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Merge pull request #32 from dfarrow0/master
modularize, implement `covid_survey` parts
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‎integrations/test_covid_survey_county_weekly.py

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"""Integration tests for the `covid_survey_county_weekly` endpoint."""
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# standard library
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import unittest
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# third party
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import mysql.connector
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import requests
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# use the local instance of the Epidata API
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BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
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class CovidSurveyCountyWeeklyTests(unittest.TestCase):
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"""Tests the `covid_survey_county_weekly` endpoint."""
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def setUp(self):
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"""Perform per-test setup."""
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# connect to the `epidata` database and clear the
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# `covid_survey_county_weekly` table
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cnx = mysql.connector.connect(
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user='user',
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password='pass',
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host='delphi_database_epidata',
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database='epidata')
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cur = cnx.cursor()
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cur.execute('truncate table covid_survey_county_weekly')
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cnx.commit()
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cur.close()
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# make connection and cursor available to test cases
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self.cnx = cnx
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self.cur = cnx.cursor()
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def tearDown(self):
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"""Perform per-test teardown."""
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self.cur.close()
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self.cnx.close()
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def test_round_trip(self):
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"""Make a simple round-trip with some sample data."""
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# insert dummy data
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self.cur.execute('''
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insert into covid_survey_county_weekly values
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(0, 202014, '42003', 1.5, 2.5, 3.5, 4.5, 5678.5)
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''')
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self.cnx.commit()
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# make the request
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response = requests.get(BASE_URL, params={
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'source': 'covid_survey_county_weekly',
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'counties': '42003',
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'epiweeks': 202014,
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})
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response.raise_for_status()
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response = response.json()
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# assert that the right data came back
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self.assertEqual(response, {
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"result": 1,
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"epidata": [{
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'epiweek': 202014,
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'county': '42003',
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'ili': 1.5,
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'ili_stdev': 2.5,
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'cli': 3.5,
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'cli_stdev': 4.5,
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'denominator': 5678.5,
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}],
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"message": "success",
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})
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def test_privacy_filtering(self):
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"""Don't return rows with too small of a denominator."""
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# shared constants
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request_params = {
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'source': 'covid_survey_county_weekly',
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'counties': '42003',
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'epiweeks': 202014,
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}
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with self.subTest(name='filtered'):
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# insert dummy data
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self.cur.execute('''
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insert into covid_survey_county_weekly values
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(0, 202014, '42003', 1.5, 2.5, 3.5, 4.5, 99.5)
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''')
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self.cnx.commit()
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# make the request
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response = requests.get(BASE_URL, params=request_params)
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response.raise_for_status()
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response = response.json()
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# assert that no data came back
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self.assertEqual(response, {
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"result": -2,
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"message": "no results",
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})
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with self.subTest(name='unfiltered'):
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# amend the denominator
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self.cur.execute('''
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update covid_survey_county_weekly set denominator = 100.5
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''')
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self.cnx.commit()
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# make the request
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response = requests.get(BASE_URL, params=request_params)
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response.raise_for_status()
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response = response.json()
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# assert that the right data came back
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self.assertEqual(response, {
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"result": 1,
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"epidata": [{
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'epiweek': 202014,
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'county': '42003',
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'ili': 1.5,
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'ili_stdev': 2.5,
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'cli': 3.5,
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'cli_stdev': 4.5,
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'denominator': 100.5,
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}],
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"message": "success",
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})

‎integrations/test_covid_survey_hrr_daily.py

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"""Integration tests for the `covid_survey_hrr_daily` endpoint."""
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# standard library
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import unittest
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# third party
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import mysql.connector
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import requests
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# use the local instance of the Epidata API
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BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
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class CovidSurveyHrrDailyTests(unittest.TestCase):
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"""Tests the `covid_survey_hrr_daily` endpoint."""
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def setUp(self):
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"""Perform per-test setup."""
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# connect to the `epidata` database and clear the `covid_survey_hrr_daily`
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# table
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cnx = mysql.connector.connect(
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user='user',
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password='pass',
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host='delphi_database_epidata',
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database='epidata')
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cur = cnx.cursor()
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cur.execute('truncate table covid_survey_hrr_daily')
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cnx.commit()
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cur.close()
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# make connection and cursor available to test cases
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self.cnx = cnx
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self.cur = cnx.cursor()
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def tearDown(self):
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"""Perform per-test teardown."""
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self.cur.close()
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self.cnx.close()
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def test_round_trip(self):
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"""Make a simple round-trip with some sample data."""
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# insert dummy data
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self.cur.execute('''
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insert into covid_survey_hrr_daily values
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(0, '2020-04-08', 123, 1.5, 2.5, 3.5, 4.5, 5678.5)
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''')
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self.cnx.commit()
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# make the request
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response = requests.get(BASE_URL, params={
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'source': 'covid_survey_hrr_daily',
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'hrrs': 123,
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'dates': 20200408,
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})
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response.raise_for_status()
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response = response.json()
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# assert that the right data came back
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self.assertEqual(response, {
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"result": 1,
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"epidata": [{
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'date': '2020-04-08',
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'hrr': 123,
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'ili': 1.5,
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'ili_stdev': 2.5,
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'cli': 3.5,
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'cli_stdev': 4.5,
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'denominator': 5678.5,
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}],
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"message": "success",
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})
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def test_privacy_filtering(self):
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"""Don't return rows with too small of a denominator."""
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# shared constants
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request_params = {
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'source': 'covid_survey_hrr_daily',
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'hrrs': 123,
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'dates': 20200408,
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}
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with self.subTest(name='filtered'):
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# insert dummy data
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self.cur.execute('''
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insert into covid_survey_hrr_daily values
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(0, '2020-04-08', 123, 1.5, 2.5, 3.5, 4.5, 99.5)
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''')
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self.cnx.commit()
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# make the request
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response = requests.get(BASE_URL, params=request_params)
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response.raise_for_status()
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response = response.json()
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# assert that no data came back
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self.assertEqual(response, {
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"result": -2,
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"message": "no results",
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})
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with self.subTest(name='unfiltered'):
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# amend the denominator
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self.cur.execute('''
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update covid_survey_hrr_daily set denominator = 100.5
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''')
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self.cnx.commit()
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# make the request
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response = requests.get(BASE_URL, params=request_params)
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response.raise_for_status()
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response = response.json()
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# assert that the right data came back
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self.assertEqual(response, {
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"result": 1,
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"epidata": [{
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'date': '2020-04-08',
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'hrr': 123,
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'ili': 1.5,
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'ili_stdev': 2.5,
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'cli': 3.5,
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'cli_stdev': 4.5,
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'denominator': 100.5,
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}],
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"message": "success",
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})

