disability weight location processing bugfix #354
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hussain-jafari
requested review from
albrja,
collijk,
patricktnast,
rmudambi and
stevebachmeier
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hussain-jafari
commented
Jul 16, 2024
src/vivarium_inputs/extract.py
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| "key", axis=1 | ||
| ) | ||
| data = pd.merge( | ||
| data.drop("year_id", axis=1, errors="ignore"), year_df, on="key" |
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Here I'm just adding errors='ignore' so we don't error out if year_id isn't in data (we usually expect it not to be after looking at the disability weight flat file, but I'm just being safe and dropping it if it is present).
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Ignoring errors is pretty scary. I think it would be a lot better to do a simple check for this column before merging so you don't inadvertently cover up a different error caused by a data schema issue.
hussain-jafari
commented
Jul 16, 2024
| disability_weights.healthstate_id == entity.healthstate.gbd_id, : | ||
| ] | ||
| # Update location_id to match original location id |
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We already do this in gbd access - Zeb was seeing duplicates in our data from these lines
rmudambi
approved these changes
Jul 16, 2024
albrja
approved these changes
Jul 16, 2024
hussain-jafari
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bugfix/MIC-5171_disability_weights_loc_processing
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disability weight location processing bugfix
Description=
Changes and notes
Don't duplicate data for locations since this is already done in gbd access.
Only drop year_id column if it is present in data.
Testing
Pulled disability weight for diarrheal diseases with no year specified, for 2021, for 2019 and 2021, and for all years.