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searx/engines/pubmed.py

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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