‎integrations/test_fluview.py

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"""Integration tests for the `fluview` endpoint."""
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# standard library
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import unittest
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# third party
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import mysql.connector
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# first party
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from delphi.epidata.client.delphi_epidata import Epidata
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class FluviewTests(unittest.TestCase):
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"""Tests the `fluview` endpoint."""
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@classmethod
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def setUpClass(cls):
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"""Perform one-time setup."""
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# use the local instance of the Epidata API
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Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
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def setUp(self):
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"""Perform per-test setup."""
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# connect to the `epidata` database and clear the `fluview` table
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cnx = mysql.connector.connect(
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user='user',
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password='pass',
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host='delphi_database_epidata',
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database='epidata')
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cur = cnx.cursor()
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cur.execute('truncate table fluview')
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cnx.commit()
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cur.close()
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# make connection and cursor available to test cases
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self.cnx = cnx
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self.cur = cnx.cursor()
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def tearDown(self):
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"""Perform per-test teardown."""
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self.cur.close()
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self.cnx.close()
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def test_round_trip(self):
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"""Make a simple round-trip with some sample data."""
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# insert dummy data
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self.cur.execute('''
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insert into fluview values
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(0, "2020-04-07", 202021, 202020, "nat", 1, 2, 3, 4, 3.14159, 1.41421,
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10, 11, 12, 13, 14, 15)
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''')
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self.cnx.commit()
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# make the request
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response = Epidata.fluview('nat', 202020)
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# assert that the right data came back
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self.assertEqual(response, {
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"result": 1,
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"epidata": [{
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"release_date": "2020-04-07",
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"region": "nat",
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"issue": 202021,
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"epiweek": 202020,
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"lag": 1,
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"num_ili": 2,
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"num_patients": 3,
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"num_providers": 4,
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"num_age_0": 10,
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"num_age_1": 11,
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"num_age_2": 12,
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"num_age_3": 13,
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"num_age_4": 14,
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"num_age_5": 15,
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"wili": 3.14159,
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"ili": 1.41421,
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}],
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"message": "success",
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})

‎src/ddl/covid_survey_county_weekly.sql

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/*
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Stores a subset of data from the COVID-19 survey, aggregated by weeks and
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counties.
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+-------------+------------+------+-----+---------+----------------+
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| Field | Type | Null | Key | Default | Extra |
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+-------------+------------+------+-----+---------+----------------+
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| id | int(11) | NO | PRI | NULL | auto_increment |
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| epiweek | int(11) | NO | MUL | NULL | |
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| county | varchar(5) | NO | | NULL | |
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| ili | double | NO | | NULL | |
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| ili_stdev | double | NO | | NULL | |
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| cli | double | NO | | NULL | |
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| cli_stdev | double | NO | | NULL | |
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| denominator | double | NO | | NULL | |
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+-------------+------------+------+-----+---------+----------------+
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id:
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unique identifier for each record
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epiweek:
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the epidemiological week during which the survey was submitted
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county:
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assumed fips 6-4 county code
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ili:
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estimated percent of sample experiencing influenza-like illness (ILI)
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ili_stdev:
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standard deviation for the ILI estimate
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cli:
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estimated percent of sample experiencing codid-19-like illness (CLI)
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cli_stdev:
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standard deviation for the CLI estimate
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denominator:
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estimated sample size
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*/
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CREATE TABLE `covid_survey_county_weekly` (
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`id` int(11) NOT NULL AUTO_INCREMENT,
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`epiweek` int(11) NOT NULL,
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`county` varchar(5) NOT NULL,
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`ili` double NOT NULL,
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`ili_stdev` double NOT NULL,
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`cli` double NOT NULL,
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`cli_stdev` double NOT NULL,
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`denominator` double NOT NULL,
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PRIMARY KEY (`id`),
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UNIQUE KEY (`epiweek`, `county`),
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KEY (`county`, `epiweek`)
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) ENGINE=InnoDB DEFAULT CHARSET=latin1;

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