first implimentation of rsv

nhsn/delphi_nhsn/constants.py

@@ -8,29 +8,36 @@
 # column name from socrata
 TOTAL_ADMISSION_COVID_COL = "totalconfc19newadm"
 TOTAL_ADMISSION_FLU_COL = "totalconfflunewadm"
+TOTAL_ADMISSION_RSV_COL = "totalconfrsvnewadm"
 NUM_HOSP_REPORTING_COVID_COL = "totalconfc19newadmhosprep"
 NUM_HOSP_REPORTING_FLU_COL = "totalconfflunewadmhosprep"
-
+NUM_HOSP_REPORTING_RSV_COL = "totalconfrsvnewadmhosprep"
 # signal name
 TOTAL_ADMISSION_COVID = "confirmed_admissions_covid_ew"
 TOTAL_ADMISSION_FLU = "confirmed_admissions_flu_ew"
+TOTAL_ADMISSION_RSV = "confirmed_admissions_rsv_ew"
 NUM_HOSP_REPORTING_COVID = "hosprep_confirmed_admissions_covid_ew"
 NUM_HOSP_REPORTING_FLU = "hosprep_confirmed_admissions_flu_ew"
+NUM_HOSP_REPORTING_RSV = "hosprep_confirmed_admissions_rsv_ew"
 
 SIGNALS_MAP = {
     TOTAL_ADMISSION_COVID: TOTAL_ADMISSION_COVID_COL,
     TOTAL_ADMISSION_FLU: TOTAL_ADMISSION_FLU_COL,
+    TOTAL_ADMISSION_RSV: TOTAL_ADMISSION_RSV_COL,
     NUM_HOSP_REPORTING_COVID: NUM_HOSP_REPORTING_COVID_COL,
     NUM_HOSP_REPORTING_FLU: NUM_HOSP_REPORTING_FLU_COL,
+    NUM_HOSP_REPORTING_RSV: NUM_HOSP_REPORTING_RSV_COL,
 }
 
 TYPE_DICT = {
     "timestamp": "datetime64[ns]",
     "geo_id": str,
     TOTAL_ADMISSION_COVID: float,
     TOTAL_ADMISSION_FLU: float,
+    TOTAL_ADMISSION_RSV: float,
     NUM_HOSP_REPORTING_COVID: float,
     NUM_HOSP_REPORTING_FLU: float,
+    NUM_HOSP_REPORTING_RSV: float,
 }
 
 # signal mapping for secondary, preliminary source
@@ -39,15 +46,19 @@
 PRELIM_SIGNALS_MAP = {
     f"{TOTAL_ADMISSION_COVID}_prelim": TOTAL_ADMISSION_COVID_COL,
     f"{TOTAL_ADMISSION_FLU}_prelim": TOTAL_ADMISSION_FLU_COL,
+    f"{TOTAL_ADMISSION_RSV}_prelim": TOTAL_ADMISSION_RSV_COL,
     f"{NUM_HOSP_REPORTING_COVID}_prelim": NUM_HOSP_REPORTING_COVID_COL,
     f"{NUM_HOSP_REPORTING_FLU}_prelim": NUM_HOSP_REPORTING_FLU_COL,
+    f"{NUM_HOSP_REPORTING_RSV}_prelim": NUM_HOSP_REPORTING_RSV_COL,
 }
 
 PRELIM_TYPE_DICT = {
     "timestamp": "datetime64[ns]",
     "geo_id": str,
     f"{TOTAL_ADMISSION_COVID}_prelim": float,
     f"{TOTAL_ADMISSION_FLU}_prelim": float,
+    f"{TOTAL_ADMISSION_RSV}_prelim": float,
     f"{NUM_HOSP_REPORTING_COVID}_prelim": float,
     f"{NUM_HOSP_REPORTING_FLU}_prelim": float,
+    f"{NUM_HOSP_REPORTING_RSV}_prelim": float,
 }

nhsn/delphi_nhsn/pull.py

@@ -58,7 +58,10 @@ def check_last_updated(socrata_token, dataset_id, logger):
 def pull_data(socrata_token: str, dataset_id: str, backup_dir: str, logger):
     """Pull data from Socrata API."""
     client = Socrata("data.cdc.gov", socrata_token)
-    logger.info("Pulling data from Socrata API")
+    logger.info(
+        f"Pulling {'main' if dataset_id == MAIN_DATASET_ID else 'preliminary'} data from Socrata API",
+        dataset_id=dataset_id,
+    )
     results = []
     offset = 0
     limit = 50000  # maximum limit allowed by SODA 2.0

nhsn/delphi_nhsn/run.py

@@ -92,6 +92,7 @@ def run_module(params, logger=None):
 
             df["se"] = np.nan
             df["sample_size"] = np.nan
+
             dates = create_export_csv(
                 df,
                 geo_res=geo,