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[FIX] ADNI-to-BIDS : incorporate the fix for KeyError "APGEN" #1342

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merged 4 commits into from
Oct 24, 2024
Merged

[FIX] ADNI-to-BIDS : incorporate the fix for KeyError "APGEN" #1342

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a0b7543
Proposition
AliceJoubert Oct 21, 2024
fbf55b1
Changes upon suggestions
AliceJoubert Oct 21, 2024
5e279dd
Modify unit test
AliceJoubert Oct 23, 2024
3706242
Small fix
AliceJoubert Oct 24, 2024
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11 changes: 11 additions & 0 deletions clinica/iotools/bids_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -401,6 +401,17 @@ def create_participants_df(
file_to_read = load_clinical_csv(
clinical_data_dir, location.split(".")[0]
)
if location == "APOERES.csv":
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if (
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"APGEN1" not in file_to_read.columns
and "GENOTYPE" in file_to_read.columns
):
# Split the 'GENOTYPE' column into 'APGEN1' and 'APGEN2'
genotype = file_to_read["GENOTYPE"].str.split(
"/", expand=True
)
file_to_read.assign(APGEN1=genotype[0], APGEN2=genotype[1])

prev_location = location
prev_sheet = sheet

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