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Support chng-fips county group reporting in chng for privacy #1883

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d852db5
turn sircal alerts back on for all chng signals
nmdefries Aug 4, 2023
af20af7
support county groups
nmdefries Aug 4, 2023
e0d12ad
swap county out for chng-fips in template params
nmdefries Aug 4, 2023
04ab8b5
prevent sircal from alerting about missing county signals
nmdefries Aug 4, 2023
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2 changes: 1 addition & 1 deletion ansible/templates/changehc-params-prod.json.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
"n_waiting_days": 3,
"se": false,
"parallel": false,
"geos": ["state", "msa", "hrr", "county", "hhs", "nation"],
"geos": ["state", "msa", "hrr", "chng-fips", "hhs", "nation"],
"weekday": [true, false],
"types": ["covid","cli","flu"],
"wip_signal": "",
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9 changes: 8 additions & 1 deletion ansible/templates/sir_complainsalot-params-prod.json.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,14 @@
"chng": {
"max_age": 6,
"maintainers": ["U01AP8GSWG3","U01069KCRS7"],
"retired-signals": ["smoothed_outpatient_covid", "smoothed_adj_outpatient_covid", "smoothed_outpatient_cli", "smoothed_adj_outpatient_cli"]
"retired-signals": [
["smoothed_outpatient_covid", "county"],
["smoothed_adj_outpatient_covid", "county"],
["smoothed_outpatient_cli", "county"],
["smoothed_adj_outpatient_cli", "county"],
["smoothed_outpatient_flu", "county"],
["smoothed_adj_outpatient_flu", "county"]
]
},
"google-symptoms": {
"max_age": 6,
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21 changes: 14 additions & 7 deletions changehc/delphi_changehc/update_sensor.py
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Expand Up @@ -91,7 +91,7 @@ def __init__(self,
startdate: first sensor date (YYYY-mm-dd)
enddate: last sensor date (YYYY-mm-dd)
dropdate: data drop date (YYYY-mm-dd)
geo: geographic resolution, one of ["county", "state", "msa", "hrr", "hhs", "nation"]
geo: geographic resolution, one of ["county", "chng-fips", "state", "msa", "hrr", "hhs", "nation"]
parallel: boolean to run the sensor update in parallel
weekday: boolean to adjust for weekday effects
numtype: type of count data used, one of ["covid", "cli"]
Expand Down Expand Up @@ -149,19 +149,26 @@ def geo_reindex(self, data):
# get right geography
geo = self.geo
gmpr = GeoMapper()
if geo not in {"county", "state", "msa", "hrr", "nation", "hhs"}:
self.logger.error("{0} is invalid, pick one of 'county', "
if geo not in {"county", "chng-fips", "state", "msa", "hrr", "nation", "hhs"}:
self.logger.error("{0} is invalid, pick one of 'county', 'chng-fips', "
"'state', 'msa', 'hrr', 'hss','nation'".format(geo))
return False
if geo == "county":
data_frame = gmpr.fips_to_megacounty(data,
if geo == "county" or geo == "chng-fips":
if geo == "chng-fips":
data_frame = gmpr.replace_geocode(data, "fips", geo, new_col="chng-fips-raw", date_col=Config.DATE_COL)
fips_col = "chng-fips-raw"
else:
data_frame = data
fips_col = "fips"
data_frame = gmpr.fips_to_megacounty(data_frame,
Config.MIN_DEN,
Config.MAX_BACKFILL_WINDOW,
thr_col="den",
mega_col=geo,
date_col=Config.DATE_COL)
date_col=Config.DATE_COL,
fips_col=fips_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('_')))]
data_frame = data_frame[~((data_frame[geo].str.len() > 5) | (data_frame[geo].str.contains('_')))]
elif geo == "state":
data_frame = gmpr.replace_geocode(data, "fips", "state_id", new_col="state",
date_col=Config.DATE_COL)
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4 changes: 2 additions & 2 deletions changehc/params.json.template
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@
"n_waiting_days": 3,
"se": false,
"parallel": false,
"geos": ["state", "msa", "hrr", "county", "nation", "hhs"],
"geos": ["state", "msa", "hrr", "chng-fips", "nation", "hhs"],
"weekday": [true, false],
"types": ["covid","cli"],
"types": ["covid","cli", "flu"],
"wip_signal": "",
"ftp_conn": {
"host": "",
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10 changes: 9 additions & 1 deletion sir_complainsalot/params.json.template
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,15 @@
},
"chng": {
"max_age": 6,
"maintainers": ["U01AP8GSWG3","U01069KCRS7"]
"maintainers": ["U01AP8GSWG3","U01069KCRS7"],
"retired-signals": [
["smoothed_outpatient_covid", "county"],
["smoothed_adj_outpatient_covid", "county"],
["smoothed_outpatient_cli", "county"],
["smoothed_adj_outpatient_cli", "county"],
["smoothed_outpatient_flu", "county"],
["smoothed_adj_outpatient_flu", "county"]
]
},
"google-symptoms": {
"max_age": 6,
Expand Down