[de07e6]: / src / Preporcessor / preprocessing.py

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import joblib
from tqdm.auto import tqdm
from preprocessing_utils import eic_text_preprocessing
from TrialMatchAI.src.Preporcessor.preprocess_clinical_notes import tokenize_clinical_note
import pandas as pd
import os
memory = joblib.Memory(".")
def ParallelExecutor(use_bar="tqdm", **joblib_args):
"""Utility for tqdm progress bar in joblib.Parallel"""
all_bar_funcs = {
"tqdm": lambda args: lambda x: tqdm(x, **args),
"False": lambda args: iter,
"None": lambda args: iter,
}
def aprun(bar=use_bar, **tq_args):
def tmp(op_iter):
if str(bar) in all_bar_funcs.keys():
bar_func = all_bar_funcs[str(bar)](tq_args)
else:
raise ValueError("Value %s not supported as bar type" % bar)
# Pass n_jobs from joblib_args
return joblib.Parallel(n_jobs=joblib_args.get("n_jobs", 10))(bar_func(op_iter))
return tmp
return aprun
class Preprocessor:
def __init__(self, id_list, n_jobs):
self.id_list = id_list
self.n_jobs = n_jobs
def preprocess_clinical_trials_text(self):
parallel_runner = ParallelExecutor(n_jobs=self.n_jobs)(total=len(self.id_list))
X = parallel_runner(
joblib.delayed(eic_text_preprocessing)(
[_id]
)
for _id in self.id_list
)
return pd.concat(X).reset_index(drop=True)
def preprocess_patient_clinical_notes(self):
parallel_runner = ParallelExecutor(n_jobs=self.n_jobs)(total=len(self.id_list))
X = parallel_runner(
joblib.delayed(tokenize_clinical_note)(
[_id]
)
for _id in self.id_list
)
return pd.concat(X).reset_index(drop=True)