Support streaming

bionlp_st_2011_epi.py

@@ -15,7 +15,7 @@
 
 
 from pathlib import Path
-from typing import List
+from typing import Iterable, List
 
 import datasets
 
@@ -32,7 +32,7 @@ _DISPLAYNAME = "BioNLP 2011 EPI"
 _SOURCE_VIEW_NAME = "source"
 _UNIFIED_VIEW_NAME = "bigbio"
 
-_LANGUAGES = ['English']
+_LANGUAGES = ["English"]
 _PUBMED = True
 _LOCAL = False
 _CITATION = """\
@@ -59,11 +59,12 @@ of BioNLP Shared Task 2011.
 
 _HOMEPAGE = "https://github.com/openbiocorpora/bionlp-st-2011-epi"
 
-_LICENSE = 'GENIA Project License for Annotated Corpora'
+_LICENSE = "GENIA Project License for Annotated Corpora"
 
 _URLs = {
-    "source": "https://github.com/openbiocorpora/bionlp-st-2011-epi/archive/refs/heads/master.zip",
-    "bigbio_kb": "https://github.com/openbiocorpora/bionlp-st-2011-epi/archive/refs/heads/master.zip",
+    "train": "data/train.zip",
+    "validation": "data/devel.zip",
+    "test": "data/test.zip",
 }
 
 _SUPPORTED_TASKS = [
@@ -198,46 +199,44 @@ class bionlp_st_2011_epi(datasets.GeneratorBasedBuilder):
         self, dl_manager: datasets.DownloadManager
     ) -> List[datasets.SplitGenerator]:
 
-        my_urls = _URLs[self.config.schema]
-        data_dir = Path(dl_manager.download_and_extract(my_urls))
-        data_files = {
-            "train": data_dir
-            / f"bionlp-st-2011-epi-master"
-            / "original-data"
-            / "train",
-            "dev": data_dir / f"bionlp-st-2011-epi-master" / "original-data" / "devel",
-            "test": data_dir / f"bionlp-st-2011-epi-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"])},
             ),
         ]
 
-    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):
-                example = brat_parse_to_bigbio_kb(
-                    parse_brat_file(txt_file)
-                )
+            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["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 sha256:4f439291f13c6f04f1c669dce40f5abfd539a82529e0e99cc7164462ed775738
+size 318525

data/test.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5f1d5d6b552661be4e3c7988db8c1e534e00a9c5afbb12838af36b9f6c597ed3
+size 646940

data/train.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b10532f594a23c5ff0a66e88cdb5f731814c529a282701746df44edd72c182f2
+size 942875