Fix loading and support streaming (#2)

- Add data files (daf3e25da921ef394ca09c4951645041c41d8318)
- Update loading script with hosted data (e0421fe90a9d25b05fe6acca257ac7eccfb69544)
- Support streaming in parse_brat_file (2ee733db8c9f630266b93e7d1ea1ad67cd213518)
- Fix style (054eb3272a28b702827325bc6c099a262eb04b8f)


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

bionlp_st_2019_bb.py

@@ -31,7 +31,7 @@ _DISPLAYNAME = "BioNLP 2019 BB"
 _SOURCE_VIEW_NAME = "source"
 _UNIFIED_VIEW_NAME = "bigbio"
 
-_LANGUAGES = ['English']
+_LANGUAGES = ["English"]
 _PUBMED = True
 _LOCAL = False
 _CITATION = """\
@@ -76,48 +76,16 @@ and applications in microbiology.
 
 _HOMEPAGE = "https://sites.google.com/view/bb-2019/dataset"
 
-_LICENSE = 'License information unavailable'
+_LICENSE = "License information unavailable"
 
+_SUBTASKS = ["norm", "norm+ner", "rel", "rel+ner", "kb", "kb+ner"]
+_FILENAMES = ["train", "dev", "test"]
 _URLs = {
-    "source": {
-        "norm": {
-            "train": "https://drive.google.com/uc?export=download&id=1aXbshxgytZ1Dhbmw7OULPFarPO1FbcM3",
-            "dev": "https://drive.google.com/uc?export=download&id=14jRZWF8VeluEYrV9EybV3LeGm4q5nH6s",
-            "test": "https://drive.google.com/uc?export=download&id=1BPDCFTVMmIlOowYA-DkeNNFjwTfHYPG6",
-        },
-        "norm+ner": {
-            "train": "https://drive.google.com/uc?export=download&id=1yKxBPMej8EYdVeU4QS1xquFfXM76F-2K",
-            "dev": "https://drive.google.com/uc?export=download&id=1Xk7h9bax533QWclO3Ur7aS07OATBF_bG",
-            "test": "https://drive.google.com/uc?export=download&id=1Cb5hQIPS3LIeUL-UWdqyWfKB52xUz9cp",
-        },
-        "rel": {
-            "train": "https://drive.google.com/uc?export=download&id=1gnc-ScNpssC3qrA7cVox4Iei7i96sYqC",
-            "dev": "https://drive.google.com/uc?export=download&id=1wJM9XOfmvIBcX23t9bzQX5fLZwWQJIwS",
-            "test": "https://drive.google.com/uc?export=download&id=1smhKA4LEPK5UJEyBLseq0mBaT9REUevu",
-        },
-        "rel+ner": {
-            "train": "https://drive.google.com/uc?export=download&id=1CPx9NxTPQbygqMtxw3d0hNFajhecqgss",
-            "dev": "https://drive.google.com/uc?export=download&id=1lVyCCuAJ5TmmTDz4S0dISBNiWGR745_7",
-            "test": "https://drive.google.com/uc?export=download&id=1uE8oY5m-7mSA-W-e6vownnAVV97IwHhA",
-        },
-        "kb": {
-            "train": "https://drive.google.com/uc?export=download&id=1Iuce3T_IArXWBbIJ7RXb_STaPnWKQBN-",
-            "dev": "https://drive.google.com/uc?export=download&id=14yON_Tc9dm8esWYDVxL-krw23sgTCcdL",
-            "test": "https://drive.google.com/uc?export=download&id=1wVqI_t9mirGUk71BkwkcKJv0VNGyaHDs",
-        },
-        "kb+ner": {
-            "train": "https://drive.google.com/uc?export=download&id=1WMl9eD4OZXq8zkkmHp3hSEvAqaAVui6L",
-            "dev": "https://drive.google.com/uc?export=download&id=1oOfOfjIfg1XnesXwaKvSDfqgnchuximG",
-            "test": "https://drive.google.com/uc?export=download&id=1_dRbgpGJUBCfF-iN2qOAgOBRvYmE7byW",
-        },
-    },
-    "bigbio_kb": {
-        "kb+ner": {
-            "train": "https://drive.google.com/uc?export=download&id=1WMl9eD4OZXq8zkkmHp3hSEvAqaAVui6L",
-            "dev": "https://drive.google.com/uc?export=download&id=1oOfOfjIfg1XnesXwaKvSDfqgnchuximG",
-            "test": "https://drive.google.com/uc?export=download&id=1_dRbgpGJUBCfF-iN2qOAgOBRvYmE7byW",
-        },
-    },
+    subtask: {
+        filename: f"data/{subtask}/BioNLP-OST-2019_BB-{subtask}_{filename}.zip"
+        for filename in _FILENAMES
+    }
+    for subtask in _SUBTASKS
 }
 
