Fix JHU bug that renamed fips to county in receiving

* change valid geo_res
* change GEO_RESOLUTIOSN in run.py
* update tests to use "county"

Author: dshemetov

jhu/delphi_jhu/geo.py

@@ -27,12 +27,12 @@ def geo_map(df: pd.DataFrame, geo_res: str):
         Columns: geo_id, timestamp, ...
     """
     df = df.copy()
-    VALID_GEO_RES = ("fips", "state", "msa", "hrr")
+    VALID_GEO_RES = ("county", "state", "msa", "hrr")
     if geo_res not in VALID_GEO_RES:
         raise ValueError(f"geo_res must be one of {VALID_GEO_RES}")
 
     gmpr = GeoMapper()
-    if geo_res == "fips":
+    if geo_res == "county":
         df.rename(columns={'fips': 'geo_id'}, inplace=True)
     elif geo_res == "state":
         df = gmpr.replace_geocode(df, "fips", "state_id", new_col="geo_id", date_col="timestamp")

jhu/delphi_jhu/run.py

@@ -59,7 +59,7 @@
     "seven_day_average":    (seven_day_moving_average, '7dav_'),
 }
 GEO_RESOLUTIONS = [
-    "fips",
+    "county",
     "state",
     "msa",
     "hrr",

jhu/tests/test_geo.py

@@ -45,7 +45,7 @@ def test_fips(self):
 
         df = df.append(df_mega)
 
-        new_df = geo_map(df, "fips")
+        new_df = geo_map(df, "county")
 
         exp_incidence = df["new_counts"] / df["population"] * 100000
         exp_cprop = df["cumulative_counts"] / df["population"] * 100000