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mostafaalishahi / eICU_Benchmark

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KeyError: "['hospitaladmityear'] not in index" #5

Open PiasTanmoy opened 1 week ago

PiasTanmoy commented 1 week ago

Traceback (most recent call last): File "data_extraction_root.py", line 51, in main() File "data_extraction_root.py", line 49, in main data_extraction_root(args) File "data_extraction_root.py", line 16, in data_extraction_root patients = utils.read_patients_table(args.eicu_dir, args.output_dir) File "/home/danfeng/LLM-HC/eICU/eICU_Benchmark/data_extraction/utils.py", line 82, in read_patients_table pats = filter_patients_on_columns(pats) File "/home/danfeng/LLM-HC/eICU/eICU_Benchmark/data_extraction/utils.py", line 119, in filter_patients_on_columns return patients[columns] File "/home/danfeng/LLM-HC/eICU/.venv3.5/lib/python3.5/site-packages/pandas/core/frame.py", line 2934, in getitem raise_missing=True) File "/home/danfeng/LLM-HC/eICU/.venv3.5/lib/python3.5/site-packages/pandas/core/indexing.py", line 1354, in _convert_to_indexer return self._get_listlike_indexer(obj, axis, **kwargs)[1] File "/home/danfeng/LLM-HC/eICU/.venv3.5/lib/python3.5/site-packages/pandas/core/indexing.py", line 1161, in _get_listlike_indexer raise_missing=raise_missing) File "/home/danfeng/LLM-HC/eICU/.venv3.5/lib/python3.5/site-packages/pandas/core/indexing.py", line 1252, in _validate_read_indexer raise KeyError("{} not in index".format(not_found)) KeyError: "['hospitaladmityear'] not in index"

My virtual environment is (Python 3.5.10)

Package Version

joblib 0.14.1 numpy 1.15.0 pandas 0.24.1 pip 20.3.4 python-dateutil 2.9.0.post0 pytz 2024.1 scikit-learn 0.21.2 scipy 1.2.0 setuptools 50.3.2 six 1.16.0 wheel 0.37.1

mostafaalishahi commented 1 week ago

for any reasons, you do not have 'hospitaladmityear' column in your data. Either you could check your data or you just drop this column hospitaladmityear as it is not being used anywhere in the next steps.