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