Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -6,6 +6,7 @@ import datasets
 import pickle
 #import cohort
 from .test import print_test
+import subprocess
 
 _DESCRIPTION = """\
 Dataset for mimic4 data, by default for the Mortality task.
@@ -16,7 +17,7 @@ mimic path should have this form :
 
 _HOMEPAGE = "https://huggingface.co/datasets/thbndi/Mimic4Dataset"
 _CITATION = "https://proceedings.mlr.press/v193/gupta22a.html"
-_URL = "https://github.com/healthylaife/MIMIC-IV-Data-Pipeline/archive/master.zip"
+_URL = "https://github.com/healthylaife/MIMIC-IV-Data-Pipeline"
 
 class Mimic4DatasetConfig(datasets.BuilderConfig):
     """BuilderConfig for Mimic4Dataset."""
@@ -132,13 +133,10 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         data_dir = self.config.data_dir + "/dataDic"
         #mimic=self.mimic_path
         data_dir = self.config.data_dir + "/dataDic"
-        
-        path_git = dl_manager.download(_URL)
-        print(path_git)
-        local_path_git = dl_manager.extract(path_git)
-        local_path_git = dl_manager.extract(local_path_git)
-        print(local_path_git)
-        path_bench = local_path_git + "/MIMIC-IV-Data-Pipeline-main"
+        repodir = os.getcwd()
+        path_bench = repodir+'/MIMIC-IV-Data-Pipeline-main'
+        repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
+        subprocess.run(["git", "clone", repo_url, repodir+'/MIMIC-IV-Data-Pipeline-main'])
         
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir, "benchmark": path_bench}),