pubmed-bibtex/pubmed_bibtex/__init__.py

"""
Generate BibTeX Entries for PubMed Publications

This module utilizes the API of TeXMed,
a BibTeX interface for PubMed.

TeXMed was written by Arne Muller
https://www.bioinformatics.org/texmed/

Command Line Example:
$ pubmed-bibtex 31025164
@Article{pmid31025164,
   Author="...",
   Title="...",
   Journal="...",
   ...
}

Python Example:
>>> from pubmed_bibtex import bibtex_entry_from_pmid
>>> print(bibtex_entry_from_pmid(123456789))

Copyright (C) 2019 Fabian Peter Hammerle <fabian@hammerle.me>

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.
"""

import html.parser
import logging
import re
import typing
import urllib.parse
import urllib.request

from pubmed_bibtex.version import __version__

__all__ = ["__version__", "bibtex_entry_from_pmid"]

_TEXMED_URL_PATTERN = (
    "https://www.bioinformatics.org/texmed/cgi-bin/list.cgi?PMID={pmid}&linkOut"
)

_LOGGER = logging.getLogger(__name__)


class _TeXMedHtmlParser(html.parser.HTMLParser):
    def __init__(self) -> None:
        self.bibtex_entry: typing.Optional[str] = None
        super().__init__()

    @staticmethod
    def _strip_bibtex_entry(data: str) -> str:
        return re.sub(r"\n\% \d+\s?\n", "", data).strip() + "\n"

    def handle_data(self, data: str) -> None:
        if "Author" in data:
            self.bibtex_entry = self._strip_bibtex_entry(data)

    @staticmethod
    def error(message: str) -> None:
        raise Exception(message)  # pragma: no cover


def bibtex_entry_from_pmid(pmid: str, retries: int = 2) -> typing.Optional[str]:
    assert pmid.isdigit(), pmid
    parser = _TeXMedHtmlParser()
    for attempt_index in range(1, retries + 2):
        with urllib.request.urlopen(  # raises urllib.error.HTTPError
            _TEXMED_URL_PATTERN.format(pmid=urllib.parse.quote(pmid))
        ) as resp:
            parser.feed(resp.read().decode("utf-8"))
        if parser.bibtex_entry is None:
            _LOGGER.log(
                logging.WARNING if attempt_index <= retries else logging.ERROR,
                "attempt #%d/%d to fetch bibtex entry failed",
                attempt_index,
                retries + 1,
            )
        else:
            break
    return parser.bibtex_entry