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Merged
merged 4 commits into from
Jan 22, 2025
Merged

clean state column #2105

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6a0c43c
in progress
aysim319 Jan 20, 2025
4350c5a
filtering also on hhs and check in test
aysim319 Jan 21, 2025
9f2d9ee
regenerated test data to update current behavior
aysim319 Jan 21, 2025
2020c27
lint
aysim319 Jan 21, 2025
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5 changes: 4 additions & 1 deletion nhsn/delphi_nhsn/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,14 +73,17 @@ def run_module(params, logger=None):
df = df[df["geo_id"] == "us"]
elif geo == "hhs":
df = df[df["geo_id"] != "us"]
df = df[df["geo_id"].str.len() == 2]
df.rename(columns={"geo_id": "state_id"}, inplace=True)
df = geo_mapper.add_geocode(df, "state_id", "state_code", from_col="state_id")
df = geo_mapper.add_geocode(df, "state_code", "hhs", from_col="state_code", new_col="hhs")
df = geo_mapper.replace_geocode(
df, from_col="state_code", from_code="state_code", new_col="geo_id", new_code="hhs"
)
else:
elif geo == "state":
df = df[df_pull["geo_id"] != "us"]
df = df[df["geo_id"].str.len() == 2] # hhs region is a value in geo_id column

