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#!/usr/bin/env python
"""
PubMed (Scholar publications)
@website https://www.ncbi.nlm.nih.gov/pubmed/
@provide-api yes (https://www.ncbi.nlm.nih.gov/home/develop/api/)
@using-api yes
@results XML
@stable yes
@parse url, title, publishedDate, content
More info on api: https://www.ncbi.nlm.nih.gov/books/NBK25501/
"""
from flask_babel import gettext
from lxml import etree
from datetime import datetime
from searx.url_utils import urlencode
from searx.poolrequests import get
categories = ['science']
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 = dict(query=urlencode({'term': query}),
offset=offset,
hits=number_of_results)
params['url'] = base_url.format(**string_args)
return params
def response(resp):
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 = dict(pmids_string=pmids_string)
retrieve_url_encoded = pubmed_retrieve_api_url.format(**retrieve_notice_args)
search_results_xml = get(retrieve_url_encoded).content
search_results = etree.XML(search_results_xml).xpath('//PubmedArticleSet/PubmedArticle/MedlineCitation')
for entry in search_results:
title = entry.xpath('.//Article/ArticleTitle')[0].text
pmid = entry.xpath('.//PMID')[0].text
url = pubmed_url + pmid
try:
content = entry.xpath('.//Abstract/AbstractText')[0].text
except:
content = gettext('No abstract is available for this publication.')
# If a doi is available, add it to the snipppet
try:
doi = entry.xpath('.//ELocationID[@EIdType="doi"]')[0].text
content = 'DOI: {doi} Abstract: {content}'.format(doi=doi, content=content)
except:
pass
if len(content) > 300:
content = content[0:300] + "..."
# TODO: center snippet on query term
publishedDate = datetime.strptime(entry.xpath('.//DateCreated/Year')[0].text
+ '-' + entry.xpath('.//DateCreated/Month')[0].text
+ '-' + entry.xpath('.//DateCreated/Day')[0].text, '%Y-%m-%d')
res_dict = {'url': url,
'title': title,
'publishedDate': publishedDate,
'content': content}
results.append(res_dict)
return results
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