diff --git a/cdc_covidnet/delphi_cdc_covidnet/update_sensor.py b/cdc_covidnet/delphi_cdc_covidnet/update_sensor.py index a434f1e40..50414c73d 100644 --- a/cdc_covidnet/delphi_cdc_covidnet/update_sensor.py +++ b/cdc_covidnet/delphi_cdc_covidnet/update_sensor.py @@ -92,7 +92,7 @@ def update_sensor( new_code="state_id", dropna=False) # To use the original column name, reassign original column and drop new one - hosp_df[APIConfig.STATE_COL] = hosp_df["state_id"].str.upper() + hosp_df[APIConfig.STATE_COL] = hosp_df["state_id"] hosp_df.drop("state_id", axis=1, inplace=True) assert not hosp_df.duplicated(["date", "geo_id"]).any(), "Non-unique (date, geo_id) pairs" hosp_df.set_index(["date", "geo_id"], inplace=True) @@ -105,7 +105,6 @@ def update_sensor( signals = add_prefix(SIGNALS, wip_signal=read_params()["wip_signal"], prefix="wip_") for signal in signals: write_to_csv(hosp_df, signal, output_path) - return hosp_df diff --git a/cdc_covidnet/tests/receiving_test/202010_state_wip_covidnet.csv b/cdc_covidnet/tests/receiving_test/202010_state_wip_covidnet.csv index 9e73eb600..c978738ad 100644 --- a/cdc_covidnet/tests/receiving_test/202010_state_wip_covidnet.csv +++ b/cdc_covidnet/tests/receiving_test/202010_state_wip_covidnet.csv @@ -1,15 +1,15 @@ geo_id,val,se,sample_size -CA,0.2,NA,NA -CO,0.1,NA,NA -CT,0.1,NA,NA -GA,0.5,NA,NA -MD,0.1,NA,NA -MN,0.0,NA,NA -NM,0.0,NA,NA -NY,0.1,NA,NA -OR,0.1,NA,NA -TN,0.1,NA,NA -IA,0.0,NA,NA -MI,0.1,NA,NA -OH,0.0,NA,NA -UT,0.0,NA,NA +ca,0.2,NA,NA +co,0.1,NA,NA +ct,0.1,NA,NA +ga,0.5,NA,NA +md,0.1,NA,NA +mn,0.0,NA,NA +nm,0.0,NA,NA +ny,0.1,NA,NA +or,0.1,NA,NA +tn,0.1,NA,NA +ia,0.0,NA,NA +mi,0.1,NA,NA +oh,0.0,NA,NA +ut,0.0,NA,NA diff --git a/cdc_covidnet/tests/receiving_test/202011_state_wip_covidnet.csv b/cdc_covidnet/tests/receiving_test/202011_state_wip_covidnet.csv index b5eeac60f..366d951ee 100644 --- a/cdc_covidnet/tests/receiving_test/202011_state_wip_covidnet.csv +++ b/cdc_covidnet/tests/receiving_test/202011_state_wip_covidnet.csv @@ -1,15 +1,15 @@ geo_id,val,se,sample_size -CA,1.0,NA,NA -CO,0.8,NA,NA -CT,1.0,NA,NA -GA,2.7,NA,NA -MD,0.4,NA,NA -MN,0.1,NA,NA -NM,0.2,NA,NA -NY,0.7,NA,NA -OR,0.5,NA,NA -TN,0.7,NA,NA -IA,0.0,NA,NA -MI,0.2,NA,NA -OH,0.3,NA,NA -UT,0.2,NA,NA +ca,1.0,NA,NA +co,0.8,NA,NA +ct,1.0,NA,NA +ga,2.7,NA,NA +md,0.4,NA,NA +mn,0.1,NA,NA +nm,0.2,NA,NA +ny,0.7,NA,NA +or,0.5,NA,NA +tn,0.7,NA,NA +ia,0.0,NA,NA +mi,0.2,NA,NA +oh,0.3,NA,NA +ut,0.2,NA,NA diff --git a/cdc_covidnet/tests/test_update_sensor.py b/cdc_covidnet/tests/test_update_sensor.py index fe9499e23..e85d48d53 100644 --- a/cdc_covidnet/tests/test_update_sensor.py +++ b/cdc_covidnet/tests/test_update_sensor.py @@ -76,17 +76,16 @@ def test_syn_update_sensor(self): # Generate the csvs hosp_df = update_sensor(state_files, mmwr_info, temp_dir, start_date, end_date) - # Check dataframe returned assert hosp_df.index.nlevels == 2 assert set(hosp_df.index.names) == {"date", "geo_id"} - assert set(hosp_df.index.get_level_values("geo_id")) == {"CA", "PA"} + assert set(hosp_df.index.get_level_values("geo_id")) == {"ca", "pa"} assert set(hosp_df.index.get_level_values("date")) == \ {datetime(2020, 3, 7), datetime(2020, 3, 14)} assert set(hosp_df["epiweek"].unique()) == {10, 11} geo_index = hosp_df.index.get_level_values("geo_id") - assert np.allclose(hosp_df.loc[geo_index == "CA", "val"], [2.5, 3.5]) - assert np.allclose(hosp_df.loc[geo_index == "PA", "val"], [10.3, 11.2]) + assert np.allclose(hosp_df.loc[geo_index == "ca", "val"], [2.5, 3.5]) + assert np.allclose(hosp_df.loc[geo_index == "pa", "val"], [10.3, 11.2]) assert pd.isna(hosp_df["se"]).all() assert pd.isna(hosp_df["sample_size"]).all() @@ -108,7 +107,7 @@ def test_syn_update_sensor(self): assert pd.isna(data["sample_size"]).all() # Check values are right - assert set(data["geo_id"].unique()) == {"CA", "PA"} + assert set(data["geo_id"].unique()) == {"ca", "pa"} assert np.allclose( data["val"], [ state_1["datadownload"][i]["cumulative-rate"],