async-retriever

A part of HyRiver software stack for asynchronous requests with persistent caching

https://github.com/hyriver/async-retriever

Keywords

Keywords from Contributors

Repository

A part of HyRiver software stack for asynchronous requests with persistent caching

README.rst

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/async_retriever_logo.png
    :target: https://github.com/hyriver/HyRiver

|

.. image:: https://joss.theoj.org/papers/b0df2f6192f0a18b9e622a3edff52e77/status.svg
    :target: https://joss.theoj.org/papers/b0df2f6192f0a18b9e622a3edff52e77
    :alt: JOSS

|

.. |pygeohydro| image:: https://github.com/hyriver/pygeohydro/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pygeohydro/actions/workflows/test.yml
    :alt: Github Actions

.. |pygeoogc| image:: https://github.com/hyriver/pygeoogc/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pygeoogc/actions/workflows/test.yml
    :alt: Github Actions

.. |pygeoutils| image:: https://github.com/hyriver/pygeoutils/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pygeoutils/actions/workflows/test.yml
    :alt: Github Actions

.. |pynhd| image:: https://github.com/hyriver/pynhd/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pynhd/actions/workflows/test.yml
    :alt: Github Actions

.. |py3dep| image:: https://github.com/hyriver/py3dep/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/py3dep/actions/workflows/test.yml
    :alt: Github Actions

.. |pydaymet| image:: https://github.com/hyriver/pydaymet/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pydaymet/actions/workflows/test.yml
    :alt: Github Actions

.. |pygridmet| image:: https://github.com/hyriver/pygridmet/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pygridmet/actions/workflows/test.yml
    :alt: Github Actions

.. |pynldas2| image:: https://github.com/hyriver/pynldas2/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/pynldas2/actions/workflows/test.yml
    :alt: Github Actions

.. |async| image:: https://github.com/hyriver/async-retriever/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/async-retriever/actions/workflows/test.yml
    :alt: Github Actions

.. |signatures| image:: https://github.com/hyriver/hydrosignatures/actions/workflows/test.yml/badge.svg
    :target: https://github.com/hyriver/hydrosignatures/actions/workflows/test.yml
    :alt: Github Actions

================ ====================================================================
Package          Description
================ ====================================================================
PyNHD_           Navigate and subset NHDPlus (MR and HR) using web services
Py3DEP_          Access topographic data through National Map's 3DEP web service
PyGeoHydro_      Access NWIS, NID, WQP, eHydro, NLCD, CAMELS, and SSEBop databases
PyDaymet_        Access daily, monthly, and annual climate data via Daymet
PyGridMET_       Access daily climate data via GridMET
PyNLDAS2_        Access hourly NLDAS-2 data via web services
HydroSignatures_ A collection of tools for computing hydrological signatures
AsyncRetriever_  High-level API for asynchronous requests with persistent caching
PyGeoOGC_        Send queries to any ArcGIS RESTful-, WMS-, and WFS-based services
PyGeoUtils_      Utilities for manipulating geospatial, (Geo)JSON, and (Geo)TIFF data
================ ====================================================================

.. _PyGeoHydro: https://github.com/hyriver/pygeohydro
.. _AsyncRetriever: https://github.com/hyriver/async-retriever
.. _PyGeoOGC: https://github.com/hyriver/pygeoogc
.. _PyGeoUtils: https://github.com/hyriver/pygeoutils
.. _PyNHD: https://github.com/hyriver/pynhd
.. _Py3DEP: https://github.com/hyriver/py3dep
.. _PyDaymet: https://github.com/hyriver/pydaymet
.. _PyGridMET: https://github.com/hyriver/pygridmet
.. _PyNLDAS2: https://github.com/hyriver/pynldas2
.. _HydroSignatures: https://github.com/hyriver/hydrosignatures

AsyncRetriever: Asynchronous requests with persistent caching
-------------------------------------------------------------

.. image:: https://img.shields.io/pypi/v/async-retriever.svg
    :target: https://pypi.python.org/pypi/async-retriever
    :alt: PyPi

.. image:: https://img.shields.io/conda/vn/conda-forge/async-retriever.svg
    :target: https://anaconda.org/conda-forge/async-retriever
    :alt: Conda Version

.. image:: https://codecov.io/gh/hyriver/async-retriever/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/hyriver/async-retriever
    :alt: CodeCov

.. image:: https://img.shields.io/pypi/pyversions/async-retriever.svg
    :target: https://pypi.python.org/pypi/async-retriever
    :alt: Python Versions

.. image:: https://static.pepy.tech/badge/async-retriever
    :target: https://pepy.tech/project/async-retriever
    :alt: Downloads

|

.. image:: https://img.shields.io/badge/security-bandit-green.svg
    :target: https://github.com/PyCQA/bandit
    :alt: Security Status

.. image:: https://www.codefactor.io/repository/github/hyriver/async-retriever/badge
   :target: https://www.codefactor.io/repository/github/hyriver/async-retriever
   :alt: CodeFactor

