Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -9,6 +9,7 @@ from urllib.request import urlretrieve
 from sklearn.model_selection import train_test_split
 from sklearn.preprocessing import LabelEncoder
 import yaml
+from git import Repo
 import numpy as np
 from .dataset_utils import vocab, concat_data, generate_deep, generate_ml, generate_text
 from .task_cohort import create_cohort
@@ -113,13 +114,12 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         mimic_complete_path='/'+mimic_folder+'/'+version
 
         current_directory = os.getcwd()
-        if os.path.exists(os.path.dirname(current_directory)+'/MIMIC-IV-Data-Pipeline-main'):
+        if os.path.exists(os.path.dirname(current_directory)+'/MIMIC-IV-Data-Pipeline'):
             dir =os.path.dirname(current_directory) 
             os.chdir(dir)
         else:
             #move to parent directory of mimic data
             dir = self.mimic_path.replace(mimic_complete_path,'')
-            print('dir : ',dir)
             if dir[-1]!='/':
                 dir=dir+'/'
             elif dir=='':
@@ -131,7 +131,9 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
         path_bench = './MIMIC-IV-Data-Pipeline'
         if not os.path.exists(path_bench):
-            subprocess.run(["git", "clone", repo_url, path_bench],shell = True,capture_output=True)
+            # subprocess.run(["git", "clone", repo_url, path_bench],shell = True,capture_output=True)
+ 
+            Repo.clone_from(repo_url, path_bench)
             os.makedirs(path_bench+'/'+'mimic-iv')
             shutil.move(version,path_bench+'/'+'mimic-iv')