Merge pull request #1341 from cmu-delphi/krivard/hhs-flu

Add flu hospitalizations to hhs_hosp

Author: krivard

hhs_hosp/delphi_hhs/constants.py

@@ -5,12 +5,16 @@
 SUM_CONF_SUSP = "sum_confirmed_suspected_admissions_covid_1d"
 CONFIRMED_PROP = "confirmed_admissions_covid_1d_prop"
 SUM_CONF_SUSP_PROP = "sum_confirmed_suspected_admissions_covid_1d_prop"
+CONFIRMED_FLU = "confirmed_admissions_influenza_1d"
+CONFIRMED_FLU_PROP = CONFIRMED_FLU+"_prop"
 
 SIGNALS = [
     CONFIRMED,
     SUM_CONF_SUSP,
     CONFIRMED_PROP,
-    SUM_CONF_SUSP_PROP
+    SUM_CONF_SUSP_PROP,
+    CONFIRMED_FLU,
+    CONFIRMED_FLU_PROP
 ]
 
 GEOS = [

hhs_hosp/delphi_hhs/run.py

@@ -15,7 +15,7 @@
 import numpy as np
 import pandas as pd
 
-from .constants import SIGNALS, GEOS, SMOOTHERS, CONFIRMED, SUM_CONF_SUSP
+from .constants import SIGNALS, GEOS, SMOOTHERS, CONFIRMED, SUM_CONF_SUSP, CONFIRMED_FLU
 
 def _date_to_int(d):
     """Return a date object as a yyyymmdd int."""
@@ -190,6 +190,13 @@ def make_signal(all_columns, sig):
             all_columns.previous_day_admission_pediatric_covid_confirmed + \
             all_columns.previous_day_admission_pediatric_covid_suspected,
         })
+    elif sig.startswith(CONFIRMED_FLU):
+        df = pd.DataFrame({
+            "state": all_columns.state.apply(str.lower),
+            "timestamp":int_date_to_previous_day_datetime(all_columns.date),
+            "val": \
+            all_columns.previous_day_admission_influenza_confirmed
+        })
     else:
         raise Exception(
             "Bad programmer: signal '{sig}' in SIGNALS but not handled in make_signal"

hhs_hosp/tests/test_response.json

@@ -6,7 +6,8 @@
 
 from delphi_hhs.run import _date_to_int, int_date_to_previous_day_datetime, generate_date_ranges, \
     make_signal, make_geo, run_module, pop_proportion
-from delphi_hhs.constants import CONFIRMED, SUM_CONF_SUSP, SMOOTHERS, GEOS, SIGNALS, CONFIRMED_PROP, SUM_CONF_SUSP_PROP
+from delphi_hhs.constants import SMOOTHERS, GEOS, SIGNALS, \
+    CONFIRMED, SUM_CONF_SUSP, CONFIRMED_FLU, CONFIRMED_PROP, SUM_CONF_SUSP_PROP, CONFIRMED_FLU_PROP
 from delphi_utils.geomap import GeoMapper
 from freezegun import freeze_time
 import numpy as np
@@ -57,7 +58,8 @@ def test_make_signal():
         'previous_day_admission_adult_covid_confirmed': [1],
         'previous_day_admission_adult_covid_suspected': [2],
         'previous_day_admission_pediatric_covid_confirmed': [4],
-        'previous_day_admission_pediatric_covid_suspected': [8]
+        'previous_day_admission_pediatric_covid_suspected': [8],
+        'previous_day_admission_influenza_confirmed': [16]
     })
 
     expected_confirmed = pd.DataFrame({
@@ -76,6 +78,14 @@ def test_make_signal():
     pd.testing.assert_frame_equal(expected_sum, make_signal(data, SUM_CONF_SUSP))
     pd.testing.assert_frame_equal(expected_sum, make_signal(data, SUM_CONF_SUSP_PROP))
 
+    expected_flu = pd.DataFrame({
+        'state': ['na'],
+        'timestamp': [datetime(year=2020, month=1, day=1)],
+        'val': [16.],
+    })
+    pd.testing.assert_frame_equal(expected_flu, make_signal(data, CONFIRMED_FLU))
+    pd.testing.assert_frame_equal(expected_flu, make_signal(data, CONFIRMED_FLU_PROP))
+    
     with pytest.raises(Exception):
         make_signal(data, "zig")
 
@@ -184,7 +194,8 @@ def test_ignore_last_range_no_results(mock_covid_hosp, mock_export):
               "previous_day_admission_adult_covid_confirmed": [0],
               "previous_day_admission_adult_covid_suspected": [0],
               "previous_day_admission_pediatric_covid_confirmed": [0],
-              "previous_day_admission_pediatric_covid_suspected": [0]
+              "previous_day_admission_pediatric_covid_suspected": [0],
+              "previous_day_admission_influenza_confirmed": [0]
               }
          },
         {"result": -2, "message": "no results"}