Use JSON Lines data files hosted in the Hub

biomrc.py

@@ -33,7 +33,7 @@ from .bigbiohub import qa_features
 from .bigbiohub import BigBioConfig
 from .bigbiohub import Tasks
 
-_LANGUAGES = ['English']
+_LANGUAGES = ["English"]
 _PUBMED = True
 _LOCAL = False
 _CITATION = """\
@@ -69,40 +69,37 @@ sizes, also releasing our code, and providing a leaderboard.
 
 _HOMEPAGE = "https://github.com/PetrosStav/BioMRC_code"
 
-_LICENSE = 'License information unavailable'
+_LICENSE = "License information unavailable"
 
+_BASE_URL = "https://huggingface.co/datasets/biomrc/resolve/main/data/"
 _URLS = {
     "large": {
         "A": {
-            "train": "https://archive.org/download/biomrc_dataset/biomrc_large/dataset_train.json.gz",
-            "val": "https://archive.org/download/biomrc_dataset/biomrc_large/dataset_val.json.gz",
-            "test": "https://archive.org/download/biomrc_dataset/biomrc_large/dataset_test.json.gz",
+            "train": _BASE_URL + "biomrc_large/dataset_train.jsonl.gz",
+            "val": _BASE_URL + "biomrc_large/dataset_val.jsonl.gz",
+            "test": _BASE_URL + "biomrc_large/dataset_test.jsonl.gz",
         },
         "B": {
-            "train": "https://archive.org/download/biomrc_dataset/biomrc_large/dataset_train_B.json.gz",
-            "val": "https://archive.org/download/biomrc_dataset/biomrc_large/dataset_val_B.json.gz",
-            "test": "https://archive.org/download/biomrc_dataset/biomrc_large/dataset_test_B.json.gz",
+            "train": _BASE_URL + "biomrc_large/dataset_train_B.jsonl.gz",
+            "val": _BASE_URL + "biomrc_large/dataset_val_B.jsonl.gz",
+            "test": _BASE_URL + "biomrc_large/dataset_test_B.jsonl.gz",
         },
     },
     "small": {
         "A": {
-            "train": "https://archive.org/download/biomrc_dataset/biomrc_small/dataset_train_small.json.gz",
-            "val": "https://archive.org/download/biomrc_dataset/biomrc_small/dataset_val_small.json.gz",
-            "test": "https://archive.org/download/biomrc_dataset/biomrc_small/dataset_test_small.json.gz",
+            "train": _BASE_URL + "biomrc_small/dataset_train_small.jsonl.gz",
+            "val": _BASE_URL + "biomrc_small/dataset_val_small.jsonl.gz",
+            "test": _BASE_URL + "biomrc_small/dataset_test_small.jsonl.gz",
         },
         "B": {
-            "train": "https://archive.org/download/biomrc_dataset/biomrc_small/dataset_train_small_B.json.gz",
-            "val": "https://archive.org/download/biomrc_dataset/biomrc_small/dataset_val_small_B.json.gz",
-            "test": "https://archive.org/download/biomrc_dataset/biomrc_small/dataset_test_small_B.json.gz",
+            "train": _BASE_URL + "biomrc_small/dataset_train_small_B.jsonl.gz",
+            "val": _BASE_URL + "biomrc_small/dataset_val_small_B.jsonl.gz",
+            "test": _BASE_URL + "biomrc_small/dataset_test_small_B.jsonl.gz",
         },
     },
     "tiny": {
-        "A": {
-            "test": "https://archive.org/download/biomrc_dataset/biomrc_tiny/dataset_tiny.json.gz"
-        },
-        "B": {
-            "test": "https://archive.org/download/biomrc_dataset/biomrc_tiny/dataset_tiny_B.json.gz"
-        },
+        "A": {"test": _BASE_URL + "biomrc_tiny/dataset_tiny.jsonl.gz"},
+        "B": {"test": _BASE_URL + "biomrc_tiny/dataset_tiny_B.jsonl.gz"},
     },
 }
 
@@ -212,46 +209,29 @@ class BiomrcDataset(datasets.GeneratorBasedBuilder):
 
         if self.config.schema == "source":
             with open(filepath, encoding="utf-8") as fp:
-                biomrc = json.load(fp)
-                for _id, (ab, ti, el, an) in enumerate(
-                    zip(
-                        biomrc["abstracts"],
-                        biomrc["titles"],
-                        biomrc["entities_list"],
-                        biomrc["answers"],
-                    )
-                ):
-                    el = [self._parse_dict_from_entity(entity) for entity in el]
-                    an = self._parse_dict_from_entity(an)
-                    yield _id, {
-                        "abstract": ab,
-                        "title": ti,
-                        "entities_list": el,
-                        "answer": an,
-                    }
+                for _id, line in enumerate(fp):
+                    example = json.loads(line)
+                    example["entities_list"] = [
+                        self._parse_dict_from_entity(entity) for entity in example["entities_list"]
+                    ]
+                    example["answer"] = self._parse_dict_from_entity(example["answer"])
+                    yield _id, example
         elif self.config.schema == "bigbio_qa":
             with open(filepath, encoding="utf-8") as fp:
                 uid = it.count(0)
-                biomrc = json.load(fp)
-                for _id, (ab, ti, el, an) in enumerate(
-                    zip(
-                        biomrc["abstracts"],
-                        biomrc["titles"],
-                        biomrc["entities_list"],
-                        biomrc["answers"],
-                    )
-                ):
+                for _id, line in enumerate(fp):
+                    example = json.loads(line)
                     # remove info such as code, label, synonyms from answer and choices
                     # f.e. @entity1 :: ('9606', 'Species') :: ['patients', 'patient']"
                     example = {
                         "id": next(uid),
                         "question_id": next(uid),
                         "document_id": next(uid),
-                        "question": ti,
+                        "question": example["title"],
                         "type": "multiple_choice",
-                        "choices": [x.split(" :: ")[0] for x in el],
-                        "context": ab,
-                        "answer": [an.split(" :: ")[0]],
+                        "choices": [x.split(" :: ")[0] for x in example["entities_list"]],
+                        "context": example["abstract"],
+                        "answer": [example["answer"].split(" :: ")[0]],
                     }
                     yield _id, example