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[GEN-1892] redeact pediatric YEAR_CONTACT and YEAR_DEATH #611

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Merged
danlu1 merged 5 commits into from
Sep 17, 2025
Merged

[GEN-1892] redeact pediatric YEAR_CONTACT and YEAR_DEATH #611

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redeact pediatric YEAR_CONTACT and YEAR_DEATH
danlu1 Sep 17, 2025
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add test case for _redact_ped_year
danlu1 Sep 17, 2025
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20 changes: 20 additions & 0 deletions genie/database_to_staging.py
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Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,22 @@ def _redact_year(df_col):
return df_col


def _redact_ped_year(df_col):
"""Redacts year values that have <

Args:
df_col: Dataframe column/pandas.Series of a year column

Returns:
pandas.Series: Redacted series

"""
year = df_col.astype(str)
contain_lessthan = year.str.contains("<", na=False)
df_col[contain_lessthan] = "withheld"
return df_col


# TODO: Add to transform.py
def _to_redact_difference(df_col_year1, df_col_year2):
"""Determine if difference between year2 and year1 is > 89
Expand Down Expand Up @@ -205,6 +221,10 @@ def redact_phi(
)
clinicaldf.loc[to_redact, "BIRTH_YEAR"] = "cannotReleaseHIPAA"

# redact range year for pediatric data
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@rxu17 rxu17 Sep 17, 2025

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I might have missed this in the discussion but to confirm, YEAR_CONTACT and YEAR_DEATH are also phi so that's why they are being redacted as well?

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@danlu1 danlu1 Sep 17, 2025

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I think Xindi referred to the AC of the ticket:'Keep standardizing the center uploaded masked data as "withheld"' and confirmed that we need to redact these two columns. I believe these are phi but the reason to redact should be more related to standardization.

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@rxu17 rxu17 Sep 17, 2025

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Ah I see. Sounds good as long as that's clearly documented, see JIRA comment

clinicaldf["YEAR_CONTACT"] = _redact_ped_year(clinicaldf["YEAR_CONTACT"])
clinicaldf["YEAR_DEATH"] = _redact_ped_year(clinicaldf["YEAR_DEATH"])

return clinicaldf


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