Add rvdss indicator/data source

integrations/acquisition/rvdss/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/acquisition/rvdss/test_scenarios.py

@@ -0,0 +1,99 @@
+"""Integration tests for acquisition of rvdss data."""
+# standard library
+import unittest
+from unittest.mock import MagicMock
+
+# first party
+from delphi.epidata.client.delphi_epidata import Epidata
+from delphi.epidata.acquisition.rvdss.database import update
+import delphi.operations.secrets as secrets
+
+# third party
+import mysql.connector
+
+# py3tester coverage target (equivalent to `import *`)
+# __test_target__ = 'delphi.epidata.acquisition.covid_hosp.facility.update'
+
+NEWLINE="\n"
+
+class AcquisitionTests(unittest.TestCase):
+
+  def setUp(self):
+    """Perform per-test setup."""
+
+    # configure test data
+    # self.test_utils = UnitTestUtils(__file__)
+
+    # use the local instance of the Epidata API
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata'
+    Epidata.auth = ('epidata', 'key')
+
+    # use the local instance of the epidata database
+    secrets.db.host = 'delphi_database_epidata'
+    secrets.db.epi = ('user', 'pass')
+
+    # clear relevant tables
+    u, p = secrets.db.epi
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cur = cnx.cursor()
+
+    cur.execute('truncate table rvdss_repiratory_detections')
+    cur.execute('truncate table rvdss_pct_positive')
+    cur.execute('truncate table rvdss_detections_counts')
+    cur.execute('delete from api_user')
+    cur.execute('insert into api_user(api_key, email) values ("key", "emai")')
+
+  def test_rvdss_repiratory_detections(self):
+    # make sure the data does not yet exist
+    with self.subTest(name='no data yet'):
+      response = Epidata.rvdss_repiratory_detections(
+          '450822', Epidata.range(20200101, 20210101))
+      self.assertEqual(response['result'], -2, response)
+
+    # 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'):
+      expected_spotchecks = {
+        "hospital_pk": "450822",
+        "collection_week": 20201030,
+        "publication_date": 20210315,
+        "previous_day_total_ed_visits_7_day_sum": 536,
+        "total_personnel_covid_vaccinated_doses_all_7_day_sum": 18,
+        "total_beds_7_day_avg": 69.3,
+        "previous_day_admission_influenza_confirmed_7_day_sum": -999999
+      }
+      response = Epidata.covid_hosp_facility(
+          '450822', Epidata.range(20200101, 20210101))
+      self.assertEqual(response['result'], 1)
+      self.assertEqual(len(response['epidata']), 2)
+      row = response['epidata'][0]
+      for k,v in expected_spotchecks.items():
+        self.assertTrue(
+          k in row,
+          f"no '{k}' in row:\n{NEWLINE.join(sorted(row.keys()))}"
+        )
+        if isinstance(v, float):
+          self.assertAlmostEqual(row[k], v, f"row[{k}] is {row[k]} not {v}")
+        else:
+          self.assertEqual(row[k], v, f"row[{k}] is {row[k]} not {v}")
+
+      # expect 113 fields per row (114 database columns, except `id`)
+      self.assertEqual(len(row), 113)
+
+    # 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']), 2)
+
+

