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CHNG pipeline fix #1858

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Merged
merged 5 commits into from
Jun 15, 2023
Merged

CHNG pipeline fix #1858

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8c4454b
changes to fix typeerror and temporary geo issue
Jun 15, 2023
6fce061
TypeError fixes and temporary handling for geos
Jun 15, 2023
00d03db
fix failing lint
Jun 15, 2023
0c9d0a0
add docstring to fix failing lint
Jun 15, 2023
fb90c24
Drop pdb
krivard Jun 15, 2023
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14 changes: 12 additions & 2 deletions changehc/delphi_changehc/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,16 @@ def make_asserts(params):
assert (files["denom"] is None) == (files["flu"] is None), \
"exactly one of denom and flu files are provided"

def process_dates(params, startdate_dt, enddate_dt):
"""Process the start and end dates for indicator."""
enddate = params["indicator"].get("end_date")
if enddate is None:
enddate = str(enddate_dt.date())
startdate = params["indicator"].get("start_date", str(startdate_dt.date()))
if startdate is None:
startdate = str(startdate_dt.date())
return startdate, enddate


def run_module(params: Dict[str, Dict[str, Any]]):
"""
Expand Down Expand Up @@ -144,8 +154,8 @@ def run_module(params: Dict[str, Dict[str, Any]]):
enddate_dt = dropdate_dt - timedelta(days=n_waiting_days)
startdate_dt = enddate_dt - timedelta(days=n_backfill_days)
# now allow manual overrides
enddate = enddate = params["indicator"].get("end_date",str(enddate_dt.date()))
startdate = params["indicator"].get("start_date", str(startdate_dt.date()))

startdate, enddate = process_dates(params, startdate_dt, enddate_dt)

logger.info("generating signal and exporting to CSV",
first_sensor_date = startdate,
Expand Down
5 changes: 4 additions & 1 deletion changehc/delphi_changehc/update_sensor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,6 +160,8 @@ def geo_reindex(self, data):
thr_col="den",
mega_col=geo,
date_col=Config.DATE_COL)
# this line should be removed once the fix is implemented for megacounties
data_frame = data_frame[~((data_frame['county'].str.len() > 5) | (data_frame['county'].str.contains('_')))]
elif geo == "state":
data_frame = gmpr.replace_geocode(data, "fips", "state_id", new_col="state",
date_col=Config.DATE_COL)
Expand All @@ -172,7 +174,8 @@ def geo_reindex(self, data):
multiindex = pd.MultiIndex.from_product((unique_geo_ids, self.fit_dates),
names=[geo, Config.DATE_COL])
assert (len(multiindex) <= (len(gmpr.get_geo_values(gmpr.as_mapper_name(geo))) * len(self.fit_dates))
), "more loc-date pairs than maximum number of geographies x number of dates"
), f"more loc-date pairs than maximum number of geographies x number of dates, length of multiindex is {len(multiindex)}, geo level is {geo}"

# fill dataframe with missing dates using 0
data_frame = data_frame.reindex(multiindex, fill_value=0)
data_frame.fillna(0, inplace=True)
Expand Down