leopold-franz/MIMIC-III_FHIR_Transformation

UnboundLocalError: local variable 'file_path' referenced before assignment

banderlog opened this issue · 0 comments

The following code throws an error:

from mimic_fhir_transformation import transform_table


data_path = './data/mimic-iii-clinical-database-1.4/'
output_path = './data/test/'

patient_fhir = transform_table(os.path.join(data_path, 'PATIENTS.csv.gz'),
                               os.path.join(data_path, 'ADMISSIONS.csv.gz'),
                               output_path)

And the source of error:

def transform_table(table_file_path, output_path, auxiliary_table_path=''):
    if Path(table_file_path).suffix == '':
        file_path = Path(table_file_path).stem

    if Path(file_path).name == 'ADMISSIONS.csv':
        df = transform_admissions(table_file_path, output_path)
    ...

If Path(table_file_path).suffix != '', then you have no file_path at all