clean up and fix tests

Author: aysim319

nhsn/delphi_nhsn/run.py

@@ -63,11 +63,11 @@ def run_module(params, logger=None):
     geo_mapper = GeoMapper()
     signal_df_dict = dict()
     if not nhsn_df.empty:
-        signal_df_dict.update({signal: nhsn_df for signal in SIGNALS_MAP if signal in nhsn_df.columns})
+        signal_df_dict.update({signal: nhsn_df for signal in SIGNALS_MAP})
     # some of the source backups do not include for preliminary data
     if not preliminary_nhsn_df.empty:
         signal_df_dict.update(
-            {signal: preliminary_nhsn_df for signal in PRELIM_SIGNALS_MAP if signal in preliminary_nhsn_df.columns}
+            {signal: preliminary_nhsn_df for signal in PRELIM_SIGNALS_MAP}
         )
 
     for geo, signals_df in product(GEOS, signal_df_dict.items()):
@@ -94,6 +94,7 @@ def run_module(params, logger=None):
 
             df["se"] = np.nan
             df["sample_size"] = np.nan
+
             dates = create_export_csv(
                 df,
                 geo_res=geo,

nhsn/tests/test_data/20241212.csv.gz

@@ -273,125 +273,166 @@
     "pctconfc19icubedsperchos": "0.0",
     "pctconffluicubedsperchos": "0.0",
     "pctconfrsvicubedsperchos": "0.0"
-  },
-  {
-    "weekendingdate": "2021-08-21T00:00:00.000",
-    "jurisdiction": "USA",
-    "numinptbeds": "750150.99",
-    "numinptbedsadult": "679540.51",
-    "numinptbedsped": "51335.02",
-    "numinptbedsocc": "572345.09",
-    "numinptbedsoccadult": "526399.17",
-    "numinptbedsoccped": "32810.36",
-    "numicubeds": "120768.79",
-    "numicubedsadult": "91030.4",
-    "numicubedsped": "21419.35",
-    "numicubedsocc": "89853.28",
-    "numicubedsoccadult": "70595.31",
-    "numicubedsoccped": "14112.02",
-    "numconfc19hosppatsadult": "92782.24",
-    "numconfc19hosppatsped": "1268.64",
-    "totalconfc19hosppats": "94050.88",
-    "totalconffluhosppats": "292.67",
-    "numconfc19icupatsadult": "24692.91",
-    "totalconfc19icupats": "24692.91",
-    "totalconffluicupats": "45.57",
-    "totalconfc19newadmped": "2170.0",
-    "numconfc19newadmadult18to49": "27365.0",
-    "totalconfc19newadmadult": "90776.0",
-    "numconfc19newadmunk": "4827.0",
-    "totalconfc19newadm": "92946.0",
-    "totalconfflunewadm": "280.0",
-    "pctinptbedsocc": "0.763",
-    "pctconfc19inptbeds": "0.1254",
-    "pctconffluinptbeds": "0.0004",
-    "pcticubedsocc": "0.744",
-    "pctconfc19icubeds": "0.2045",
-    "pctconffluicubeds": "0.0004",
-    "pctconfc19newadmadult": "0.9767",
-    "pctconfc19newadmped": "0.0233",
-    "numinptbedshosprep": "5396",
-    "numinptbedsocchosprep": "5396",
-    "numicubedshosprep": "5396",
-    "numicubedsocchosprep": "5396",
-    "totalconfc19hosppatshosprep": "5393",
-    "totalconffluhosppatshosprep": "4417",
-    "totalconfrsvhosppatshosprep": "0",
-    "totalconfc19icupatshosprep": "5393",
-    "totalconffluicupatshosprep": "4415",
-    "totalconfrsvicupatshosprep": "0",
-    "totalconfc19newadmpedhosprep": "5276",
-    "totalconfc19newadmadulthosprep": "5392",
-    "totalconfc19newadmhosprep": "5392",
-    "totalconfflunewadmpedhosprep": "0",
-    "totalconfflunewadmadulthosprep": "0",
-    "totalconfflunewadmhosprep": "4415",
-    "totalconfrsvnewadmpedhosprep": "0",
-    "totalconfrsvnewadmadulthosprep": "0",
-    "totalconfrsvnewadmhosprep": "0",
