Download directly TSV files

ehr_rel.py

@@ -30,7 +30,7 @@ from .bigbiohub import pairs_features
 from .bigbiohub import BigBioConfig
 from .bigbiohub import Tasks
 
-_LANGUAGES = ['English']
+_LANGUAGES = ["English"]
 _PUBMED = False
 _LOCAL = False
 _CITATION = """\
@@ -64,10 +64,13 @@ A detailed analysis of the concepts in the dataset reveals a far larger coverage
 
 _HOMEPAGE = "https://github.com/babylonhealth/EHR-Rel"
 
-_LICENSE = 'Apache License 2.0'
+_LICENSE = "Apache License 2.0"
 
 _URLS = {
-    _DATASETNAME: "https://github.com/babylonhealth/EHR-Rel/archive/refs/heads/master.zip",
+    _DATASETNAME: {
+        "ehr_rel_a": "https://raw.githubusercontent.com/babylonhealth/EHR-Rel/master/EHR-RelA.tsv",
+        "ehr_rel_b": "https://raw.githubusercontent.com/babylonhealth/EHR-Rel/master/EHR-RelB.tsv",
+    },
 }
 
 _SUPPORTED_TASKS = [Tasks.SEMANTIC_SIMILARITY]
@@ -152,30 +155,25 @@ class EHRRelDataset(datasets.GeneratorBasedBuilder):
     def _split_generators(self, dl_manager) -> List[datasets.SplitGenerator]:
         """Returns SplitGenerators."""
         urls = _URLS[_DATASETNAME]
-        data_dir = Path(dl_manager.download_and_extract(urls))
-        data_dir = data_dir.joinpath("EHR-Rel-master")
+        urls = (
+            [urls[self.config.subset_id]]
+            if self.config.subset_id in urls
+            else list(urls.values())
+        )
+        paths = dl_manager.download(urls)
         return [
             datasets.SplitGenerator(
-                name=datasets.Split.TRAIN,
-                gen_kwargs={"data_dir": data_dir},
+                name=datasets.Split.TRAIN, gen_kwargs={"paths": paths},
             ),
         ]
 
-    def _generate_examples(self, data_dir: Path) -> Iterator[Tuple[str, Dict]]:
-
-        if self.config.subset_id == "ehr_rel_a":
-            files = ["EHR-RelA.tsv"]
-        elif self.config.subset_id == "ehr_rel_b":
-            files = ["EHR-RelB.tsv"]
-        else:
-            files = ["EHR-RelA.tsv", "EHR-RelB.tsv"]
+    def _generate_examples(self, paths: List[str]) -> Iterator[Tuple[str, Dict]]:
 
         uid = -1  # want first instance to be 0
 
-        for filename in files:
-            file = data_dir.joinpath(filename)
-            document_id = str(file.stem)
-            with open(file, encoding="utf-8") as csv_file:
+        for path in paths:
+            document_id = Path(path).stem
+            with open(path, encoding="utf-8", newline="") as csv_file:
                 csv_reader = csv.reader(csv_file, quotechar='"', delimiter="\t")
                 next(csv_reader, None)  # remove column headers
                 for id_, row in enumerate(csv_reader):