upload hubscripts/meddialog_hub.py to hub from bigbio repo

meddialog.py

@@ -0,0 +1,222 @@
+# coding=utf-8
+# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import json
+import re
+
+import datasets
+
+from .bigbiohub import text_features
+from .bigbiohub import BigBioConfig
+from .bigbiohub import Tasks
+
+_DATASETNAME = "meddialog"
+_DISPLAYNAME = "MedDialog"
+
+_LANGUAGES = ['English', 'Chinese']
+_PUBMED = False
+_LOCAL = False
+_CITATION = """
+@article{DBLP:journals/corr/abs-2004-03329,
+  author    = {Shu Chen and
+               Zeqian Ju and
+               Xiangyu Dong and
+               Hongchao Fang and
+               Sicheng Wang and
+               Yue Yang and
+               Jiaqi Zeng and
+               Ruisi Zhang and
+               Ruoyu Zhang and
+               Meng Zhou and
+               Penghui Zhu and
+               Pengtao Xie},
+  title     = {MedDialog: {A} Large-scale Medical Dialogue Dataset},
+  journal   = {CoRR},
+  volume    = {abs/2004.03329},
+  year      = {2020},
+  url       = {https://arxiv.org/abs/2004.03329},
+  eprinttype = {arXiv},
+  eprint    = {2004.03329},
+  biburl    = {https://dblp.org/rec/journals/corr/abs-2004-03329.bib},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+"""
+
+_DESCRIPTION = """
+The MedDialog dataset (English) contains conversations (in English) between doctors and patients.\
+It has 0.26 million dialogues. The data is continuously growing and more dialogues will be added. \
+The raw dialogues are from healthcaremagic.com and icliniq.com.\
+
+All copyrights of the data belong to healthcaremagic.com and icliniq.com.
+"""
+
+_HOMEPAGE = "https://github.com/UCSD-AI4H/Medical-Dialogue-System"
+
+_LICENSE = 'License information unavailable'
+
+_URLs = {
+    "en": {
+        "train": "https://drive.google.com/file/d/1ria4E6IdTIPsikL4Glm3uy1tFKJKw0W8/view?usp=sharing",
+        "validation": "https://drive.google.com/file/d/1KAZneuwdfEVQQM6euCX4pMDP-9DQpiB5/view?usp=sharing",
+        "test": "https://drive.google.com/file/d/10izqL71kcgnteYsf87Vh6j_mZ8sZM2Rc/view?usp=sharing",
+    },
+    "zh": {
+        "train": "https://drive.google.com/file/d/1AaDJoHaiHAwEZwtskRH8oL1UP4FRgmgx/view?usp=sharing",
+        "validation": "https://drive.google.com/file/d/1TvfZCmQqP1kURIfEinOcj5VOPelTuGwI/view?usp=sharing",
+        "test": "https://drive.google.com/file/d/1pmmG95Yl6mMXRXDDSRb9-bYTxOE7ank5/view?usp=sharing",
+    },
+}
+
+_SUPPORTED_TASKS = [Tasks.TEXT_CLASSIFICATION]
+_SOURCE_VERSION = "1.0.0"
+_BIGBIO_VERSION = "1.0.0"
+
+
+class MedDialog(datasets.GeneratorBasedBuilder):
+    """MedDialog: Large-scale Medical Dialogue Datasets in English and Chinese."""
+
+    DEFAULT_CONFIG_NAME = "meddialog_en_source"
+    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
+    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
+
+    BUILDER_CONFIGS = [
+        # Source schemas
+        BigBioConfig(
+            name="meddialog_en_source",
+            version=SOURCE_VERSION,
+            description="MedDialog source schema",
+            schema="source",
+            subset_id="meddialog_en",
+        ),
+        BigBioConfig(
+            name="meddialog_zh_source",
+            version=SOURCE_VERSION,
+            description="MedDialog source schema",
+            schema="source",
+            subset_id="meddialog_zh",
+        ),
+        # BigBio schema: text classification
+        BigBioConfig(
+            name="meddialog_en_bigbio_text",
+            version=BIGBIO_VERSION,
+            description="MedDialog simplified BigBio schema",
+            schema="bigbio_text",
+            subset_id="meddialog_en",
+        ),
+        BigBioConfig(
+            name="meddialog_zh_bigbio_text",
+            version=BIGBIO_VERSION,
+            description="MedDialog simplified BigBio schema",
+            schema="bigbio_text",
+            subset_id="meddialog_zh",
+        ),
+    ]
+
+    def _get_gdrive_url(self, url):
+        """Converts URL from google drive shareable link to format used by dl_manager."""
+        fileid = re.match("https://drive\.google\.com/file/d/(.+)/view\?", url).group(1)
+        return f"https://drive.google.com/uc?id={fileid}"
+
+    def _info(self):
+        lang = self.config.name.split("_")[1]
+        if self.config.schema == "source":
+            if lang == "en":
+                features = datasets.Features(
+                    {
+                        "description": datasets.Value("string"),
+                        "utterances": datasets.Sequence(
+                            {
+                                "speaker": datasets.ClassLabel(
+                                    names=["patient", "doctor"]
+                                ),
+                                "utterance": datasets.Value("string"),
+                            }
+                        ),
+                    }
+                )
+            elif lang == "zh":
+                features = datasets.Features(
+                    {
+                        "utterances": datasets.Sequence(
+                            {
+                                "speaker": datasets.ClassLabel(names=["病人", "医生"]),
+                                "utterance": datasets.Value("string"),
+                            }
+                        ),
+                    }
+                )
+        elif self.config.schema == "bigbio_text":
+            features = text_features
+
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            supervised_keys=None,
+            homepage=_HOMEPAGE,
+            license=str(_LICENSE),
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager):
+        lang = self.config.name.split("_")[1]
+        my_urls = {
+            split: self._get_gdrive_url(url) for split, url in _URLs[lang].items()
+        }
+        dl_dir = dl_manager.download_and_extract(my_urls)
+        return [
+            datasets.SplitGenerator(
+                name=split,
+                gen_kwargs={"filepath": dl_dir[split], "split": split, "lang": lang},
+            )
+            for split in _URLs[lang]
+        ]
+
+    def _generate_examples(self, filepath, split, lang):
+        with open(filepath, "r") as f:
+            data = json.load(f)
+
+        # delimiter symbol differs by language
+        delimiter = "：" if lang == "zh" else ":"
+        document_id = f"{lang}_{split}"
+
+        for i, d in enumerate(data):
+            out_utterances = []
+            utterances = d["utterances"] if lang == "en" else d
+            for j, utt in enumerate(utterances):
+                elements = utt.strip().split(delimiter)
+                speaker = elements[0]
+                text = delimiter.join(elements[1:]).strip()
+                if self.config.schema == "bigbio_text":
+                    # TODO - this ignores description
+                    id = f"{document_id}_{i}_{j}"
+                    yield id, {
+                        "id": id,
+                        "document_id": document_id,
+                        "text": text,
+                        "labels": [speaker],
+                    }
+                else:
+                    out_utterances.append({"speaker": speaker, "utterance": text})
+            if self.config.schema == "source":
+                id = f"{document_id}_{i}"
+                if lang == "en":
+                    yield id, {
+                        "description": d["description"],
+                        "utterances": out_utterances,
+                    }
+                else:
+                    yield id, {
+                        "utterances": out_utterances,
+                    }