-    "pctinptbedsocchosprep": "5396",
-    "pcticubedsocchosprep": "5396",
-    "pctconfc19inptbedshosprep": "5393",
-    "pctconffluinptbedshosprep": "4417",
-    "pctconfrsvinptbedshosprep": "0",
-    "pctconfc19icubedshosprep": "5393",
-    "pctconffluicubedshosprep": "4415",
-    "pctconfrsvicubedshosprep": "0",
-    "numinptbedsperchosprep": "0.9492",
-    "numinptbedsoccperchosprep": "0.9492",
-    "numicubedsperchosprep": "0.9492",
-    "numicubedsoccperchosprep": "0.9492",
-    "totalconfc19hosppatsperc": "0.9486",
-    "totalconffluhosppatsperc": "0.777",
-    "totalconfrsvhosppatsperc": "0.0",
-    "totalconfc19icupatsperchosprep": "0.9486",
-    "totalconffluicupatsperchosprep": "0.7766",
-    "totalconfrsvicupatsperchosprep": "0.0",
-    "totalconfc19newadmpedper": "0.9281",
-    "totalconfc19newadmadultp": "0.9485",
-    "totalconfc19newadmperchosprep": "94.85",
-    "totalconfflunewadmpedper": "0.0",
-    "totalconfflunewadmadultp": "0.0",
-    "totalconfflunewadmperchosprep": "77.66",
-    "totalconfrsvnewadmpedper": "0.0",
-    "totalconfrsvnewadmadultp": "0.0",
-    "totalconfrsvnewadmperchosprep": "0.0",
-    "pctinptbedsoccperchosprep": "0.9492",
-    "pcticubedsoccperchosprep": "0.9492",
-    "pctconfc19inptbedsperchosprep": "0.9486",
-    "pctconffluinptbedsperchosprep": "0.777",
-    "pctconfrsvinptbedsperchosprep": "0.0",
-    "pctconfc19icubedsperchosprep": "0.9486",
-    "pctconffluicubedsperchosprep": "0.7766",
-    "pctconfrsvicubedsperchosprep": "0.0",
-    "numinptbedsperchosprepabschg": "0.07",
-    "numinptbedsoccperchospre": "0.07",
-    "numicubedsperchosprepabschg": "0.07",
-    "numicubedsoccperchosprepabschg": "0.07",
-    "totalconfc19hosppatsperc_1": "0.07",
-    "totalconffluhosppatsperc_1": "0.14",
-    "totalconfrsvhosppatsperc_1": "0.0",
-    "totalconfc19icupatsperch": "0.07",
-    "totalconffluicupatsperch": "0.19",
-    "totalconfrsvicupatsperch": "0.0",
-    "totalconfc19newadmpedper_1": "0.07",
-    "totalconfc19newadmadultp_1": "0.07",
-    "totalconfc19newadmpercho": "0.07",
-    "totalconfflunewadmpedper_1": "0.0",
-    "totalconfflunewadmadultp_1": "0.0",
-    "totalconfflunewadmpercho": "0.16",
-    "totalconfrsvnewadmpedper_1": "0.0",
-    "totalconfrsvnewadmadultp_1": "0.0",
-    "totalconfrsvnewadmpercho": "0.0",
-    "pctinptbedsoccperchospre": "0.0007",
-    "pcticubedsoccperchosprepabschg": "0.0007",
-    "pctconfc19inptbedspercho": "0.0007",
-    "pctconffluinptbedspercho": "0.0014",
-    "pctconfrsvinptbedspercho": "0.0",
-    "pctconfc19icubedsperchos": "0.0007",
-    "pctconffluicubedsperchos": "0.0019",
-    "pctconfrsvicubedsperchos": "0.0"
-  },
+  },{
+      "weekendingdate": "2021-08-21T00:00:00.000",
+        "jurisdiction": "USA",
+        "numinptbeds": "691631.77",
+        "numinptbedsadult": "626133.24",
+        "numinptbedsped": "37667.52",
+        "numinptbedsocc": "525785.42",
+        "numinptbedsoccadult": "479767.94",
+        "numinptbedsoccped": "26370.0",
+        "numicubeds": "98235.73",
+        "numicubedsadult": "76084.07",
+        "numicubedsped": "8987.7",
+        "numicubedsocc": "69971.29",
+        "numicubedsoccadult": "55500.93",
+        "numicubedsoccped": "6279.0",
+        "numconfc19hosppatsadult": "8413.3",
+        "numconfc19hosppatsped": "392.43",
+        "totalconfc19hosppats": "8805.73",
