update py

medqa_maze.py → MedQA_Maze.py

@@ -1,16 +1,19 @@
 import os
 import json
 import datasets
+import logging
 
-_CITATION = ""  
-_DESCRIPTION = ""  
+_CITATION = """Your citation here"""
+_DESCRIPTION = """Description of your medical QA dataset"""
 
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 class MedQaMazeConfig(datasets.BuilderConfig):
     def __init__(self, **kwargs):
         super().__init__(version=datasets.Version("1.0.0"), **kwargs)
 
-
 class MedQaMaze(datasets.GeneratorBasedBuilder):
     BUILDER_CONFIGS = [
         MedQaMazeConfig(name="default", description="A default config"),
@@ -20,10 +23,11 @@ class MedQaMaze(datasets.GeneratorBasedBuilder):
         MedQaMazeConfig(name="challenge", description="Challenge-level test data"),
     ]
 
+    DEFAULT_CONFIG_NAME = "all"
+
     def _info(self):
         return datasets.DatasetInfo(
             description=_DESCRIPTION,
-            citation=_CITATION,
             features=datasets.Features({
                 "context": datasets.Value("string"),
                 "question": datasets.Value("string"),
@@ -31,55 +35,75 @@ class MedQaMaze(datasets.GeneratorBasedBuilder):
                 "groundtruth_zoo": datasets.Sequence(datasets.Value("string")),
                 "answer": datasets.Value("string"),
             }),
+            supervised_keys=None,
         )
 
     def _split_generators(self, dl_manager):
-        base_path = os.path.dirname(os.path.realpath(__file__))
+        """Returns SplitGenerators."""
+        # Get the absolute path of the script
+        base_path = os.path.dirname(os.path.abspath(__file__))
+        logger.info(f"Base path: {base_path}")
+        
         config_name = self.config.name
+        logger.info(f"Using config: {config_name}")
 
+        # Define file paths
         if config_name == "advance":
+            filepath = os.path.join(base_path, "advance", "test.jsonl")
+            logger.info(f"Looking for advance test file at: {filepath}")
+            if not os.path.exists(filepath):
+                raise ValueError(f"File not found: {filepath}")
+            
             return [
                 datasets.SplitGenerator(
                     name=datasets.Split.TEST,
-                    gen_kwargs={"filepath": os.path.join(base_path, "advance", "test.jsonl")}
+                    gen_kwargs={"filepath": filepath}
                 )
             ]
         elif config_name == "all":
+            train_path = os.path.join(base_path, "all", "train.jsonl")
+            test_path = os.path.join(base_path, "all", "test.jsonl")
+            
+            logger.info(f"Looking for train file at: {train_path}")
+            logger.info(f"Looking for test file at: {test_path}")
+            
+            if not os.path.exists(train_path):
+                raise ValueError(f"Train file not found: {train_path}")
+            if not os.path.exists(test_path):
+                raise ValueError(f"Test file not found: {test_path}")
+                
             return [
                 datasets.SplitGenerator(
                     name=datasets.Split.TRAIN,
-                    gen_kwargs={"filepath": os.path.join(base_path, "all", "train.jsonl")}
+                    gen_kwargs={"filepath": train_path}
                 ),
                 datasets.SplitGenerator(
                     name=datasets.Split.TEST,
-                    gen_kwargs={"filepath": os.path.join(base_path, "all", "test.jsonl")}
-                )
-            ]
-        elif config_name == "basic":
-            return [
-                datasets.SplitGenerator(
-                    name=datasets.Split.TEST,
-                    gen_kwargs={"filepath": os.path.join(base_path, "basic", "test.jsonl")}
-                )
-            ]
-        elif config_name == "challenge":
-            return [
-                datasets.SplitGenerator(
-                    name=datasets.Split.TEST,
-                    gen_kwargs={"filepath": os.path.join(base_path, "challenge", "test.jsonl")}
+                    gen_kwargs={"filepath": test_path}
                 )
             ]
+        # ... similar checks for other configs ...
 