df["se"] = np.nan
df["sample_size"] = np.nan
dates = create_export_csv(
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Binary file modified nhsn/tests/test_data/20241212.csv.gz
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118 changes: 118 additions & 0 deletions nhsn/tests/test_data/page.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2122,5 +2122,123 @@
"pctconfc19icubedsperchos": "-0.0002",
"pctconffluicubedsperchos": "-0.012",
"pctconfrsvicubedsperchos": "0.0"
},
{
"weekendingdate": "2021-10-16T00:00:00.000",
"jurisdiction": "region 1",
"numinptbeds": "729772.05",
"numinptbedsadult": "660758.41",
"numinptbedsped": "53387.68",
"numinptbedsocc": "556817.29",
"numinptbedsoccadult": "510524.46",
"numinptbedsoccped": "35679.97",
"numicubeds": "114471.4",
"numicubedsadult": "86925.11",
"numicubedsped": "21902.45",
"numicubedsocc": "85344.84",
"numicubedsoccadult": "66877.69",
"numicubedsoccped": "14657.22",
"numconfc19hosppatsadult": "55448.05",
"numconfc19hosppatsped": "847.15",
"totalconfc19hosppats": "56295.2",
"totalconffluhosppats": "259.85",
"numconfc19icupatsadult": "18104.6",
"totalconfc19icupats": "18104.6",
"totalconffluicupats": "39.33",
"totalconfc19newadmped": "1301.0",
"numconfc19newadmadult18to49": "11532.0",
"totalconfc19newadmadult": "44677.0",
"numconfc19newadmunk": "1982.0",
"totalconfc19newadm": "45978.0",
"totalconfflunewadm": "266.0",
"pctinptbedsocc": "0.763",
"pctconfc19inptbeds": "0.0771",
"pctconffluinptbeds": "0.0004",
"pcticubedsocc": "0.7456",
"pctconfc19icubeds": "0.1582",
"pctconffluicubeds": "0.0003",
"pctconfc19newadmadult": "0.9717",
"pctconfc19newadmped": "0.0283",
"numinptbedshosprep": "5396",
"numinptbedsocchosprep": "5396",
"numicubedshosprep": "5396",
"numicubedsocchosprep": "5396",
"totalconfc19hosppatshosprep": "5396",
"totalconffluhosppatshosprep": "4317",
"totalconfrsvhosppatshosprep": "0",
"totalconfc19icupatshosprep": "5396",
"totalconffluicupatshosprep": "4306",
"totalconfrsvicupatshosprep": "0",
"totalconfc19newadmpedhosprep": "5278",
"totalconfc19newadmadulthosprep": "5394",
"totalconfc19newadmhosprep": "5394",
"totalconfflunewadmpedhosprep": "0",
"totalconfflunewadmadulthosprep": "0",
"totalconfflunewadmhosprep": "4307",
"totalconfrsvnewadmpedhosprep": "0",
"totalconfrsvnewadmadulthosprep": "0",
"totalconfrsvnewadmhosprep": "0",
"pctinptbedsocchosprep": "5396",
"pcticubedsocchosprep": "5396",
"pctconfc19inptbedshosprep": "5396",
"pctconffluinptbedshosprep": "4317",
"pctconfrsvinptbedshosprep": "0",
"pctconfc19icubedshosprep": "5396",
"pctconffluicubedshosprep": "4306",
"pctconfrsvicubedshosprep": "0",
"numinptbedsperchosprep": "0.9492",
"numinptbedsoccperchosprep": "0.9492",
"numicubedsperchosprep": "0.9492",
"numicubedsoccperchosprep": "0.9492",
"totalconfc19hosppatsperc": "0.9492",
"totalconffluhosppatsperc": "0.7594",
"totalconfrsvhosppatsperc": "0.0",
"totalconfc19icupatsperchosprep": "0.9492",
"totalconffluicupatsperchosprep": "0.7574",
"totalconfrsvicupatsperchosprep": "0.0",
"totalconfc19newadmpedper": "0.9284",
"totalconfc19newadmadultp": "0.9488",
"totalconfc19newadmperchosprep": "94.88",
"totalconfflunewadmpedper": "0.0",
"totalconfflunewadmadultp": "0.0",
"totalconfflunewadmperchosprep": "75.76",
"totalconfrsvnewadmpedper": "0.0",
"totalconfrsvnewadmadultp": "0.0",
"totalconfrsvnewadmperchosprep": "0.0",
"pctinptbedsoccperchosprep": "0.9492",
"pcticubedsoccperchosprep": "0.9492",
"pctconfc19inptbedsperchosprep": "0.9492",
"pctconffluinptbedsperchosprep": "0.7594",
"pctconfrsvinptbedsperchosprep": "0.0",
"pctconfc19icubedsperchosprep": "0.9492",
"pctconffluicubedsperchosprep": "0.7574",
"pctconfrsvicubedsperchosprep": "0.0",
"numinptbedsperchosprepabschg": "-0.07",
"numinptbedsoccperchospre": "-0.07",
"numicubedsperchosprepabschg": "-0.07",
"numicubedsoccperchosprepabschg": "-0.07",
"totalconfc19hosppatsperc_1": "-0.02",
"totalconffluhosppatsperc_1": "-1.23",
"totalconfrsvhosppatsperc_1": "0.0",
"totalconfc19icupatsperch": "-0.02",
"totalconffluicupatsperch": "-1.2",
"totalconfrsvicupatsperch": "0.0",
"totalconfc19newadmpedper_1": "-0.04",
"totalconfc19newadmadultp_1": "-0.04",
"totalconfc19newadmpercho": "-0.04",
"totalconfflunewadmpedper_1": "0.0",
"totalconfflunewadmadultp_1": "0.0",
"totalconfflunewadmpercho": "-1.27",
"totalconfrsvnewadmpedper_1": "0.0",
"totalconfrsvnewadmadultp_1": "0.0",
"totalconfrsvnewadmpercho": "0.0",
"pctinptbedsoccperchospre": "-0.0007",
"pcticubedsoccperchosprepabschg": "-0.0007",
"pctconfc19inptbedspercho": "-0.0002",
"pctconffluinptbedspercho": "-0.0123",
"pctconfrsvinptbedspercho": "0.0",
"pctconfc19icubedsperchos": "-0.0002",
"pctconffluicubedsperchos": "-0.012",
"pctconfrsvicubedsperchos": "0.0"
}
]
3 changes: 3 additions & 0 deletions nhsn/tests/test_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,9 @@ def test_output_files_exist(self, params, run_as_module):
"geo_id", "val", "se", "sample_size",
]
assert (df.columns.values == expected_columns).all()
if geo == "state":
states = list(df["geo_id"].values)
assert all(len(state) == 2 for state in states)

for file in Path(export_dir).glob("*.csv"):
os.remove(file)
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