Merge pull request #342 from dfarrow0/dfarrow/covid-hosp-facility3

add endpoint `covid_hosp_facility`

Author: krivard

integrations/acquisition/covid_hosp/facility/test_scenarios.py

@@ -0,0 +1,87 @@
+"""Integration tests for acquisition of COVID hospitalization facility."""
+
+# standard library
+import unittest
+from unittest.mock import MagicMock
+
+# first party
+from delphi.epidata.acquisition.covid_hosp.common.database import Database
+from delphi.epidata.acquisition.covid_hosp.common.test_utils import TestUtils
+from delphi.epidata.client.delphi_epidata import Epidata
+import delphi.operations.secrets as secrets
+
+# py3tester coverage target (equivalent to `import *`)
+__test_target__ = 'delphi.epidata.acquisition.covid_hosp.facility.update'
+
+
+class AcquisitionTests(unittest.TestCase):
+
+  def setUp(self):
+    """Perform per-test setup."""
+
+    # configure test data
+    self.test_utils = TestUtils(__file__)
+
+    # use the local instance of the Epidata API
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+
+    # use the local instance of the epidata database
+    secrets.db.host = 'delphi_database_epidata'
+    secrets.db.epi = ('user', 'pass')
+
+    # clear relevant tables
+    with Database.connect() as db:
+      with db.new_cursor() as cur:
+        cur.execute('truncate table covid_hosp_facility')
+        cur.execute('truncate table covid_hosp_meta')
+
+  def test_acquire_dataset(self):
+    """Acquire a new dataset."""
+
+    # only mock out network calls to external hosts
+    mock_network = MagicMock()
+    mock_network.fetch_metadata.return_value = \
+        self.test_utils.load_sample_metadata()
+    mock_network.fetch_dataset.return_value = \
+        self.test_utils.load_sample_dataset()
+
+    # make sure the data does not yet exist
+    with self.subTest(name='no data yet'):
+      response = Epidata.covid_hosp_facility(
+          '450822', Epidata.range(20200101, 20210101))
+      self.assertEqual(response['result'], -2)
+
+    # acquire sample data into local database
+    with self.subTest(name='first acquisition'):
+      acquired = Update.run(network=mock_network)
+      self.assertTrue(acquired)
+
+    # make sure the data now exists
+    with self.subTest(name='initial data checks'):
+      response = Epidata.covid_hosp_facility(
+          '450822', Epidata.range(20200101, 20210101))
+      self.assertEqual(response['result'], 1)
+      self.assertEqual(len(response['epidata']), 1)
+      row = response['epidata'][0]
+      self.assertEqual(row['hospital_pk'], '450822')
+      self.assertEqual(row['collection_week'], 20201030)
+      self.assertEqual(row['publication_date'], 20201208)
+      self.assertEqual(row['previous_day_total_ed_visits_7_day_sum'], 536)
+      self.assertAlmostEqual(row['total_beds_7_day_avg'], 69.3)
+      self.assertEqual(
+          row['previous_day_admission_influenza_confirmed_7_day_sum'], -999999)
+
+      # expect 94 fields per row (95 database columns, except `id`)
+      self.assertEqual(len(row), 94)
+
+    # re-acquisition of the same dataset should be a no-op
+    with self.subTest(name='second acquisition'):
+      acquired = Update.run(network=mock_network)
+      self.assertFalse(acquired)
+
+    # make sure the data still exists
+    with self.subTest(name='final data checks'):
+      response = Epidata.covid_hosp_facility(
+          '450822', Epidata.range(20200101, 20210101))
+      self.assertEqual(response['result'], 1)
+      self.assertEqual(len(response['epidata']), 1)

src/client/delphi_epidata.R

@@ -571,6 +571,25 @@ Epidata <- (function() {
     return(.request(params))
   }
 
+  # Fetch COVID hospitalization data for specific facilities
+  covid_hosp_facility <- function(hospital_pks, collection_weeks, publication_dates) {
+    # Check parameters
+    if(missing(hospital_pks) || missing(collection_weeks)) {
+      stop('`hospital_pks` and `collection_weeks` are both required')
+    }
+    # Set up request
+    params <- list(
+      source = 'covid_hosp_facility',
+      hospital_pks = .list(hospital_pks),
+      collection_weeks = .list(collection_weeks)
+    )
+    if(!missing(publication_dates)) {
+      params$publication_dates <- .list(publication_dates)
+    }
+    # Make the API call
+    return(.request(params))
+  }
+
   # Export the public methods
   return(list(
     range = range,
@@ -598,6 +617,7 @@ Epidata <- (function() {
     meta = meta,
     covidcast = covidcast,
     covidcast_meta = covidcast_meta,
-    covid_hosp = covid_hosp
+    covid_hosp = covid_hosp,
+    covid_hosp_facility = covid_hosp_facility
   ))
 })()

src/client/delphi_epidata.coffee

@@ -430,5 +430,20 @@ class Epidata
     # Make the API call
     _request(callback, params)
 
+  # Fetch COVID hospitalization data for specific facilities
+  @covid_hosp_facility: (callback, hospital_pks, collection_weeks, publication_dates) ->
+    # Check parameters
+    unless hospital_pks? and collection_weeks?
+      throw { msg: '`hospital_pks` and `collection_weeks` are both required' }
+    # Set up request
+    params =
+      'source': 'covid_hosp_facility'
+      'hospital_pks': _list(hospital_pks)
+      'collection_weeks': _list(collection_weeks)
+    if publication_dates?
+      params.publication_dates = _list(publication_dates)
+    # Make the API call
+    _request(callback, params)
+
 # Export the API to the global environment
 (exports ? window).Epidata = Epidata

src/client/delphi_epidata.js

@@ -634,6 +634,32 @@ function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _d
           } // Make the API call
 
 
+          return _request(callback, params);
+        } // Fetch COVID hospitalization data for specific facilities
+
+      }, {
+        key: "covid_hosp_facility",
+        value: function covid_hosp_facility(callback, hospital_pks, collection_weeks, publication_dates) {
+          var params; // Check parameters
+
+          if (!(hospital_pks != null && collection_weeks != null)) {
+            throw {
+              msg: '`hospital_pks` and `collection_weeks` are both required'
+            };
+          } // Set up request
+
+
+          params = {
+            'source': 'covid_hosp_facility',
+            'hospital_pks': _list(hospital_pks),
+            'collection_weeks': _list(collection_weeks)
+          };
+
+          if (publication_dates != null) {
+            params.publication_dates = _list(publication_dates);
+          } // Make the API call
+
+
           return _request(callback, params);
         }
       }]);

src/client/delphi_epidata.py

@@ -624,3 +624,22 @@ def covid_hosp(states, dates, issues=None):
       params['issues'] = Epidata._list(issues)
     # Make the API call
     return Epidata._request(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 Exception('`hospital_pks` and `collection_weeks` are both required')
+    # Set up request
+    params = {
+      'source': 'covid_hosp_facility',
+      '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(params)