used the existing subject_split to split the cohort automatically instead of doing it manually (#63)

Author: ChaoPang

src/cehrbert/data_generators/hf_data_generator/meds_utils.py

@@ -436,8 +436,12 @@ def _create_cehrbert_data_from_meds(
     assert split in ["held_out", "train", "tuning"]
     batches = []
     if data_args.cohort_folder:
-        cohort = pd.read_parquet(os.path.join(os.path.expanduser(data_args.cohort_folder), split))
-        for cohort_row in cohort.itertuples():
+        # Load the entire cohort
+        cohort = pd.read_parquet(os.path.expanduser(data_args.cohort_folder))
+        patient_split = get_subject_split(os.path.expanduser(data_args.data_folder))
+        subject_ids = patient_split[split]
+        cohort_split = cohort[cohort.subject_id.isin(subject_ids)]
+        for cohort_row in cohort_split.itertuples():
             subject_id = cohort_row.subject_id
             prediction_time = cohort_row.prediction_time
             label = int(cohort_row.boolean_value)