.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
    :target: https://github.com/astral-sh/ruff
    :alt: Ruff

.. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
    :target: https://github.com/pre-commit/pre-commit
    :alt: pre-commit

|

Features
--------

AsyncRetriever is a part of `HyRiver `__ software stack that
is designed to aid in hydroclimate analysis through web services. This package serves as HyRiver's
engine for asynchronously sending requests and retrieving responses as ``text``, ``binary``, or
``json`` objects. It uses persistent caching using
`aiohttp-client-cache `__ to speed up the retrieval
even further. Moreover, thanks to `nest_asyncio `__
you can use this package in Jupyter notebooks. Although this package is part of the HyRiver
software stack, it can be used for any web calls. There are three functions that you can
use to make web calls:

* ``retrieve_text``: Get responses as ``text`` objects.
* ``retrieve_binary``: Get responses as ``binary`` objects.
* ``retrieve_json``: Get responses as ``json`` objects.
* ``stream_write``: Stream responses and write them to disk in chunks.

You can also use the general-purpose ``retrieve`` function to get responses as any
of the three types. All responses are returned as a list that has the same order as the
input list of requests. Moreover, there is another function called ``delete_url_cache``
for removing all requests from a cache file that contains a given URL.

You can control the request/response caching behavior and verbosity of the package
by setting the following environment variables:

* ``HYRIVER_CACHE_NAME``: Path to the caching SQLite database. It defaults to
  ``./cache/aiohttp_cache.sqlite``
* ``HYRIVER_CACHE_EXPIRE``: Expiration time for cached requests in seconds. It defaults to
  one week.
* ``HYRIVER_CACHE_DISABLE``: Disable reading/writing from/to the cache. The default is false.
* ``HYRIVER_SSL_CERT``: Path to a SSL certificate file.

For example, in your code before making any requests you can do:

.. code-block:: python

    import os

    os.environ["HYRIVER_CACHE_NAME"] = "path/to/file.sqlite"
    os.environ["HYRIVER_CACHE_EXPIRE"] = "3600"
    os.environ["HYRIVER_CACHE_DISABLE"] = "true"
    os.environ["HYRIVER_SSL_CERT"] = "path/to/cert.pem"

You can find some example notebooks `here `__.

You can also try using AsyncRetriever without installing
it on your system by clicking on the binder badge. A Jupyter Lab
instance with the HyRiver stack pre-installed will be launched in your web browser, and you
can start coding!

Moreover, requests for additional functionalities can be submitted via
`issue tracker `__.

Citation
--------
If you use any of HyRiver packages in your research, we appreciate citations:

.. code-block:: bibtex

    @article{Chegini_2021,
        author = {Chegini, Taher and Li, Hong-Yi and Leung, L. Ruby},
        doi = {10.21105/joss.03175},
        journal = {Journal of Open Source Software},
        month = {10},
        number = {66},
        pages = {1--3},
        title = {{HyRiver: Hydroclimate Data Retriever}},
        volume = {6},
        year = {2021}
    }

Installation
------------

You can install ``async-retriever`` using ``pip``:

.. code-block:: console

    $ pip install async-retriever

Alternatively, ``async-retriever`` can be installed from the ``conda-forge`` repository
using `Conda `__:

.. code-block:: console

    $ conda install -c conda-forge async-retriever

Quick start
-----------

AsyncRetriever by default creates and/or uses ``./cache/aiohttp_cache.sqlite`` as the cache
that you can customize by the ``cache_name`` argument. Also, by default, the cache doesn't
have any expiration date and the ``delete_url_cache`` function should be used if you know
that a database on a server was updated, and you want to retrieve the latest data.
Alternatively, you can use the ``expire_after`` to set the expiration date for the cache.

As an example for retrieving a ``binary`` response, let's use the DAAC server to get
`NDVI `_.
The responses can be directly passed to ``xarray.open_mfdataset`` to get the data as
a ``xarray`` Dataset. We can also disable SSL certificate verification by setting
``ssl=False``.

.. code-block:: python

    import io
    import xarray as xr
    import async_retriever as ar
    from datetime import datetime

    west, south, east, north = (-69.77, 45.07, -69.31, 45.45)
    base_url = "https://thredds.daac.ornl.gov/thredds/ncss/ornldaac/1299"
    dates_itr = ((datetime(y, 1, 1), datetime(y, 1, 31)) for y in range(2000, 2005))
    urls, kwds = zip(
        *[
            (
                f"{base_url}/MCD13.A{s.year}.unaccum.nc4",
                {
                    "params": {
                        "var": "NDVI",
                        "north": f"{north}",
                        "west": f"{west}",
                        "east": f"{east}",
                        "south": f"{south}",
                        "disableProjSubset": "on",
                        "horizStride": "1",
                        "time_start": s.strftime("%Y-%m-%dT%H:%M:%SZ"),
                        "time_end": e.strftime("%Y-%m-%dT%H:%M:%SZ"),
                        "timeStride": "1",
                        "addLatLon": "true",
                        "accept": "netcdf",
                    }
                },
            )
            for s, e in dates_itr
        ]
    )
    resp = ar.retrieve_binary(urls, kwds, max_workers=8, ssl=False)
    data = xr.open_mfdataset(io.BytesIO(r) for r in resp)