 _SUPPORTED_TASKS = [
@@ -282,48 +250,47 @@ class bionlp_st_2019_bb(datasets.GeneratorBasedBuilder):
     def _split_generators(
         self, dl_manager: datasets.DownloadManager
     ) -> List[datasets.SplitGenerator]:
-        version = self.config.name.split("_")[-2]
-        if version == "bigbio":
-            version = "kb+ner"
-        my_urls = _URLs[self.config.schema][version]
-        data_files = {
-            "train": Path(dl_manager.download_and_extract(my_urls["train"]))
-            / f"BioNLP-OST-2019_BB-{version}_train",
-            "dev": Path(dl_manager.download_and_extract(my_urls["dev"]))
-            / f"BioNLP-OST-2019_BB-{version}_dev",
-            "test": Path(dl_manager.download_and_extract(my_urls["test"]))
-            / f"BioNLP-OST-2019_BB-{version}_test",
-        }
+        subtask = self.config.name.split("_")[4]
+        if subtask == "bigbio":
+            subtask = "kb+ner"
+        my_urls = _URLs[subtask]
+        data_files = dl_manager.download_and_extract(my_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["dev"])},
             ),
             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):
         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 = self.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(
-                    self.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(self.parse_brat_file(txt_file))
                 example["id"] = str(guid)
                 yield guid, example
+                guid += 1
         else:
             raise ValueError(f"Invalid config: {self.config.name}")
 
@@ -447,9 +414,11 @@ class bionlp_st_2019_bb(datasets.GeneratorBasedBuilder):
         ann_lines = []
         for suffix in annotation_file_suffixes:
             annotation_file = txt_file.with_suffix(suffix)
-            if annotation_file.exists():
+            try:
                 with annotation_file.open(encoding="utf8") as f:
                     ann_lines.extend(f.readlines())
+            except Exception:
+                continue
 
         example["text_bound_annotations"] = []
         example["events"] = []

data/kb+ner/BioNLP-OST-2019_BB-kb+ner_dev.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:826bf7711b295557ec518a7828de448741bf1f8a6e7de02771dbbb4b33b3e9e3
+size 140927

data/kb+ner/BioNLP-OST-2019_BB-kb+ner_test.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0d4875dd0a2fd8a81cba9ade5a7f12b589767e6373f7e5edd7c60177a6b6adea
+size 138265

data/kb+ner/BioNLP-OST-2019_BB-kb+ner_train.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:73845eda51d1c0f7dab64d8d1660dc8e1f7cb3109b1275819f6ee32de6e9982f
+size 278279

data/kb/BioNLP-OST-2019_BB-kb_dev.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ef774dc4df3a00577106d3fd3e9a7d5f6187a5e2aa3b15edaf91997449ec6a55
+size 133209

data/kb/BioNLP-OST-2019_BB-kb_test.zip

@@ -0,0 +1,3 @@
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+oid sha256:4bac030a47ba15b3320732adafc2e9a4a7c5df2b1e2f80c61052f65884b9f836
+size 157340

data/kb/BioNLP-OST-2019_BB-kb_train.zip

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+oid sha256:1a8c5e824b99bd2fa77cb751b059fc72d70e508181ae92db38630687d87c2564
+size 250631

data/norm+ner/BioNLP-OST-2019_BB-norm+ner_dev.zip

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+size 137838

data/norm+ner/BioNLP-OST-2019_BB-norm+ner_test.zip

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+size 139805

data/norm+ner/BioNLP-OST-2019_BB-norm+ner_train.zip

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+size 271933

data/norm/BioNLP-OST-2019_BB-norm_dev.zip

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+size 132646

data/norm/BioNLP-OST-2019_BB-norm_test.zip

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+size 162450

data/norm/BioNLP-OST-2019_BB-norm_train.zip

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+size 259327

data/rel+ner/BioNLP-OST-2019_BB-rel+ner_dev.zip

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+size 130535

data/rel+ner/BioNLP-OST-2019_BB-rel+ner_test.zip

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data/rel+ner/BioNLP-OST-2019_BB-rel+ner_train.zip

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data/rel/BioNLP-OST-2019_BB-rel_dev.zip

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data/rel/BioNLP-OST-2019_BB-rel_test.zip

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data/rel/BioNLP-OST-2019_BB-rel_train.zip

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