added meds_exclude_tables to the login meds_utils

cumc-dbmi · Oct 29, 2024 · a28d7a1 · a28d7a1
1 parent 4c93a7a
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diff --git a/src/cehrbert/data_generators/hf_data_generator/meds_utils.py b/src/cehrbert/data_generators/hf_data_generator/meds_utils.py
@@ -195,6 +195,7 @@ def create_dataset_from_meds_reader(
     LOG.info("The inpatient_att_function_type: %s", data_args.inpatient_att_function_type)
     LOG.info("The include_auxiliary_token: %s", data_args.include_auxiliary_token)
     LOG.info("The include_demographic_prompt: %s", data_args.include_demographic_prompt)
+    LOG.info("The meds_exclude_tables: %s", "\n".join(data_args.meds_exclude_tables))
 
     train_dataset = _create_cehrbert_data_from_meds(
         data_args=data_args,

diff --git a/src/cehrbert/runners/hf_runner_argument_dataclass.py b/src/cehrbert/runners/hf_runner_argument_dataclass.py
@@ -111,7 +111,7 @@ class DataTrainingArguments:
         },
     )
     meds_exclude_tables: Optional[List[str]] = dataclasses.field(
-        default=list,
+        default_factory=list,
         metadata={"help": "The tables to exclude in the conversion e.g. measurement"},
     )
     # TODO: Python 3.9/10 do not support dynamic unpacking, we have to manually provide the entire