fixed bug, module runs

Author: jsharpna

emr_hosp/delphi_emr_hosp/sensor.py

@@ -110,9 +110,6 @@ def fit(y_data, first_sensor_date, geo_id, num_col="num", den_col="den"):
             dictionary of results
 
         """
-        # values to keep
-        fitting_idxs = np.where(y_data.index >= first_sensor_date)[0] # JS: WILL CHANGE
-
         # backfill
         total_counts, total_visits = EMRHospSensor.backfill(y_data[num_col].values, y_data[den_col].values)
         # total_counts = pd.Series(total_counts.flatten(), name=num_col, index=y_data.index)

emr_hosp/delphi_emr_hosp/update_sensor.py

@@ -93,6 +93,7 @@ def __init__(self,
                 ), f"not enough data to produce estimates starting {self.startdate}"
         assert self.startdate < self.enddate, "start date >= end date"
         assert self.enddate <= self.dropdate, "end date > drop date"
+        assert geo in ['county', 'state', 'msa', 'hrr'], f"{geo} is invalid, pick one of 'county', 'state', 'msa', 'hrr'"
         self.geo, self.parallel, self.weekday = geo, parallel, weekday
 
 
@@ -162,9 +163,9 @@ def update_sensor(self,
 
         self.shift_dates()
         final_sensor_idxs = (self.burn_in_dates >= self.startdate) & (self.burn_in_dates <= self.enddate)
-        ## JS: THIS IS FINE
 
         # load data
+        ## JS: If the data is in fips then can we also put it into hrr?
         base_geo = "hrr" if self.geo == "hrr" else "fips"
         data = load_combined_data(emr_filepath, claims_filepath, self.dropdate, base_geo)
 
@@ -180,7 +181,6 @@ def update_sensor(self,
         if not self.parallel:
             for geo_id, sub_data in data_frame.groupby(level=0):
                 sub_data.reset_index(level=0,inplace=True)
-                del sub_data[base_geo]
 
                 if self.weekday:
                     sub_data = Weekday.calc_adjustment(wd_params, sub_data)
@@ -199,7 +199,6 @@ def update_sensor(self,
                 pool_results = []
                 for geo_id, sub_data in data_frame.groupby(level=0,as_index=False):
                     sub_data.reset_index(level=0, inplace=True)
-                    del sub_data[base_geo]
                     if self.weekday:
                         sub_data = Weekday.calc_adjustment(wd_params, sub_data)
 
@@ -222,7 +221,7 @@ def update_sensor(self,
             "rates": sensor_rates,
             "se": sensor_se,
             "dates": self.sensor_dates,
-            "geo_ids": self.unique_geo_ids,
+            "geo_ids": unique_geo_ids,
             "geo_level": self.geo,
             "include": sensor_include,
         }

emr_hosp/tests/test_update_sensor.py

@@ -69,23 +69,23 @@ def test_geo_reindex(self):
         assert (data_frame.sum() == (4200,19000)).all()
 
     def test_update_sensor(self):
-        td = TemporaryDirectory()
-        su_inst = EMRHospSensorUpdator(
-            "02-01-2020",
-            "06-01-2020",
-            "06-12-2020",
-            'hrr',
-            self.parallel,
-            self.weekday)
-        su_inst.update_sensor(
-            EMR_FILEPATH,
-            CLAIMS_FILEPATH,
-            td.name,
-            PARAMS["static_file_dir"]
-        )
-        assert len(os.listdir(td.name)) == len(su_inst.sensor_dates)
-        ## JS: ADD MORE TESTS HERE
-        td.cleanup()
+        for geo in ["state","hrr"]:
+            td = TemporaryDirectory()
+            su_inst = EMRHospSensorUpdator(
+                "02-01-2020",
+                "06-01-2020",
+                "06-12-2020",
+                geo,
+                self.parallel,
+                self.weekday)
+            su_inst.update_sensor(
+                EMR_FILEPATH,
+                CLAIMS_FILEPATH,
+                td.name,
+                PARAMS["static_file_dir"]
+            )
+            assert len(os.listdir(td.name)) == len(su_inst.sensor_dates), f"failed {geo} update sensor test"
+            td.cleanup()
 
 class TestWriteToCsv:
     def test_write_to_csv_results(self):