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Check whether patient_id exists in the meds_reader database #66

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Oct 25, 2024
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Check whether patient_id exists in the meds_reader database #66

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5 changes: 3 additions & 2 deletions src/cehrbert/data_generators/hf_data_generator/meds_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -221,8 +221,9 @@ def _meds_to_cehrbert_generator(
with meds_reader.SubjectDatabase(path_to_db) as patient_database:
for shard in shards:
for patient_id, prediction_time, label in shard:
patient = patient_database[patient_id]
yield convert_one_patient(patient, conversion, prediction_time, label)
if patient_id in patient_database:
patient = patient_database[patient_id]
yield convert_one_patient(patient, conversion, prediction_time, label)


def _create_cehrbert_data_from_meds(
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