        elif fips_code is not None:
            params["fips_code"] = fips_code
        else:
            raise EpidataBadRequestException(
                "one of `state`, `ccn`, `city`, `zip`, or `fips_code` is required"
            )
        # Make the API call
        return Epidata._request("covid_hosp_facility_lookup", params)

    # Fetch Delphi's COVID-19 Nowcast sensors
    @staticmethod
    def covidcast_nowcast(
        data_source,
        signals,
        sensor_names,
        time_type,
        geo_type,
        time_values,
        geo_value,
        as_of=None,
        issues=None,
        lag=None,
        **kwargs,
    ):
        """Fetch Delphi's COVID-19 Nowcast sensors"""
        # Check parameters
        # fmt: off
        if None in (data_source, signals, time_type, geo_type, time_values, geo_value, sensor_names):
            # fmt: on
            raise EpidataBadRequestException(
                "`data_source`, `signals`, `sensor_names`, `time_type`, `geo_type`, "
                "`time_values`, and `geo_value` are all required"
            )
        if issues is not None and lag is not None:
            raise EpidataBadRequestException(REGIONS_EPIWEEKS_REQUIRED)
        # Set up request
        params = {
            "data_source": data_source,
            "signals": Epidata._list(signals),
            "sensor_names": Epidata._list(sensor_names),
            "time_type": time_type,
            "geo_type": geo_type,
            "time_values": Epidata._list(time_values),
        }

        if isinstance(geo_value, (list, tuple)):
            params["geo_values"] = ",".join(geo_value)
        else:
            params["geo_value"] = geo_value
        if as_of is not None:
            params["as_of"] = as_of
        if issues is not None:
            params["issues"] = Epidata._list(issues)
        if lag is not None:
            params["lag"] = lag

        if "format" in kwargs:
            params["format"] = kwargs["format"]

        # Make the API call
        return Epidata._request("covidcast_nowcast", params)

    @staticmethod
    def async_epidata(endpoint, param_list, batch_size=50):
        """Make asynchronous Epidata calls for a list of parameters."""

        request_url = f"{Epidata.BASE_URL}/{endpoint}"

        async def async_get(params, session):
            """Helper function to make Epidata GET requests."""
            async with session.get(request_url, params=params) as response:
                response.raise_for_status()
                return await response.json(), params

        async def async_make_calls(param_combos):
            """Helper function to asynchronously make and aggregate Epidata GET requests."""
            tasks = []
            connector = TCPConnector(limit=batch_size)
            if isinstance(Epidata.auth, tuple):
                auth = BasicAuth(login=Epidata.auth[0], password=Epidata.auth[1], encoding="utf-8")
            else:
                auth = Epidata.auth
            async with ClientSession(connector=connector, headers=_HEADERS, auth=auth) as session:
                for param in param_combos:
                    task = asyncio.ensure_future(async_get(param, session))
                    tasks.append(task)
                responses = await asyncio.gather(*tasks)
                return responses

        loop = asyncio.get_event_loop()
        future = asyncio.ensure_future(async_make_calls(param_list))
        responses = loop.run_until_complete(future)
        return responses