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Add flu hospitalizations to hhs_hosp #1341

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Merged
merged 2 commits into from
Oct 27, 2021
Merged

Add flu hospitalizations to hhs_hosp #1341

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90f63a4
Add flu hospitalizations
krivard Oct 26, 2021
8a1ef20
Update tests with flu hospitalizations
krivard Oct 26, 2021
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6 changes: 5 additions & 1 deletion hhs_hosp/delphi_hhs/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,16 @@
SUM_CONF_SUSP = "sum_confirmed_suspected_admissions_covid_1d"
CONFIRMED_PROP = "confirmed_admissions_covid_1d_prop"
SUM_CONF_SUSP_PROP = "sum_confirmed_suspected_admissions_covid_1d_prop"
CONFIRMED_FLU = "confirmed_admissions_influenza_1d"
CONFIRMED_FLU_PROP = CONFIRMED_FLU+"_prop"

SIGNALS = [
CONFIRMED,
SUM_CONF_SUSP,
CONFIRMED_PROP,
SUM_CONF_SUSP_PROP
SUM_CONF_SUSP_PROP,
CONFIRMED_FLU,
CONFIRMED_FLU_PROP
]

GEOS = [
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9 changes: 8 additions & 1 deletion hhs_hosp/delphi_hhs/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
import numpy as np
import pandas as pd

from .constants import SIGNALS, GEOS, SMOOTHERS, CONFIRMED, SUM_CONF_SUSP
from .constants import SIGNALS, GEOS, SMOOTHERS, CONFIRMED, SUM_CONF_SUSP, CONFIRMED_FLU

def _date_to_int(d):
"""Return a date object as a yyyymmdd int."""
Expand Down Expand Up @@ -190,6 +190,13 @@ def make_signal(all_columns, sig):
all_columns.previous_day_admission_pediatric_covid_confirmed + \
all_columns.previous_day_admission_pediatric_covid_suspected,
})
elif sig.startswith(CONFIRMED_FLU):
df = pd.DataFrame({
"state": all_columns.state.apply(str.lower),
"timestamp":int_date_to_previous_day_datetime(all_columns.date),
"val": \
all_columns.previous_day_admission_influenza_confirmed
})
else:
raise Exception(
"Bad programmer: signal '{sig}' in SIGNALS but not handled in make_signal"
Expand Down
1,087 changes: 1,086 additions & 1 deletion hhs_hosp/tests/test_response.json
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17 changes: 14 additions & 3 deletions hhs_hosp/tests/test_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@

from delphi_hhs.run import _date_to_int, int_date_to_previous_day_datetime, generate_date_ranges, \
make_signal, make_geo, run_module, pop_proportion
from delphi_hhs.constants import CONFIRMED, SUM_CONF_SUSP, SMOOTHERS, GEOS, SIGNALS, CONFIRMED_PROP, SUM_CONF_SUSP_PROP
from delphi_hhs.constants import SMOOTHERS, GEOS, SIGNALS, \
CONFIRMED, SUM_CONF_SUSP, CONFIRMED_FLU, CONFIRMED_PROP, SUM_CONF_SUSP_PROP, CONFIRMED_FLU_PROP
from delphi_utils.geomap import GeoMapper
from freezegun import freeze_time
import numpy as np
Expand Down Expand Up @@ -57,7 +58,8 @@ def test_make_signal():
'previous_day_admission_adult_covid_confirmed': [1],
'previous_day_admission_adult_covid_suspected': [2],
'previous_day_admission_pediatric_covid_confirmed': [4],
'previous_day_admission_pediatric_covid_suspected': [8]
'previous_day_admission_pediatric_covid_suspected': [8],
'previous_day_admission_influenza_confirmed': [16]
})

expected_confirmed = pd.DataFrame({
Expand All @@ -76,6 +78,14 @@ def test_make_signal():
pd.testing.assert_frame_equal(expected_sum, make_signal(data, SUM_CONF_SUSP))
pd.testing.assert_frame_equal(expected_sum, make_signal(data, SUM_CONF_SUSP_PROP))

expected_flu = pd.DataFrame({
'state': ['na'],
'timestamp': [datetime(year=2020, month=1, day=1)],
'val': [16.],
})
pd.testing.assert_frame_equal(expected_flu, make_signal(data, CONFIRMED_FLU))
pd.testing.assert_frame_equal(expected_flu, make_signal(data, CONFIRMED_FLU_PROP))

with pytest.raises(Exception):
make_signal(data, "zig")

Expand Down Expand Up @@ -184,7 +194,8 @@ def test_ignore_last_range_no_results(mock_covid_hosp, mock_export):
"previous_day_admission_adult_covid_confirmed": [0],
"previous_day_admission_adult_covid_suspected": [0],
"previous_day_admission_pediatric_covid_confirmed": [0],
"previous_day_admission_pediatric_covid_suspected": [0]
"previous_day_admission_pediatric_covid_suspected": [0],
"previous_day_admission_influenza_confirmed": [0]
}
},
{"result": -2, "message": "no results"}
Expand Down