Format Pubmed for Citaion
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#!/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() |
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