Create sci_lay.py

sci_lay.py

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+"""SciLay Dataset."""
+
+import gzip
+import json
+import os
+
+import datasets
+from datasets.download.streaming_download_manager import FilesIterable
+
+_HOMEPAGE = ""
+
+_CITATION = """
+"""
+
+_DESCRIPTION = """
+SCILAY comprises 46,486 instances, each representing a scientific article in the biomedical domain. 
+Each instance in the dataset includes the following components:
+    - plain_text: Containing a plain language summary of the scientific article. This section is written in a simple and accessible language, and is intended to be understandable by a wide audience.
+    - technical_text: This section contains the abstract of the scientific article. It provides a detailed and technical description of the research conducted in the article.
+In addition to the textual content, each instance is associated with the following metadata:
+    - Keywords: Keywords that capture the main topics and themes addressed in the article.
+    - Journal: The journal in which the article is published, providing context about the source of the research.
+    - DOI (Digital Object Identifier): A unique identifier for the article, facilitating easy referencing.
+The main objective of the SCILAY dataset is to support the development and evaluation of text summarization models that can effectively simplify complex scientific language while retaining the essential information. 
+"""
+
+_LICENSE = "Creative Commons Attribution 4.0 International"
+
+_SPLIT_NAMES = {datasets.Split.TRAIN: "train", datasets.Split.VALIDATION: "validation", datasets.Split.TEST: "test"}
+_URL = "data/{version}/{split_name}.zip"
+
+_DOI = "doi"
+_PMCID = "pmcid"
+_SUMMARY = "plain_text"
+_ABSTRACT = "technical_text"
+_JOURNAL = "journal"
+_TOPICS = "topics"
+_KEYWORDS = "keywords"
+
+_JOURNALS = {
+    "NC": "Nature Communications",
+    "A": "Animals: an Open Access Journal from MDPI",
+    "NIHR": "NIHR Journals Library",
+    "PLGEN": "PLoS Genetics",
+    "PLPAT": "PLoS Pathogens",
+    "PLCB": "PLoS Computational Biology",
+    "PLNTD": "PLoS Neglected Tropical Diseases",
+    "B": "Biology",
+    "I": "Insects",
+    "EL": "eLife",
+    "PLB": "PLoS Biology",
+    "CB": "Communications Biology",
+    "SD": "Scientific Data",
+    "MBIO": "mBio",
+    "C": "Cancers",
+    "OTHER": "Others"
+}
+
+# Available versions:
+# 1.0.0 cased raw strings.
+
+_VERSION = "1.0.0"
+
+class SciLayConfig(datasets.BuilderConfig):
+    """BuilderConfig for SciLay."""
+
+    def __init__(self, journals="all", version=_VERSION, **kwargs):
+        """BuilderConfig for SciLay.
+        Args:
+            journals (str or list, default 'all'): List of journal names. Either 'all' or a combination
+                of {'NC', 'A', 'NIHR', 'PLGEN', 'PLPAT', 'PLCB', 'PLNTD', 'B', 'I', 'EL', 'PLB', 'CB', 'SD', 'MBIO', 'C', 'OTHER'}.
+            **kwargs: keyword arguments forwarded to super.
+        """
+        if isinstance(journals, str):
+            journals = [journals]
+        name = "+".join(journals)
+        if name == "all":
+            journals = list(_JOURNALS) 
+        if version != _VERSION:
+            name = f"{name}-{version}"
+        super().__init__(name=name, version=version, **kwargs)
+        self.journals = journals
+
+class SciLay(datasets.GeneratorBasedBuilder):
+    """SciLay datasets."""
+
+    BUILDER_CONFIG_CLASS = SciLayConfig
+    BUILDER_CONFIGS = [
+        SciLayConfig(
+            journals="all",
+            description="Articles from all journals.",
+        ),
+    ] + [
+        SciLayConfig(
+            journals=k,
+            description=f"Articles from journals {k}: {v}",
+        )
+        for k, v in sorted(_JOURNALS.items())
+    ]
+    DEFAULT_CONFIG_NAME = "all"
+    VERSION = _VERSION
+
+    def _info(self):
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=datasets.Features({
+                _DOI: datasets.Value("string"),
+                _PMCID: datasets.Value("string"),
+                _SUMMARY: datasets.Value("string"),
+                _ABSTRACT: datasets.Value("string"),
+                _JOURNAL: datasets.Value("string"),
+                _TOPICS: datasets.Sequence(datasets.Value("string")),
+                _KEYWORDS: datasets.Sequence(datasets.Value("string"))
+            }),
+            supervised_keys=(_ABSTRACT, _SUMMARY),
+            homepage=_HOMEPAGE,
+            license=_LICENSE,
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager):
+            """Returns SplitGenerators."""
+            urls = {
+                split: _URL.format(version=self.config.version, split_name=split_name)
+                for split, split_name in _SPLIT_NAMES.items()
+            }
+            dl_paths = dl_manager.download_and_extract(urls)
+            paths = {
+                split: [
+                    dl_manager.iter_files(os.path.join(dl_paths[split], split_name, code)) for code in self.config.journals
+                ]
+                for split, split_name in _SPLIT_NAMES.items()
+            }
+            raise Exception(f"paths creati = {[file_path.__repr__ for file_path in paths]}")
+            return [
+                datasets.SplitGenerator(
+                    name=split,
+                    gen_kwargs={"paths": paths[split]},
+                )
+                for split in _SPLIT_NAMES
+            ]
+
+    def _generate_examples(self, paths=None):
+        """Yields examples."""
+        for paths_per_journal in paths:
+            for path in paths_per_journal:
+                with open(path, "rb") as fin:
+                    fin = gzip.GzipFile(fileobj=fin)
+                    for row in fin:
+                        json_obj = json.loads(row)
+                        yield json_obj["doi"], {
+                            _DOI: json_obj[_DOI],
+                            _PMCID: json_obj[_PMCID],
+                            _SUMMARY: json_obj[_SUMMARY],
+                            _ABSTRACT: json_obj[_ABSTRACT],
+                            _JOURNAL: json_obj[_JOURNAL],
+                            _TOPICS: json_obj[_TOPICS],
+                            _KEYWORDS: json_obj[_KEYWORDS]
+                        }
+