integrations/server/test_rvdss.py

@@ -0,0 +1,152 @@
+# first party
+from delphi.epidata.common.integration_test_base_class import DelphiTestBase
+
+
+class rvdssTest(DelphiTestBase):
+    """Basic integration tests for rvdss endpoint."""
+
+    def localSetUp(self):
+        self.truncate_tables_list = ["rvdss_repiratory_detections",
+                                     "rvdss_pct_positive",
+                                     "rvdss_detections_counts"]
+
+    def test_rvdss_repiratory_detections(self):
+        """Basic integration test for rvdss_repiratory_detections endpoint"""
+        self.cur.execute(
+            "INSERT INTO `rvdss_repiratory_detections`(`epiweek`, `time_value`, `issue`, `geo_type`, `geo_value`, `sarscov2_tests`, `sarscov2_positive_tests`, `flu_tests`, `flu_positive_tests`, `fluah1n1pdm09_positive_tests`, `fluah3_positive_tests`, `fluauns_positive_tests`, `flua_positive_tests`, `flub_positive_tests`, `rsv_tests`, `rsv_positive_tests`, `hpiv_tests`, `hpiv1_positive_tests`, `hpiv2_positive_tests`, `hpiv3_positive_tests`, `hpiv4_positive_tests`, `hpivother_positive_tests`, `adv_tests`, `adv_positive_tests`, `hmpv_tests`, `hmpv_positive_tests`, `evrv_tests`, `evrv_positive_tests`, `hcov_tests`, `hcov_positive_tests`, `week`, `weekorder`, `year`) VALUES(%(epiweek)s, %(time_value)s, %(issue)s, %(geo_type)s, %(geo_value)s, %(sarscov2_tests)s, %(sarscov2_positive_tests)s, %(flu_tests)s, %(flu_positive_tests)s, %(fluah1n1pdm09_positive_tests)s, %(fluah3_positive_tests)s, %(fluauns_positive_tests)s, %(flua_positive_tests)s, %(flub_positive_tests)s, %(rsv_tests)s, %(rsv_positive_tests)s, %(hpiv_tests)s, %(hpiv1_positive_tests)s, %(hpiv2_positive_tests)s, %(hpiv3_positive_tests)s, %(hpiv4_positive_tests)s, %(hpivother_positive_tests)s, %(adv_tests)s, %(adv_positive_tests)s, %(hmpv_tests)s, %(hmpv_positive_tests)s, %(evrv_tests)s, %(evrv_positive_tests)s, %(hcov_tests)s, %(hcov_positive_tests)s, %(week)s, %(weekorder)s, %(year)s)",
+            ("201212", "2012-04-12", "2012-04-17", "region","on", "10", "1", "9", "1", "0", "0", "2", "3", "1", "8", "2", "7", "1", "1", "1", "1","1", "6", "5", "100", "13", "92", "9", "167", "52", "12", "34", "2012"),
+        )
+        self.cnx.commit()
+        response = self.epidata_client.rvdss_repiratory_detections(epiweeks=201212, geo_value="on")
+        self.assertEqual(
+            response,
+            {
+                "epidata": [
+                    {'epiweek':201212,
+                     'time_value':"2012-04-12",
+                     'issue':"2012-04-17",
+                     'geo_type':"region",
+                     'geo_value':"on",
+                     'sarscov2_tests':10,
+                     'sarscov2_positive_tests':1,
+                     'flu_tests':9,
+                     'flu_positive_tests':1,
+                     'fluah1n1pdm09_positive_tests':0,
+                     'fluah3_positive_tests':0,
+                     'fluauns_positive_tests':2,
+                     'flua_positive_tests':3,
+                     'flub_positive_tests':1,
+                     'rsv_tests':8,
+                     'rsv_positive_tests':2,
+                     'hpiv_tests':8,
+                     'hpiv1_positive_tests':1,
+                     'hpiv2_positive_tests':1,
+                     'hpiv3_positive_tests':1,
+                     'hpiv4_positive_tests':1,
+                     'hpivother_positive_tests':1,
+                     'adv_tests':6,
+                     'adv_positive_tests':5,
+                     'hmpv_tests':100,
+                     'hmpv_positive_tests':13,
+                     'evrv_tests':92,
+                     'evrv_positive_tests':9,
+                     'hcov_tests':167,
+                     'hcov_positive_tests':52,
+                     'week':12,
+                     'weekorder':34,
+                     'year':2012
+                    }
+                ],
+                "result": 1,
+                "message": "success",
+            },
+        )
+
+    def test_rvdss_pct_positive(self):
+        """Basic integration test for rvdss_pct_positive endpoint"""
+        self.cur.execute(
+            "INSERT INTO rvdss_pct_positive (`epiweek`, `time_value`, `issue`, `geo_type`, `geo_value`, `evrv_pct_positive`, `evrv_tests`, `evrv_positive_tests`, `hpiv_pct_positive`, `hpiv_tests`, `hpiv_positive_tests`, `adv_pct_positive`, `adv_tests`, `adv_positive_tests`,`hcov_pct_positive`, `hcov_tests`, `hcov_positive_tests`, `flua_pct_positive`, `flub_pct_positive`, `flu_tests`, `flua_positive_tests`, `flua_tests`, `flub_tests`, `flub_positive_tests`, `flu_positive_tests`, `flu_pct_positive`, `hmpv_pct_positive`, `hmpv_tests`, `hmpv_positive_tests`, `rsv_pct_positive`, `rsv_tests`, `rsv_positive_tests`, `sarscov2_pct_positive`, `sarscov2_tests`, `sarscov2_positive_tests`, `region`, `week`, `weekorder`, `year`) VALUES (%(epiweek)s, %(time_value)s, %(issue)s, %(geo_type)s, %(geo_value)s, %(evrv_pct_positive)s, %(evrv_tests)s, %(evrv_positive_tests)s, %(hpiv_pct_positive)s, %(hpiv_tests)s, %(hpiv_positive_tests)s, %(adv_pct_positive)s, %(adv_tests)s, %(hcov_pct_positive)s, %(hcov_tests)s, %(hcov_positive_tests)s, %(flua_pct_positive)s, %(flub_pct_positive)s, %(flu_tests)s, %(flua_positive_tests)s, %(flua_tests)s, %(flub_tests)s, %(flub_positive_tests)s, %(flu_positive_tests)s, %(flu_pct_positive)s, %(hmpv_pct_positive)s, %(hmpv_tests)s, %(hmpv_positive_tests)s, %(rsv_pct_positive)s, %(rsv_tests)s, %(rsv_positive_tests)s, %(sarscov2_pct_positive)s, %(sarscov2_tests)s, %(sarscov2_positive_tests)s, %(region)s, %(week)s, %(weekorder)s, %(year)s)",
