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Merge pull request #6 from cmu-delphi/master
sync to delphi
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‎docs/api/covidcast.md

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@@ -77,7 +77,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a
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# Example URLs
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### Delphi's COVID-19 Surveillance Streams from Facebook Survey ILI on 2020-04-06 - 2010-04-10 (county 06001)
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### Delphi's COVID-19 Surveillance Streams from Facebook Survey ILI on 2020-04-06 - 2020-04-10 (county 06001)
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https://delphi.midas.cs.cmu.edu/epidata/api.php?source=covidcast&data_source=fb_survey&signal=ili&time_type=day&geo_type=county&time_values=20200406-20200410&geo_value=06001
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```json
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{
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# Code Samples
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No client support yet.
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Libraries are available for [CoffeeScript](../../src/client/delphi_epidata.coffee), [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R).
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The following samples show how to import the library and fetch Delphi's COVID-19 Surveillance Streams from Facebook Survey ILI for county 06001 and days `20200401` and `20200405-20200414` (11 days total).
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### CoffeeScript (in Node.js)
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````coffeescript
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# Import
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{Epidata} = require('./delphi_epidata')
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# Fetch data
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callback = (result, message, epidata) ->
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console.log(result, message, epidata?.length)
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Epidata.covidcast(callback, 'fb_survey', 'ili', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001')
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````
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### JavaScript (in a web browser)
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````html
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<!-- Imports -->
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<script src="jquery.js"></script>
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<script src="delphi_epidata.js"></script>
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<!-- Fetch data -->
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<script>
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var callback = function(result, message, epidata) {
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console.log(result, message, epidata != null ? epidata.length : void 0);
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};
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Epidata.covidcast(callback, 'fb_survey', 'ili', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001');
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</script>
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````
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### Python
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Optionally install the package using pip(env):
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````bash
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pip install delphi-epidata
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````
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Otherwise, place `delphi_epidata.py` from this repo next to your python script.
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````python
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# Import
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from delphi_epidata import Epidata
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# Fetch data
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res = Epidata.covidcast('fb_survey', 'ili', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001')
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print(res['result'], res['message'], len(res['epidata']))
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````
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### R
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````R
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# Import
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source('delphi_epidata.R')
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# Fetch data
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res <- Epidata$covidcast('fb_survey', 'ili', 'day', 'county', list(20200401, Epidata$range(20200405, 20200414)), '06001')
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cat(paste(res$result, res$message, length(res$epidata), "\n"))
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````

‎docs/api/covidcast_meta.md

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@@ -93,4 +93,58 @@ https://delphi.midas.cs.cmu.edu/epidata/api.php?source=covidcast_meta
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# Code Samples
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<!-- TODO: fix -->
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Libraries are available for [CoffeeScript](../../src/client/delphi_epidata.coffee), [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R).
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The following samples show how to import the library and fetch Delphi's COVID-19 Surveillance Streams metadata.
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### CoffeeScript (in Node.js)
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````coffeescript
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# Import
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{Epidata} = require('./delphi_epidata')
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# Fetch data
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callback = (result, message, epidata) ->
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console.log(result, message, epidata?.length)
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Epidata.covidcast_meta(callback)
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````
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### JavaScript (in a web browser)
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````html
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<!-- Imports -->
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<script src="jquery.js"></script>
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<script src="delphi_epidata.js"></script>
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<!-- Fetch data -->
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<script>
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var callback = function(result, message, epidata) {
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console.log(result, message, epidata != null ? epidata.length : void 0);
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};
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Epidata.covidcast_meta(callback);
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</script>
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````
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### Python
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Optionally install the package using pip(env):
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````bash
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pip install delphi-epidata
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````
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Otherwise, place `delphi_epidata.py` from this repo next to your python script.
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````python
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# Import
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from delphi_epidata import Epidata
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# Fetch data
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res = Epidata.covidcast_meta()
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print(res['result'], res['message'], len(res['epidata']))
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````
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### R
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````R
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# Import
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source('delphi_epidata.R')
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# Fetch data
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res <- Epidata$covidcast_meta()
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cat(paste(res$result, res$message, length(res$epidata), "\n"))
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````

‎docs/api/wiki.md

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# Import
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source('delphi_epidata.R')
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# Fetch data
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res <- Epidata$fluview_clinical(list('nat'), NULL, list(201940, Epidata$range(202001, 202010)), list(0, 12), 'en')
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res <- Epidata$wiki(list('nat'), NULL, list(201940, Epidata$range(202001, 202010)), list(0, 12), 'en')
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cat(paste(res$result, res$message, length(res$epidata), "\n"))
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````

