Use iter_files

chebi_nactem.py

@@ -14,8 +14,9 @@
 # limitations under the License.
 
 import os.path
+from itertools import count
 from pathlib import Path
-from typing import Dict, List, Tuple
+from typing import Dict, Iterable, List, Tuple
 
 import datasets
 
@@ -25,7 +26,7 @@ from .bigbiohub import Tasks
 from .bigbiohub import parse_brat_file
 
 
-_LANGUAGES = ['English']
+_LANGUAGES = ["English"]
 _PUBMED = True
 _LOCAL = False
 _CITATION = """\
@@ -66,7 +67,7 @@ and over 6,000 relations between entities.
 
 _HOMEPAGE = "http://www.nactem.ac.uk/chebi"
 
-_LICENSE = 'Creative Commons Attribution 4.0 International'
+_LICENSE = "Creative Commons Attribution 4.0 International"
 
 _URLS = {
     _DATASETNAME: "http://www.nactem.ac.uk/chebi/ChEBI.zip",
@@ -154,86 +155,75 @@ class ChebiNactemDatasset(datasets.GeneratorBasedBuilder):
             "chebi_nactem_abstr_ann2": os.path.join("ChEBI", "abstracts", "Annotator2"),
             "chebi_nactem_fullpaper": os.path.join("ChEBI", "fullpapers"),
         }
-
-        subset_dir = Path(data_dir) / subset_paths[self.config.subset_id]
-
+        subset_dir = os.path.join(data_dir, subset_paths[self.config.subset_id])
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
-                # Whatever you put in gen_kwargs will be passed to _generate_examples
-                gen_kwargs={
-                    "data_dir": subset_dir,
-                },
+                gen_kwargs={"file_paths": dl_manager.iter_files(subset_dir)},
             )
         ]
 
-    def _generate_examples(self, data_dir: Path) -> Tuple[int, Dict]:
+    def _generate_examples(self, file_paths: Iterable[str]) -> Tuple[int, Dict]:
         """Yields examples as (key, example) tuples."""
 
-        def uid_gen():
-            _uid = 0
-            while True:
-                yield str(_uid)
-                _uid += 1
-
-        uid = iter(uid_gen())
-
-        txt_files = (f for f in sorted(os.listdir(data_dir)) if f.endswith(".txt"))
-        for idx, file_name in enumerate(txt_files):
-
-            brat_file = data_dir / file_name
-            contents = parse_brat_file(brat_file)
-
-            if self.config.schema == "source":
-                yield idx, {
-                    "document_id": contents["document_id"],
-                    "text": contents["text"],
-                    "entities": contents["text_bound_annotations"],
-                    "relations": [
-                        {
-                            "id": relation["id"],
-                            "type": relation["type"],
-                            "arg1": relation["head"]["ref_id"],
-                            "arg2": relation["tail"]["ref_id"],
-                        }
-                        for relation in contents["relations"]
-                    ],
-                }
-
-            elif self.config.schema == "bigbio_kb":
-                yield idx, {
-                    "id": next(uid),
-                    "document_id": contents["document_id"],
-                    "passages": [
-                        {
-                            "id": next(uid),
-                            "type": "",
-                            "text": [contents["text"]],
-                            "offsets": [(0, len(contents["text"]))],
-                        }
-                    ],
-                    "entities": [
-                        {
-                            "id": f"{idx}_{entity['id']}",
-                            "type": entity["type"],
-                            "offsets": entity["offsets"],
-                            "text": entity["text"],
-                            "normalized": [],
-                        }
-                        for entity in contents["text_bound_annotations"]
-                    ],
-                    "events": [],
-                    "coreferences": [],
-                    "relations": [
-                        {
-                            "id": f"{idx}_{relation['id']}",
-                            "type": relation["type"],
-                            "arg1_id": f"{idx}_{relation['head']['ref_id']}",
-                            "arg2_id": f"{idx}_{relation['tail']['ref_id']}",
-                            "normalized": [],
-                        }
-                        for relation in contents["relations"]
-                    ],
-                }
-            else:
-                raise NotImplementedError(self.config.schema)
+        uid = count(0)
+
+        for idx, file_path in enumerate(file_paths):
+            if os.path.basename(file_path).endswith(".txt"):
+                contents = parse_brat_file(
+                    Path(file_path), annotation_file_suffixes=[".ann"]
+                )
+
+                if self.config.schema == "source":
+                    yield idx, {
+                        "document_id": contents["document_id"],
+                        "text": contents["text"],
+                        "entities": contents["text_bound_annotations"],
+                        "relations": [
+                            {
+                                "id": relation["id"],
+                                "type": relation["type"],
+                                "arg1": relation["head"]["ref_id"],
+                                "arg2": relation["tail"]["ref_id"],
+                            }
+                            for relation in contents["relations"]
+                        ],
+                    }
+
+                elif self.config.schema == "bigbio_kb":
+                    yield idx, {
+                        "id": next(uid),
+                        "document_id": contents["document_id"],
+                        "passages": [
+                            {
+                                "id": next(uid),
+                                "type": "",
+                                "text": [contents["text"]],
+                                "offsets": [(0, len(contents["text"]))],
+                            }
+                        ],
+                        "entities": [
+                            {
+                                "id": f"{idx}_{entity['id']}",
+                                "type": entity["type"],
+                                "offsets": entity["offsets"],
+                                "text": entity["text"],
+                                "normalized": [],
+                            }
+                            for entity in contents["text_bound_annotations"]
+                        ],
+                        "events": [],
+                        "coreferences": [],
+                        "relations": [
+                            {
+                                "id": f"{idx}_{relation['id']}",
+                                "type": relation["type"],
+                                "arg1_id": f"{idx}_{relation['head']['ref_id']}",
+                                "arg2_id": f"{idx}_{relation['tail']['ref_id']}",
+                                "normalized": [],
+                            }
+                            for relation in contents["relations"]
+                        ],
+                    }
+                else:
+                    raise NotImplementedError(self.config.schema)