Upload e3c.py

e3c.py

@@ -1,18 +1,19 @@
 import os
+from typing import Iterator
 
 import datasets
-from bs4 import ResultSet, BeautifulSoup
+from bs4 import BeautifulSoup, ResultSet
 from datasets import DownloadManager
 
 _CITATION = """\
 @report{Magnini2021,
-   author = {Bernardo Magnini and Begoña Altuna and Alberto Lavelli and Manuela Speranza 
-   and Roberto Zanoli and Fondazione Bruno Kessler},
-   keywords = {Clinical data,clinical enti-ties,corpus,multilingual,temporal information},
-   title = {The E3C Project: 
-   European Clinical Case Corpus El proyecto E3C: European Clinical Case Corpus},
-   url = {https://uts.nlm.nih.gov/uts/umls/home},
-   year = {2021},
+author = {Bernardo Magnini and Begoña Altuna and Alberto Lavelli and Manuela Speranza
+and Roberto Zanoli and Fondazione Bruno Kessler},
+keywords = {Clinical data,clinical enti-ties,corpus,multilingual,temporal information},
+title = {The E3C Project:
+European Clinical Case Corpus El proyecto E3C: European Clinical Case Corpus},
+url = {https://uts.nlm.nih.gov/uts/umls/home},
+year = {2021},
 }
 
 """
@@ -29,14 +30,13 @@ _URL = "https://github.com/hltfbk/E3C-Corpus/archive/refs/tags/v2.0.0.zip"
 
 
 class E3CConfig(datasets.BuilderConfig):
-    """BuilderConfig for SQUAD."""
+    """BuilderConfig for NCBIDisease"""
 
     def __init__(self, **kwargs):
-        """BuilderConfig for SQUAD.
+        """BuilderConfig for NCBIDisease.
         Args:
           **kwargs: keyword arguments forwarded to super.
         """
-        self.layer = kwargs.pop("layer")
         super(E3CConfig, self).__init__(**kwargs)
 
 
@@ -44,34 +44,9 @@ class E3C(datasets.GeneratorBasedBuilder):
     VERSION = datasets.Version("1.1.0")
     BUILDER_CONFIGS = [
         E3CConfig(
-            name="en",
+            name="e3c",
             version=VERSION,
             description="this is the split of the layer 1 for English of E3C dataset",
-            layer="1",
-        ),
-        E3CConfig(
-            name="es",
-            version=VERSION,
-            description="this is the split of the layer 1 for Spanish of E3C dataset",
-            layer="1",
-        ),
-        E3CConfig(
-            name="eu",
-            version=VERSION,
-            description="this is the split of the layer 1 for Basque of E3C dataset",
-            layer="1",
-        ),
-        E3CConfig(
-            name="fr",
-            version=VERSION,
-            description="this is the split of the layer 1 for French of E3C dataset",
-            layer="1",
-        ),
-        E3CConfig(
-            name="it",
-            version=VERSION,
-            description="this is the split of the layer 1 for Italian of E3C dataset",
-            layer="1",
         ),
     ]
 
@@ -118,22 +93,115 @@ class E3C(datasets.GeneratorBasedBuilder):
         """
         url = _URL
         data_dir = dl_manager.download_and_extract(url)
-        language = {
-            "en": "English",
-            "es": "Spanish",
-            "eu": "Basque",
-            "fr": "French",
-            "it": "Italian",
-        }[self.config.name]
+
         return [
             datasets.SplitGenerator(
-                name=self.config.name,
+                name="en.layer1",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "English",
+                        "layer1",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="en.layer2",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "English",
+                        "layer2",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="es.layer1",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "Spanish",
+                        "layer1",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="es.layer2",
                 gen_kwargs={
                     "filepath": os.path.join(
                         data_dir,
                         "E3C-Corpus-2.0.0/data_annotation",
-                        language,
-                        f"layer{self.config.layer}",
+                        "Spanish",
+                        "layer2",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="eu.layer1",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "Basque",
+                        "layer1",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="eu.layer2",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "Basque",
+                        "layer2",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="fr.layer1",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "French",
+                        "layer1",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="fr.layer2",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "French",
+                        "layer2",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="it.layer1",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "Italian",
+                        "layer1",
+                    ),
+                },
+            ),
+            datasets.SplitGenerator(
+                name="it.layer2",
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        data_dir,
+                        "E3C-Corpus-2.0.0/data_annotation",
+                        "Italian",
+                        "layer2",
                     ),
                 },
             ),
@@ -190,7 +258,7 @@ class E3C(datasets.GeneratorBasedBuilder):
                         "TOKENS": self.get_annotations(soup.find_all("type4:Token"), text),
                     }
 
-    def _generate_examples(self, filepath) -> tuple[str, dict]:
+    def _generate_examples(self, filepath) -> Iterator:
         """Yields examples as (key, example) tuples.
         Args:
             filepath: The path to the folder containing the files to parse.
@@ -233,8 +301,8 @@ class E3C(datasets.GeneratorBasedBuilder):
                                     labels[idx_token] = f"{entity_type}"
                                 else:
                                     labels[idx_token] = f"{entity_type}"
-                guid += 1
                 yield guid, {
                     "tokens": list(map(lambda tokens: tokens[2], filtered_tokens)),
                     "ner_tags": labels,
                 }
+                guid += 1