Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -20,6 +20,11 @@ _HOMEPAGE = "https://huggingface.co/datasets/thbndi/Mimic4Dataset"
 _CITATION = "https://proceedings.mlr.press/v193/gupta22a.html"
 _URL = "https://github.com/healthylaife/MIMIC-IV-Data-Pipeline"
 _DATA_GEN = 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/blob/main/data_generation_icu_modify.py'
+_CONFIG_URLS = {'los' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/blob/main/config/los.config',
+                'mortality' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/blob/main/config/mortality.config',
+                'phenotype' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/blob/main/config/phenotype.config',
+                'readmission' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/blob/main/config/readmission.config'
+        }
 class Mimic4DatasetConfig(datasets.BuilderConfig):
     """BuilderConfig for Mimic4Dataset."""
 
@@ -52,25 +57,25 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         Mimic4DatasetConfig(
             name="Phenotype",
             version=VERSION,
-            config_path = './config/phenotype.config',
+            config_path = _CONFIG_URLS['phenotype'],
             description="Dataset for mimic4 Phenotype task"
         ),
         Mimic4DatasetConfig(
             name="Readmission",
             version=VERSION,
-            config_path = './config/readmission.config',
+            config_path = _CONFIG_URLS['readmission'],
             description="Dataset for mimic4 Readmission task"
         ),
         Mimic4DatasetConfig(
             name="Length of Stay",
             version=VERSION,
-            config_path = './config/los.config',
+            config_path = _CONFIG_URLS['los'],
             description="Dataset for mimic4 Length of Stay task"
         ),
         Mimic4DatasetConfig(
             name="Mortality",
             version=VERSION,
-            config_path = './config/mortality.config',
+            config_path = _CONFIG_URLS['mortality'],
             description="Dataset for mimic4 Mortality task"
         ),
     ]
@@ -137,13 +142,13 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
 
     def _split_generators(self, dl_manager: datasets.DownloadManager()):
         if self.config_path is None and self.name == 'Phenotype':
-            self.config_path = './config/phenotype.config'
+            self.config_path = _CONFIG_URLS['phenotype']
         elif self.config_path is None and self.name == 'Readmission':
-            self.config_path = './config/readmission.config'
+            self.config_path = _CONFIG_URLS['readmission']
         elif self.config_path is None and self.name == 'Length of Stay':
-            self.config_path = './config/los.config'
+            self.config_path = _CONFIG_URLS['los']
         elif self.config_path is None and self.name == 'Mortality':
-            self.config_path = './config/mortality.config'
+            self.config_path = _CONFIG_URLS['mortality']
 
         repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
         if os.path.exists(os.path.dirname(os.path.abspath('MIMIC-IV-Data-Pipeline-main'))):
@@ -152,13 +157,17 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             repodir = os.getcwd()
             path_bench = repodir+'/MIMIC-IV-Data-Pipeline-main'
             subprocess.run(["git", "clone", repo_url, path_bench])
-            
+        
+        if not os.path.exists(path_bench+'/config'):
+            os.makedirs(path_bench+'/config')
+        file_path, head = urlretrieve(self.config_path)
+        shutil.move(file_path, path_bench+'/config')
+        
         file_path, head = urlretrieve(_DATA_GEN, "data_generation_icu_modify.py")
         shutil.move(file_path, path_bench+'/model')
         
         data_dir = path_bench + "/data/dataDic"
-        print(data_dir)
-        #task_cohort(self.name,self.mimic_path, path_bench, self.config_path)
+        task_cohort(self.name,self.mimic_path, path_bench, self.config_path)
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir}),
         ]