modularize, implement covid_survey parts

integrations/test_covid_survey_county_weekly.py

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

integrations/test_covid_survey_hrr_daily.py

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

integrations/test_fluview.py

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

src/ddl/covid_survey_county_weekly.sql

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