+        "numconffluhosppatsadult": "131.21",
+        "numconffluhosppatsped": "21.74",
+        "totalconffluhosppats": "4869.7",
+        "numconfrsvhosppatsadult": "55.84",
+        "numconfrsvhosppatsped": "17.13",
+        "totalconfrsvhosppats": "72.96",
+        "numconfc19icupatsadult": "1209.86",
+        "numconfc19icupatsped": "81.13",
+        "totalconfc19icupats": "1290.99",
+        "numconffluicupatsadult": "12.76",
+        "numconffluicupatsped": "3.0",
+        "totalconffluicupats": "812.94",
+        "numconfrsvicupatsadult": "4.86",
+        "numconfrsvicupatsped": "2.14",
+        "totalconfrsvicupats": "7.0",
+        "numconfc19newadmped0to4": "277.0",
+        "numconfc19newadmped5to17": "190.0",
+        "totalconfc19newadmped": "533.0",
+        "numconfc19newadmadult18to49": "1260.0",
+        "totalconfc19newadmadult": "9851.0",
+        "numconfc19newadmunk": "337.0",
+        "totalconfc19newadm": "10384.0",
+        "totalconfflunewadmped": "19.0",
+        "totalconfflunewadmadult": "140.0",
+        "totalconfflunewadm": "6049.0",
+        "totalconfrsvnewadmped": "35.0",
+        "totalconfrsvnewadmadult": "49.0",
+        "totalconfrsvnewadm": "84.0",
+        "pctinptbedsocc": "0.7602",
+        "pctconfc19inptbeds": "0.0127",
+        "pctconffluinptbeds": "0.007",
+        "pctconfrsvinptbeds": "0.0001",
+        "pcticubedsocc": "0.7123",
+        "pctconfc19icubeds": "0.0131",
+        "pctconffluicubeds": "0.0083",
+        "pctconfrsvicubeds": "0.0001",
+        "pctconfc19newadmadult": "0.9487",
+        "pctconfc19newadmped": "0.0513",
+        "pctconfflunewadmadult": "0.0231",
+        "pctconfflunewadmped": "0.0031",
+        "pctconfrsvnewadmadult": "0.5833",
+        "pctconfrsvnewadmped": "0.4167",
+        "numinptbedshosprep": "5426",
+        "numinptbedsocchosprep": "5426",
+        "numicubedshosprep": "5426",
+        "numicubedsocchosprep": "5426",
+        "totalconfc19hosppatshosprep": "5426",
+        "totalconffluhosppatshosprep": "5426",
+        "totalconfrsvhosppatshosprep": "470",
+        "totalconfc19icupatshosprep": "5426",
+        "totalconffluicupatshosprep": "5426",
+        "totalconfrsvicupatshosprep": "469",
+        "totalconfc19newadmpedhosprep": "5304",
+        "totalconfc19newadmadulthosprep": "5426",
+        "totalconfc19newadmhosprep": "5426",
+        "totalconfflunewadmpedhosprep": "287",
+        "totalconfflunewadmadulthosprep": "292",
+        "totalconfflunewadmhosprep": "5426",
+        "totalconfrsvnewadmpedhosprep": "465",
+        "totalconfrsvnewadmadulthosprep": "467",
+        "totalconfrsvnewadmhosprep": "469",
+        "pctinptbedsocchosprep": "5426",
+        "pcticubedsocchosprep": "5426",
+        "pctconfc19inptbedshosprep": "5426",
+        "pctconffluinptbedshosprep": "5426",
+        "pctconfrsvinptbedshosprep": "470",
+        "pctconfc19icubedshosprep": "5426",
+        "pctconffluicubedshosprep": "5426",
+        "pctconfrsvicubedshosprep": "469",
+        "numinptbedsperchosprep": "0.9489",
+        "numinptbedsoccperchosprep": "0.9489",
+        "numicubedsperchosprep": "0.9489",
+        "numicubedsoccperchosprep": "0.9489",
+        "totalconfc19hosppatsperc": "0.9489",
+        "totalconffluhosppatsperc": "0.9489",
+        "totalconfrsvhosppatsperc": "0.0822",