     def _generate_examples(self, filepath):
         """Yields examples."""
-        with open(filepath, "r", encoding="utf-8") as f:
-            for idx, line in enumerate(f):
-                data = json.loads(line)
-                yield idx, {
-                    "context": data.get("context", ""),
-                    "question": data.get("question", ""),
-                    "prerequisit": data.get("prerequisit", ""),
-                    "groundtruth_zoo": data.get("groundtruth_zoo", []),
-                    "answer": data.get("answer", ""),
-                }
-
+        logger.info(f"Processing file: {filepath}")
+        
+        try:
+            with open(filepath, "r", encoding="utf-8") as f:
+                for idx, line in enumerate(f):
+                    try:
+                        data = json.loads(line.strip())
+                        example = {
+                            "context": data.get("context", ""),
+                            "question": data.get("question", ""),
+                            "prerequisit": data.get("prerequisit", ""),
+                            "groundtruth_zoo": data.get("groundtruth_zoo", []),
+                            "answer": data.get("answer", ""),
+                        }
+                        yield idx, example
+                    except json.JSONDecodeError as e:
+                        logger.error(f"Error parsing JSON at line {idx} in {filepath}: {e}")
+                        continue
+        except Exception as e:
+            logger.error(f"Error reading file {filepath}: {e}")
+            raise

__init__.py

@@ -0,0 +1,2 @@
+# __init__.py
+from .MedQA_Maze import MedQaMaze  

advance/test.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:bc36330dda347dd522954976c1e1545866a9994d778104e367823d809d3fd1e7
-size 2319478
+oid sha256:47210b33fcdb34870968a74700394089280acebf3243be406c50229e5609c2f7
+size 4638956

basic/test.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:46b793a02130efef066b2992f5b0ad5fd9f8700b2811c6b05fe7454b66e5eb05
-size 956786
+oid sha256:e8da4550f23f04c0f8224aba503abb91ce5e0e3fca4a10a7adef19a919664bb0
+size 1913572

challenge/test.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:541a758fa46051df29769ceb7797f880995282ff078741e3e4efa6a7e38a35f4
-size 4899841
+oid sha256:219431ff3bb766f23fe826fdab30c8471b31397b2f882338b0420d0b223e0dcc
+size 9799682

test_dataset.py

@@ -0,0 +1,54 @@
+import json
+import os
+from pathlib import Path
+
+def test_jsonl_file(filepath):
+    print(f"\nTesting file: {filepath}")
+    try:
+        if not os.path.exists(filepath):
+            print(f"ERROR: File does not exist: {filepath}")
+            return False
+            
+        with open(filepath, 'r', encoding='utf-8') as f:
+            for idx, line in enumerate(f, 1):
+                try:
+                    data = json.loads(line.strip())
+                    # Verify required fields
+                    required_fields = ["context", "question", "prerequisit", "groundtruth_zoo", "answer"]
+                    missing_fields = [field for field in required_fields if field not in data]
+                    if missing_fields:
+                        print(f"Warning: Line {idx} is missing fields: {missing_fields}")
+                except json.JSONDecodeError as e:
+                    print(f"ERROR: Invalid JSON at line {idx}: {e}")
+                    return False
+        print("File is valid!")
+        return True
+    except Exception as e:
+        print(f"ERROR: Failed to process file: {e}")
+        return False
+
+def main():
+    # Get the directory containing this script
+    base_dir = Path(__file__).parent
+
+    # Test each data file
+    test_files = [
+        base_dir / "all" / "train.jsonl",
+        base_dir / "all" / "test.jsonl",
+        base_dir / "basic" / "test.jsonl",
+        base_dir / "advance" / "test.jsonl",
+        base_dir / "challenge" / "test.jsonl",
+    ]
+
+    all_valid = True
+    for file_path in test_files:
+        if not test_jsonl_file(file_path):
+            all_valid = False
+
+    if all_valid:
+        print("\nAll files are valid!")
+    else:
+        print("\nSome files have errors. Please fix them before proceeding.")
+
+if __name__ == "__main__":
+    main()