We can remove these requests and their responses from the cache like so:

.. code-block:: python

    ar.delete_url_cache(base_url)

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/ndvi.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/async.ipynb

For a ``json`` response example, let's get water level recordings of an NOAA's water level station,
8534720 (Atlantic City, NJ), during 2012, using CO-OPS API. Note that this CO-OPS product has a
31-day limit for a single request, so we have to break the request down accordingly.

.. code-block:: python

    import pandas as pd

    station_id = "8534720"
    start = pd.to_datetime("2012-01-01")
    end = pd.to_datetime("2012-12-31")

    s = start
    dates = []
    for e in pd.date_range(start, end, freq="m"):
        dates.append((s.date(), e.date()))
        s = e + pd.offsets.MonthBegin()

    url = "https://api.tidesandcurrents.noaa.gov/api/prod/datagetter"

    urls, kwds = zip(
        *[
            (
                url,
                {
                    "params": {
                        "product": "water_level",
                        "application": "web_services",
                        "begin_date": f'{s.strftime("%Y%m%d")}',
                        "end_date": f'{e.strftime("%Y%m%d")}',
                        "datum": "MSL",
                        "station": f"{station_id}",
                        "time_zone": "GMT",
                        "units": "metric",
                        "format": "json",
                    }
                },
            )
            for s, e in dates
        ]
    )

    resp = ar.retrieve_json(urls, kwds)
    wl_list = []
    for rjson in resp:
        wl = pd.DataFrame.from_dict(rjson["data"])
        wl["t"] = pd.to_datetime(wl.t)
        wl = wl.set_index(wl.t).drop(columns="t")
        wl["v"] = pd.to_numeric(wl.v, errors="coerce")
        wl_list.append(wl)
    water_level = pd.concat(wl_list).sort_index()
    water_level.attrs = rjson["metadata"]

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/water_level.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/async.ipynb

Now, let's see an example without any payload or headers. Here's how we can retrieve
harmonic constituents of several NOAA stations from CO-OPS:

.. code-block:: python

    stations = [
        "8410140",
        "8411060",
        "8413320",
        "8418150",
        "8419317",
        "8419870",
        "8443970",
        "8447386",
    ]

    base_url = "https://api.tidesandcurrents.noaa.gov/mdapi/prod/webapi/stations"
    urls = [f"{base_url}/{i}/harcon.json?units=metric" for i in stations]
    resp = ar.retrieve_json(urls)

    amp_list = []
    phs_list = []
    for rjson in resp:
        sid = rjson["self"].rsplit("/", 2)[1]
        const = pd.DataFrame.from_dict(rjson["HarmonicConstituents"]).set_index("name")
        amp = const.rename(columns={"amplitude": sid})[sid]
        phase = const.rename(columns={"phase_GMT": sid})[sid]
        amp_list.append(amp)
        phs_list.append(phase)

    amp = pd.concat(amp_list, axis=1)
    phs = pd.concat(phs_list, axis=1)

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/tides.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/async.ipynb

Contributing
------------

Contributions are appreciated and very welcomed. Please read
`CONTRIBUTING.rst `__
for instructions.

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Chegini"
  given-names: "Taher"
  orcid: "https://orcid.org/0000-0002-5430-6000"
- family-names: "Li"
  given-names: "Hong-Yi"
  orcid: "https://orcid.org/0000-0002-9807-3851"
- family-names: "Leung"
  given-names: "L. Ruby"
  orcid: "https://orcid.org/0000-0002-3221-9467"
title: "HyRiver: Hydroclimate Data Retriever"
version: 0.11
doi: 10.21105/joss.03175
date-released: 2021-10-27
url: "https://github.com/cheginit/HyRiver"
preferred-citation:
  type: article
  authors:
  - family-names: "Chegini"
    given-names: "Taher"
    orcid: "https://orcid.org/0000-0002-5430-6000"
  - family-names: "Li"
    given-names: "Hong-Yi"
    orcid: "https://orcid.org/0000-0002-9807-3851"
  - family-names: "Leung"
    given-names: "L. Ruby"
    orcid: "https://orcid.org/0000-0002-3221-9467"
  doi: "10.21105/joss.03175"
  journal: "Journal of Open Source Software"
  month: 10
  start: 1
  end: 3
  title: "HyRiver: Hydroclimate Data Retriever"
  issue: 66
  volume: 6
  year: 2021

GitHub Events

Committers

Last synced: about 2 years ago

Issues and Pull Requests

Last synced: 6 months ago

Packages