Fix patient merging on null patient_id tables (per-partition reset_index) - #1193
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fbonc wants to merge 1 commit into
Open
Fix patient merging on null patient_id tables (per-partition reset_index)#1193fbonc wants to merge 1 commit into
fbonc wants to merge 1 commit into
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Problem
For tables configured with
patient_id: null(one patient per row), the code assignedpatient_idviadf.reset_index(drop=True)thendf.index. In Daskreset_indexresets per partition, so rows at the same position in different partitions collide onto the same id and get silently merged into one "patient". This corrupts several shipped configs (covid19_cxr,medical_transcriptions,clinvar, eICU hospital) and defeatssplit_by_patient/split_by_patient_conformal, whose entire purpose is to prevent cross-patient leakage.Fix
Assign a globally-unique id with a
cumsum(global across partitions) instead of the per-partition index, in bothbase_dataset.pyandfhir/base.py.Tests
Added a regression test for each path that builds a null-
patient_idtable across multiple Dask partitions and asserts everypatient_idis unique. Both fail on the old code and pass on the fix.