Format Pubmed for Citaion

pubmed-format.py

#!/usr/bin/env python3

import argparse
import xml.etree.ElementTree as ET


def _main():
    parser = argparse.ArgumentParser(description='')
    parser.add_argument('pubmed_xml')
    options = parser.parse_args()

    tree = ET.parse(options.pubmed_xml)
    root = tree.getroot()
    print(root)
    for one in tree.findall('.//PubmedArticle'):
        pub_year = one.find('.//PubDate/Year').text
        # pub_month = one.find('.//PubDate/Month').text
        # pub_day = one.find('.//PubDate/Day').text

        title = one.find('.//ArticleTitle').text
        journal = one.find('.//Journal/Title').text

        # volume = one.find('.//Journal/JournalIssue/Volume').text
        #issue = one.find('.//Journal/JournalIssue/Issue')
        doi = one.find('.//ArticleId[@IdType=\'doi\']').text

        author_list = []
        for one_author in one.findall('.//Author'):
            last_name = one_author.find('./LastName').text
            initials = one_author.find('./Initials').text
            author_list.append(f"{initials}, {last_name}.")
        author_text = ', '.join(author_list)
        print(
            f"{author_text} ({pub_year}) \"{title}\" {journal}. https://doi.org/{doi}")

    pass


if __name__ == '__main__':
    _main()