Find corresponding MeSH terms from CUIs in evaluation datasets

cui2mesh.py

#!/usr/bin/env python3
# pylint: disable=invalid-name
"""Reads UMNSRS datasets where CUIs are used, add corresponding MeSHes to the
CUIs"""

from pathlib import Path
import csv
from tqdm import tqdm
from BMET.uts_api_client import UtsClient

file_in = Path('')
while not file_in.is_file():
    user_input = input("Enter path to a csv reference file containing CUIs: ")
    file_in = Path(user_input)
    file_out = Path(file_in.with_suffix('').as_posix() + '_mesh' +
                    file_in.suffix)

# Gather all the CUI codes
uts_client = UtsClient()
rows = sum(1 for line in open(file_in)) - 1
with open(file_in) as fin, open(file_out, 'w') as fout:
    csv_reader = csv.DictReader(fin)
    csv_writer = csv.writer(fout, quotechar='"')
    csv_writer.writerow(csv_reader.fieldnames + ['MESH1', 'MESH2'])
    pbar = tqdm(total=rows)
    for flds in csv_reader:
        pbar.update()
        for i in '12':
            cui = flds['CUI'+i]
            tok = flds['TERM'+i]
            try:
                rst = uts_client.get_concept_mesh_atoms(cui, tok)
                if rst is None:
                    flds['MESH'+i] = 'None'
                else:
                    mesh = rst['result'][0]['code'].split('/')[-1]
                    flds['MESH'+i] = mesh
            except Exception as e:
                print(f"Error: {e} Cui: {cui} Rec: {flds}")
                raise
        csv_writer.writerow(flds.values())
    pbar.close()
print(f"Finished writing records on {file_out}")