Support streaming (#2)

- Add data files (e1fff319d851fcad28e4d95c2642aca7c1157d12)
- Update loading script (f90d0eff0db2a4daa9d10fd66245277d03244e35)


Co-authored-by: Albert Villanova <[email protected]>

bionlp_st_2013_pc.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 
 from pathlib import Path
-from typing import Dict, List
+from typing import Dict, Iterable, List
 
 import datasets
 
@@ -70,7 +70,9 @@ _HOMEPAGE = "https://github.com/openbiocorpora/bionlp-st-2013-pc"
 _LICENSE = 'GENIA Project License for Annotated Corpora'
 
 _URLs = {
-    "bionlp_st_2013_pc": "https://github.com/openbiocorpora/bionlp-st-2013-pc/archive/refs/heads/master.zip",
+    "train": "data/train.zip",
+    "validation": "data/devel.zip",
+    "test": "data/test.zip",
 }
 
 _SUPPORTED_TASKS = [
@@ -224,26 +226,19 @@ class bionlp_st_2013_pc(datasets.GeneratorBasedBuilder):
     def _split_generators(
         self, dl_manager: datasets.DownloadManager
     ) -> List[datasets.SplitGenerator]:
-        my_urls = _URLs[_DATASETNAME]
-        data_dir = Path(dl_manager.download_and_extract(my_urls))
-        data_files = {
-            "train": data_dir / f"bionlp-st-2013-pc-master" / "original-data" / "train",
-            "dev": data_dir / f"bionlp-st-2013-pc-master" / "original-data" / "devel",
-            "test": data_dir / f"bionlp-st-2013-pc-master" / "original-data" / "test",
-        }
-
+        data_files = dl_manager.download_and_extract(_URLs)
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
-                gen_kwargs={"data_files": data_files["train"]},
+                gen_kwargs={"data_files": dl_manager.iter_files(data_files["train"])},
             ),
             datasets.SplitGenerator(
                 name=datasets.Split.VALIDATION,
-                gen_kwargs={"data_files": data_files["dev"]},
+                gen_kwargs={"data_files": dl_manager.iter_files(data_files["validation"])},
             ),
             datasets.SplitGenerator(
                 name=datasets.Split.TEST,
-                gen_kwargs={"data_files": data_files["test"]},
+                gen_kwargs={"data_files": dl_manager.iter_files(data_files["test"])},
             ),
         ]
 
@@ -256,21 +251,29 @@ class bionlp_st_2013_pc(datasets.GeneratorBasedBuilder):
 
         return kb_example
 
-    def _generate_examples(self, data_files: Path):
+    def _generate_examples(self, data_files: Iterable[str]):
         if self.config.schema == "source":
-            txt_files = list(data_files.glob("*txt"))
-            for guid, txt_file in enumerate(txt_files):
+            guid = 0
+            for data_file in data_files:
+                txt_file = Path(data_file)
+                if txt_file.suffix != ".txt":
+                    continue
                 example = parse_brat_file(txt_file)
                 example["id"] = str(guid)
                 yield guid, example
+                guid += 1
         elif self.config.schema == "bigbio_kb":
-            txt_files = list(data_files.glob("*txt"))
-            for guid, txt_file in enumerate(txt_files):
+            guid = 0
+            for data_file in data_files:
+                txt_file = Path(data_file)
+                if txt_file.suffix != ".txt":
+                    continue
                 example = brat_parse_to_bigbio_kb(
                     parse_brat_file(txt_file)
                 )
                 example = self._standardize_arguments_roles(example)
                 example["id"] = str(guid)
                 yield guid, example
+                guid += 1
         else:
             raise ValueError(f"Invalid config: {self.config.name}")

data/devel.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7d960658be6c8baf12924aa3fe08da392002c11353791b4867554a89adf050f0
+size 202006

data/test.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:760f575d41bbd17f37375f2c694ee50bc2441571ea734a45ef75e40654641ea9
+size 260734

data/train.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d3b6b85373d120b97f76489af9e68da0132eef6ac8617bafe0453d4f2385432a
+size 578917