+        "totalconfc19icupatsperchosprep": "0.9489",
+        "totalconffluicupatsperchosprep": "0.9489",
+        "totalconfrsvicupatsperchosprep": "0.082",
+        "totalconfc19newadmpedper": "0.9276",
+        "totalconfc19newadmadultp": "0.9489",
+        "totalconfc19newadmperchosprep": "0.9489",
+        "totalconfflunewadmpedper": "0.0502",
+        "totalconfflunewadmadultp": "0.0511",
+        "totalconfflunewadmperchosprep": "0.9489",
+        "totalconfrsvnewadmpedper": "0.0813",
+        "totalconfrsvnewadmadultp": "0.0817",
+        "totalconfrsvnewadmperchosprep": "0.082",
+        "pctinptbedsoccperchosprep": "0.9489",
+        "pcticubedsoccperchosprep": "0.9489",
+        "pctconfc19inptbedsperchosprep": "0.9489",
+        "pctconffluinptbedsperchosprep": "0.9489",
+        "pctconfrsvinptbedsperchosprep": "0.0822",
+        "pctconfc19icubedsperchosprep": "0.9489",
+        "pctconffluicubedsperchosprep": "0.9489",
+        "pctconfrsvicubedsperchosprep": "0.082",
+        "numinptbedsperchosprepabschg": "-0.0014",
+        "numinptbedsoccperchospre": "-0.0014",
+        "numicubedsperchosprepabschg": "-0.0014",
+        "numicubedsoccperchosprepabschg": "-0.0014",
+        "totalconfc19hosppatsperc_1": "-0.0014",
+        "totalconffluhosppatsperc_1": "-0.0014",
+        "totalconfrsvhosppatsperc_1": "0.0003",
+        "totalconfc19icupatsperch": "-0.0014",
+        "totalconffluicupatsperch": "-0.0014",
+        "totalconfrsvicupatsperch": "0.0002",
+        "totalconfc19newadmpedper_1": "-0.0012",
+        "totalconfc19newadmadultp_1": "-0.0014",
+        "totalconfc19newadmpercho": "-0.0014",
+        "totalconfflunewadmpedper_1": "0.0",
+        "totalconfflunewadmadultp_1": "0.0003",
+        "totalconfflunewadmpercho": "-0.0014",
+        "totalconfrsvnewadmpedper_1": "0.0002",
+        "totalconfrsvnewadmadultp_1": "0.0",
+        "totalconfrsvnewadmpercho": "0.0",
+        "pctinptbedsoccperchospre": "-0.0014",
+        "pcticubedsoccperchosprepabschg": "-0.0014",
+        "pctconfc19inptbedspercho": "-0.0014",
+        "pctconffluinptbedspercho": "-0.0014",
+        "pctconfrsvinptbedspercho": "0.0003",
+        "pctconfc19icubedsperchos": "-0.0014",
+        "pctconffluicubedsperchos": "-0.0014",
+        "pctconfrsvicubedsperchos": "0.0002",
+        "numconfc19newadmped0to4per100k": "1.49",
+        "numconfc19newadmped5to17per100k": "0.35",
+        "totalconfc19newadmpedper100k": "0.73",
+        "numconfc19newadmadult18to49per100k": "0.9",
+        "totalconfc19newadmadultper100k": "3.73",
+        "totalconfc19newadmper100k": "3.08",
+        "totalconfflunewadmpedper100k": "0.03",
+        "totalconfflunewadmadultper100k": "0.05",
+        "totalconfflunewadmper100k": "1.79",
+        "totalconfrsvnewadmpedper100k": "0.05",
+        "totalconfrsvnewadmadultper100k": "0.02",
+        "totalconfrsvnewadmper100k": "0.02",
+        "totalconfc19newadmperchosprepabove80pct": "1",
+        "totalconfc19newadmperchosprepabove90pct": "1",
+        "totalconfflunewadmperchosprepabove80pct": "1",
+        "totalconfflunewadmperchosprepabove90pct": "1",
+        "totalconfrsvnewadmperchosprepabove80pct": "0",
+        "totalconfrsvnewadmperchosprepabove90pct": "0"
+    },
   {
     "weekendingdate": "2021-08-28T00:00:00.000",
     "jurisdiction": "CO",