‎integrations/test_delphi_epidata.py

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"""Integration tests for delphi_epidata.py."""
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import unittest
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# first party
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from delphi.epidata.client.delphi_epidata import Epidata
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# py3tester coverage target
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__test_target__ = 'delphi.epidata.client.delphi_epidata'
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class DelphiEpidataPythonClientTests(unittest.TestCase):
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"""Tests the Python client."""
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def test_covidcast_happy_path(self):
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"""Test that the covidcast endpoint returns expected data."""
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# Fetch data
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res = Epidata.covidcast('fb_survey', 'ili', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001')
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# Check result
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self.assertEqual(res['result'], 1)
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self.assertEqual(res['message'], 'success')
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self.assertGreater(len(res['epidata']), 0)
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item = res['epidata'][0]
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self.assertIn('geo_value', item)
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self.assertIn('time_value', item)
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self.assertIn('direction', item)
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self.assertIn('value', item)
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self.assertIn('stderr', item)
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self.assertIn('sample_size', item)
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def test_covidcast_meta(self):
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"""Test that the covidcast_meta endpoint returns expected data."""
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# Fetch data
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res = Epidata.covidcast_meta()
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# Check result
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self.assertEqual(res['result'], 1)
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self.assertEqual(res['message'], 'success')
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self.assertGreater(len(res['epidata']), 0)
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item = res['epidata'][0]
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self.assertIn('data_source', item)
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self.assertIn('time_type', item)
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self.assertIn('geo_type', item)
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self.assertIn('min_time', item)
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self.assertIn('max_time', item)
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self.assertIn('num_locations', item)
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if __name__ == '__main__':
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unittest.main()

‎src/client/delphi_epidata.R

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@@ -492,6 +492,31 @@ Epidata <- (function() {
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return(.request(list(source='meta')))
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}
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# Fetch Delphi's COVID-19 Surveillance Streams
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covidcast <- function(data_source, signal, time_type, geo_type, time_values, geo_value) {
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# Check parameters
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if(missing(data_source) || missing(signal) || missing(time_type) || missing(geo_type) || missing(time_values) || missing(geo_value)) {
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stop('`data_source`, `signal`, `time_type`, `geo_type`, `time_values`, and `geo_value` are all required')
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}
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# Set up request
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params <- list(
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source = 'covidcast',
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data_source = data_source,
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signal = signal,
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time_type = time_type,
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geo_type = geo_type,
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time_values = .list(time_values),
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geo_value = geo_value
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)
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# Make the API call
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return(.request(params))
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}
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# Fetch Delphi's COVID-19 Surveillance Streams metadata
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covidcast_meta <- function() {
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return(.request(list(source='covidcast_meta')))
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}
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# Export the public methods
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return(list(
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range = range,
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dengue_sensors = dengue_sensors,
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nowcast = nowcast,
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dengue_nowcast = dengue_nowcast,
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meta = meta
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meta = meta,
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covidcast = covidcast,
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covidcast_meta = covidcast_meta
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))
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})()

‎src/client/delphi_epidata.coffee

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@meta: (callback) ->
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_request(callback, {'source': 'meta'})
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# Fetch Delphi's COVID-19 Surveillance Streams
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@covidcast: (callback, data_source, signal, time_type, geo_type, time_values, geo_value) ->
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# Check parameters
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unless data_source? and signal? and time_type? and geo_type? and time_values? and geo_values?
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throw { msg: '`data_source`, `signal`, `time_type`, `geo_type`, `time_values`, and `geo_value` are all required' }
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# Set up request
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params =
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'source': 'covidcast'
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'data_source': data_source
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'signal': signal
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'time_type': time_type
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'geo_type': geo_type
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'time_values': _list(time_values)
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'geo_value': geo_value
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# Make the API call
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_request(callback, params)
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# Fetch Delphi's COVID-19 Surveillance Streams metadata
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@covidcast_meta: (callback) ->
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_request(callback, {'source': 'covidcast_meta'})
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# Export the API to the global environment
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(exports ? window).Epidata = Epidata

‎src/client/delphi_epidata.js

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‎src/client/delphi_epidata.py

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def meta():
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"""Fetch API metadata."""
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return Epidata._request({'source': 'meta'})
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# Fetch Delphi's COVID-19 Surveillance Streams
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@staticmethod
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def covidcast(data_source, signal, time_type, geo_type, time_values, geo_value):
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"""Fetch Delphi's COVID-19 Surveillance Streams"""
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# Check parameters
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if data_source is None or signal is None or time_type is None or geo_type is None or time_values is None or geo_value is None:
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raise Exception('`data_source`, `signal`, `time_type`, `geo_type`, `time_values`, and `geo_value` are all required')
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# Set up request
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params = {
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'source': 'covidcast',
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'data_source': data_source,
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'signal': signal,
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'time_type': time_type,
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'geo_type': geo_type,
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'time_values': Epidata._list(time_values),
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'geo_value': geo_value,
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}
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# Make the API call
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return Epidata._request(params)
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# Fetch Delphi's COVID-19 Surveillance Streams metadata
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@staticmethod
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def covidcast_meta():
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"""Fetch Delphi's COVID-19 Surveillance Streams metadata"""
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return Epidata._request({'source': 'covidcast_meta'})

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