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# SPDX-License-Identifier: AGPL-3.0-or-later
"""PubMed (Scholar publications)
"""
from datetime import datetime
from urllib.parse import urlencode
from lxml import etree
from searx.network import get
from searx.utils import (
eval_xpath_getindex,
eval_xpath_list,
extract_text,
)
# about
about = {
"website": 'https://www.ncbi.nlm.nih.gov/pubmed/',
"wikidata_id": 'Q1540899',
"official_api_documentation": {
'url': 'https://www.ncbi.nlm.nih.gov/home/develop/api/',
'comment': 'More info on api: https://www.ncbi.nlm.nih.gov/books/NBK25501/',
},
"use_official_api": True,
"require_api_key": False,
"results": 'XML',
}
categories = ['science', 'scientific publications']
base_url = (
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' + '?db=pubmed&{query}&retstart={offset}&retmax={hits}'
)
# engine dependent config
number_of_results = 10
pubmed_url = 'https://www.ncbi.nlm.nih.gov/pubmed/'
def request(query, params):
# basic search
offset = (params['pageno'] - 1) * number_of_results
string_args = {
'query': urlencode({'term': query}),
'offset': offset,
'hits': number_of_results,
}
params['url'] = base_url.format(**string_args)
return params
def response(resp): # pylint: disable=too-many-locals
results = []
# First retrieve notice of each result
pubmed_retrieve_api_url = (
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?' + 'db=pubmed&retmode=xml&id={pmids_string}'
)
pmids_results = etree.XML(resp.content)
pmids = pmids_results.xpath('//eSearchResult/IdList/Id')
pmids_string = ''
for item in pmids:
pmids_string += item.text + ','
retrieve_notice_args = {'pmids_string': pmids_string}
retrieve_url_encoded = pubmed_retrieve_api_url.format(**retrieve_notice_args)
search_results_response = get(retrieve_url_encoded).content
search_results = etree.XML(search_results_response)
for entry in eval_xpath_list(search_results, '//PubmedArticle'):
medline = eval_xpath_getindex(entry, './MedlineCitation', 0)
title = eval_xpath_getindex(medline, './/Article/ArticleTitle', 0).text
pmid = eval_xpath_getindex(medline, './/PMID', 0).text
url = pubmed_url + pmid
content = extract_text(
eval_xpath_getindex(medline, './/Abstract/AbstractText//text()', 0, default=None), allow_none=True
)
doi = extract_text(
eval_xpath_getindex(medline, './/ELocationID[@EIdType="doi"]/text()', 0, default=None), allow_none=True
)
journal = extract_text(
eval_xpath_getindex(medline, './Article/Journal/Title/text()', 0, default=None), allow_none=True
)
issn = extract_text(
eval_xpath_getindex(medline, './Article/Journal/ISSN/text()', 0, default=None), allow_none=True
)
authors = []
for author in eval_xpath_list(medline, './Article/AuthorList/Author'):
f = eval_xpath_getindex(author, './ForeName', 0, default=None)
l = eval_xpath_getindex(author, './LastName', 0, default=None)
f = '' if f is None else f.text
l = '' if l is None else l.text
authors.append((f + ' ' + l).strip())
res_dict = {
'template': 'paper.html',
'url': url,
'title': title,
'content': content or "",
'journal': journal,
'issn': [issn],
'authors': authors,
'doi': doi,
}
accepted_date = eval_xpath_getindex(
entry, './PubmedData/History//PubMedPubDate[@PubStatus="accepted"]', 0, default=None
)
if accepted_date is not None:
year = eval_xpath_getindex(accepted_date, './Year', 0)
month = eval_xpath_getindex(accepted_date, './Month', 0)
day = eval_xpath_getindex(accepted_date, './Day', 0)
try:
publishedDate = datetime.strptime(
year.text + '-' + month.text + '-' + day.text,
'%Y-%m-%d',
)
res_dict['publishedDate'] = publishedDate
except Exception as e: # pylint: disable=broad-exception-caught
print(e)
results.append(res_dict)
return results
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