Merge pull request #1309 from cmu-delphi/release/delphi-epidata-4.1.11

Release Delphi Epidata 4.1.11

Author: melange396

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.10
+current_version = 4.1.11
 commit = False
 tag = False
 

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.10
+version = 4.1.11
 
 [options]
 packages =

docs/new_endpoint_tutorial.md

@@ -123,11 +123,9 @@ Here's what we add to each client:
     def fluview_meta():
       """Fetch FluView metadata."""
       # Set up request
-      params = {
-        'endpoint': 'fluview_meta',
-      }
+      params = {}
       # Make the API call
-      return Epidata._request(params)
+      return Epidata._request("fluview_meta", params)
     ```
 
 - [`delphi_epidata.R`](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R)

docs/symptom-survey/publications.md

@@ -26,6 +26,10 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*:
 
 Research publications using the survey data include:
 
+- Ma, M.Z., Chen, S.X. (2023). [Beyond the surface: accounting for confounders
+  in understanding the link between collectivism and COVID-19 pandemic in the
+  United States](https://doi.org/10.1186/s12889-023-16384-2). *BMC Public
+  Health* 23, 1513.
 - C.K. Ettman, E. Badillo Goicoechea, and E.A. Stuart (2023). [Evolution of
   depression and anxiety over the COVID-19 pandemic and across demographic
   groups in a large sample of U.S. adults](https://doi.org/10.1016/j.focus.2023.100140).
@@ -62,7 +66,7 @@ Research publications using the survey data include:
 - Rönn MM, Menzies NA, Salomon JA (2023). [Vaccination and voting patterns in
   the United States: analysis of COVID-19 and flu surveys from 2010 to
   2022](https://doi.org/10.1016/j.amepre.2023.03.001). *American Journal of
-  Preventive Medicine.*
+  Preventive Medicine* 65 (3), 458-466.
 - Taube JC, Susswein Z, Bansal S (2023). [Spatiotemporal Trends in Self-Reported
   Mask-Wearing Behavior in the United States: Analysis of a Large
   Cross-sectional Survey](https://doi.org/10.2196/42128). *JMIR Public Health

integrations/acquisition/covid_hosp/facility/test_scenarios.py

@@ -28,7 +28,7 @@ def setUp(self):
     self.test_utils = UnitTestUtils(__file__)
 
     # use the local instance of the Epidata API
-    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata'
     Epidata.auth = ('epidata', 'key')
 
     # use the local instance of the epidata database

integrations/acquisition/covid_hosp/state_daily/test_scenarios.py

@@ -32,7 +32,7 @@ def setUp(self):
     self.test_utils = UnitTestUtils(__file__)
 
     # use the local instance of the Epidata API
-    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata'
     Epidata.auth = ('epidata', 'key')
 
     # use the local instance of the epidata database

integrations/acquisition/covid_hosp/state_timeseries/test_scenarios.py

@@ -28,7 +28,7 @@ def setUp(self):
     self.test_utils = UnitTestUtils(__file__)
 
     # use the local instance of the Epidata API
-    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata'
     Epidata.auth = ('epidata', 'key')
 
     # use the local instance of the epidata database

integrations/acquisition/covidcast/test_covidcast_meta_caching.py

@@ -22,7 +22,7 @@
 )
 
 # use the local instance of the Epidata API
-BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+BASE_URL = 'http://delphi_web_epidata/epidata'
 
 
 class CovidcastMetaCacheTests(unittest.TestCase):
@@ -82,8 +82,8 @@ def tearDown(self):
 
   @staticmethod
   def _make_request():
-    params = {'endpoint': 'covidcast_meta', 'cached': 'true'}
-    response = requests.get(Epidata.BASE_URL, params=params, auth=Epidata.auth)
+    params = {'cached': 'true'}
+    response = requests.get(f"{Epidata.BASE_URL}/covidcast_meta", params=params, auth=Epidata.auth)
     response.raise_for_status()
     return response.json()
 

integrations/acquisition/covidcast/test_csv_uploading.py

@@ -69,7 +69,7 @@ def setUp(self):
     epidata_cnx.close()
 
     # use the local instance of the Epidata API
-    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata'
     Epidata.auth = ('epidata', 'key')
 
   def tearDown(self):
@@ -132,7 +132,7 @@ def test_uploading(self):
       main(args)
       response = Epidata.covidcast('src-name', signal_name, 'day', 'state', 20200419, '*')
 
-      expected_values = pd.concat([values, pd.DataFrame({ "time_value": [20200419] * 3, "signal": [signal_name] * 3, "direction": [None] * 3})], axis=1).rename(columns=uploader_column_rename).to_dict(orient="records")
+      expected_values = pd.concat([values, pd.DataFrame({ "geo_type": "state", "source": "src-name", "time_type": "day", "time_value": [20200419] * 3, "signal": [signal_name] * 3, "direction": [None] * 3})], axis=1).rename(columns=uploader_column_rename).to_dict(orient="records")
       expected_response = {'result': 1, 'epidata': self.apply_lag(expected_values), 'message': 'success'}
 
       self.assertEqual(response, expected_response)
@@ -161,6 +161,9 @@ def test_uploading(self):
       response = Epidata.covidcast('src-name', signal_name, 'day', 'state', 20200419, '*')
 
       expected_values = pd.concat([values, pd.DataFrame({
+        "geo_type": "state",
+        "source": "src-name",
+        "time_type": "day",
         "time_value": [20200419] * 3,
         "signal": [signal_name] * 3,
         "direction": [None] * 3,
@@ -194,7 +197,7 @@ def test_uploading(self):
       main(args)
       response = Epidata.covidcast('src-name', signal_name, 'day', 'state', 20200419, '*')
 
-      expected_response = {'result': -2, 'message': 'no results'}
+      expected_response = {'epidata': [], 'result': -2, 'message': 'no results'}
 
       self.assertEqual(response, expected_response)
       self.verify_timestamps_and_defaults()
@@ -220,6 +223,9 @@ def test_uploading(self):
       response = Epidata.covidcast('src-name', signal_name, 'day', 'state', 20200419, '*')
 
       expected_values_df = pd.concat([values, pd.DataFrame({
+        "geo_type": "state",
+        "source": "src-name",
+        "time_type": "day", 
         "time_value": [20200419],
         "signal": [signal_name],
         "direction": [None]})], axis=1).rename(columns=uploader_column_rename)
@@ -253,6 +259,9 @@ def test_uploading(self):
       response = Epidata.covidcast('src-name', signal_name, 'day', 'state', 20200419, '*')
 
       expected_values = pd.concat([values, pd.DataFrame({
+        "geo_type": "state",
+        "source": "src-name",
+        "time_type": "day", 
         "time_value": [20200419],
         "signal": [signal_name],
         "direction": [None]
@@ -283,7 +292,7 @@ def test_uploading(self):
       main(args)
       response = Epidata.covidcast('src-name', signal_name, 'day', 'state', 20200419, '*')
 
-      expected_response = {'result': -2, 'message': 'no results'}
+      expected_response = {'epidata': [], 'result': -2, 'message': 'no results'}
 
       self.assertEqual(response, expected_response)
       self.verify_timestamps_and_defaults()

integrations/acquisition/covidcast_nowcast/test_csv_uploading.py

@@ -55,7 +55,7 @@ def setUp(self):
     secrets.db.epi = ('user', 'pass')
 
     # use the local instance of the Epidata API
-    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
+    Epidata.BASE_URL = 'http://delphi_web_epidata/epidata'
     Epidata.auth = ('epidata', 'key')
 
   def tearDown(self):