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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 flask_babel import gettext
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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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# 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']
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base_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'\
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+ '?db=pubmed&{query}&retstart={offset}&retmax={hits}'
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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}),
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offset=offset,
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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 = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'\
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+ 'db=pubmed&retmode=xml&id={pmids_string}'
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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_xml = get(retrieve_url_encoded).content
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search_results = etree.XML(search_results_xml).xpath('//PubmedArticleSet/PubmedArticle/MedlineCitation')
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for entry in search_results:
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title = entry.xpath('.//Article/ArticleTitle')[0].text
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pmid = entry.xpath('.//PMID')[0].text
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url = pubmed_url + pmid
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try:
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content = entry.xpath('.//Abstract/AbstractText')[0].text
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except:
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content = gettext('No abstract is available for this publication.')
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# If a doi is available, add it to the snipppet
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try:
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doi = entry.xpath('.//ELocationID[@EIdType="doi"]')[0].text
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content = 'DOI: {doi} Abstract: {content}'.format(doi=doi, content=content)
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except:
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pass
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if len(content) > 300:
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content = content[0:300] + "..."
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# TODO: center snippet on query term
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res_dict = {'url': url,
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'title': title,
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'content': content}
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try:
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publishedDate = datetime.strptime(entry.xpath('.//DateCreated/Year')[0].text
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+ '-' + entry.xpath('.//DateCreated/Month')[0].text
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+ '-' + entry.xpath('.//DateCreated/Day')[0].text, '%Y-%m-%d')
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res_dict['publishedDate'] = publishedDate
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except:
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pass
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results.append(res_dict)
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return results
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