|
# 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
|