+            ("201212", "2012-04-12", "2012-04-17", "region","on","0.1","10","1","0.1","10","1","0.1","10","1","0.1","10","1","0.05","0.05","100", "10", "100","100", "10", "20", "0.1","0.1","10","1","0.1","10","1","0.1","10","1","on","12","34","2012")
+        )
+        self.cnx.commit()
+        response = self.epidata_client.rvdss_pct_positive(epiweeks=201212, geo_value="on")
+        self.assertEqual(
+            response,
+            {
+                "epidata": [
+                    {'epiweek':201212,
+                     'time_value':"2012-04-12",
+                     'issue':"2012-04-17",
+                     'geo_type':"region",
+                     'geo_value':"on",
+                     'evrv_pct_positive':0.1,
+                     'evrv_tests':10,
+                     'evrv_positive_tests':1,
+                     'hpiv_pct_positive':0.1,
+                     'hpiv_tests':10,
+                     'hpiv_positive_tests':1,
+                     'adv_pct_positive':0.1,
+                     'adv_tests':10,
+                     'adv_positive_tests':1,
+                     'hcov_pct_positive':0.1,
+                     'hcov_tests':10,
+                     'hcov_positive_tests':1,
+                     'flua_pct_positive':0.05,
+                     'flub_pct_positive':0.05,
+                     'flu_tests':100,
+                     'flua_positive_tests':10,
+                     'flua_tests':100,
+                     'flub_tests':100,
+                     'flub_positive_tests':10,
+                     'flu_positive_tests':20,
+                     'flu_pct_positive':0.1,
+                     'hmpv_pct_positive':0.1,
+                     'hmpv_tests':10,
+                     'hmpv_positive_tests':1,
+                     'rsv_pct_positive':0.1,
+                     'rsv_tests':10,
+                     'rsv_positive_tests':1,
+                     'sarscov2_pct_positive':0.1,
+                     'sarscov2_tests':10,
+                     'sarscov2_positive_tests':1,
+                     'region':"on",
+                     'week':12,
+                     'weekorder':34,
+                     'year':2012
+                    }
+                ],
+                "result": 1,
+                "message": "success",
+            },
+        )
+
+    def test_rvdss_detections_counts(self):
+        """Basic integration test for rvdss_detections_counts endpoint"""
+        self.cur.execute(
+            "INSERT INTO rvdss_detections_counts (`epiweek`, `time_value`, `issue`, `geo_type`, `geo_value`, `hpiv_positive_tests`, `adv_positive_tests`, `hmpv_positive_tests`, `evrv_positive_tests`, `hcov_positive_tests`, `rsv_positive_tests`, `flu_positive_tests`) VALUES (%(epiweek)s, %(time_value)s, %(issue)s, %(geo_type)s, %(geo_value)s, %(hpiv_positive_tests)s, %(adv_positive_tests)s, %(hmpv_positive_tests)s, %(evrv_positive_tests)s, %(hcov_positive_tests)s, %(rsv_positive_tests)s, %(flu_positive_tests)s)",
+            ("201212", "2012-04-12", "2012-04-17", "nation","ca", "10", "9", "8", "7", "6", "5", "4"),
+        )
+        self.cnx.commit()
+        response = self.epidata_client.rvdss_detections_counts(epiweeks=201212, geo_value="ca")
+        self.assertEqual(
+            response,
+            {
+                "epidata": [
+                    {'epiweek':201212,
+                     'time_value':"2012-04-12",
+                     'issue':"2012-04-17",
+                     'geo_type':"nation",
+                     'geo_value':"ca",
+                     'hpiv_positive_tests':10,
+                     'adv_positive_tests':9,
+                     'hmpv_positive_tests':8,
+                     'evrv_positive_tests':7,
+                     'hcov_positive_tests':6,
+                     'rsv_positive_tests':5,
+                     'flu_positive_tests':4
+                    }
+                ],
+                "result": 1,
+                "message": "success",
+            },
+        )

requirements.api.txt

@@ -10,11 +10,13 @@ pandas==1.2.3
 python-dotenv==0.15.0
 pyyaml
 redis==3.5.3
+regex
 requests==2.32.0
 scipy==1.10.0
 sentry-sdk[flask]
 SQLAlchemy==1.4.40
 structlog==22.1.0
 tenacity==7.0.0
 typing-extensions
+unidecode
 werkzeug==2.3.8

requirements.dev.txt

@@ -19,3 +19,6 @@ selenium==4.7.2
 sqlalchemy-stubs>=0.3
 tenacity==7.0.0
 xlrd==2.0.1
+bs4
+mock
+requests_file