Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -4,7 +4,7 @@ import os
 import pandas as pd
 import datasets
 import pickle
-#import cohort
+from .cohort import task_cohort
 from .test import print_test
 import subprocess
 
@@ -25,14 +25,10 @@ class Mimic4DatasetConfig(datasets.BuilderConfig):
     def __init__(
         self,
         mimic_path,
-        #config,
         **kwargs,
     ):
         super().__init__(**kwargs)
         self.mimic_path =mimic_path
-        
-        #self.config = config
-        #cohort.task_cohort(self.task,self.mimic_path)
 
         
 class Mimic4Dataset(datasets.GeneratorBasedBuilder):
@@ -41,24 +37,28 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         Mimic4DatasetConfig(
             name="Phenotype",
             version=VERSION,
+            config_path = './config/phenotype.config'
             description="Dataset for mimic4 Phenotype task",
             mimic_path = None
         ),
         Mimic4DatasetConfig(
             name="Readmission",
             version=VERSION,
+            config_path = './config/readmission.config'
             description="Dataset for mimic4 Readmission task",
             mimic_path = None
         ),
         Mimic4DatasetConfig(
             name="Length of Stay",
             version=VERSION,
+            config_path = './config/los.config'
             description="Dataset for mimic4 Length of Stay task",
             mimic_path = None
         ),
         Mimic4DatasetConfig(
             name="Mortality",
             version=VERSION,
+            config_path = './config/mortality.config'
             description="Dataset for mimic4 Mortality task",
             mimic_path = None
         ),
@@ -131,16 +131,14 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
         data_dir = path_bench + "/data/dataDic"
         if not os.path.exists(path_bench):
-            #subprocess.run(["git", "clone", repo_url, path_bench])
-            print('ok')
-        
+            subprocess.run(["git", "clone", repo_url, path_bench])
+        task_cohort(self.task,self.mimic_path, path_bench, self.config_path)
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir, "benchmark": path_bench}),
         ]
 
 
     def _generate_examples(self, filepath,benchmark):
-        print_test('hello',benchmark)
         with open(filepath, 'rb') as fp:
             dataDic = pickle.load(fp)
         for hid, data in dataDic.items():