[add] pubmed engine

searx/engines/pubmed.py

@@ -0,0 +1,101 @@
+#!/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 lxml import etree
+from datetime import datetime
+from searx.url_utils import urlencode, urlopen
+
+
+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}'
+
+    # handle Python2 vs Python3 management of bytes and strings
+    try:
+        pmids_results = etree.XML(resp.text.encode('utf-8'))
+    except AttributeError:
+        pmids_results = etree.XML(resp.text)
+
+    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 = urlopen(retrieve_url_encoded).read()
+    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 = '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
+        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

searx/settings.yml

@@ -460,6 +460,12 @@ engines:
     url: https://pirateproxy.red/
     timeout : 3.0
 
+  - name : pubmed
+    engine : pubmed
+    shortcut : pub
+    categories: science
+    oa_first : false
+
   - name : qwant
     engine : qwant
     shortcut : qw

searx/url_utils.py

@@ -3,6 +3,7 @@ from sys import version_info
 if version_info[0] == 2:
     from urllib import quote, quote_plus, unquote, urlencode
     from urlparse import parse_qs, parse_qsl, urljoin, urlparse, urlunparse, ParseResult
+    from urllib2 import urlopen
 else:
     from urllib.parse import (
         parse_qs,
@@ -16,6 +17,7 @@ else:
         urlunparse,
         ParseResult
     )
+    from urllib.request import urlopen
 
 
 __export__ = (parse_qs,

tests/unit/engines/pubmed.py

@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+from collections import defaultdict
+import mock
+from searx.engines import pubmed
+from searx.testing import SearxTestCase
+
+
+class TestPubmedEngine(SearxTestCase):
+
+    def test_request(self):
+        query = 'test_query'
+        dicto = defaultdict(dict)
+        dicto['pageno'] = 1
+        params = pubmed.request(query, dicto)
+        self.assertIn('url', params)
+        self.assertIn('eutils.ncbi.nlm.nih.gov/', params['url'])
+        self.assertIn('term', params['url'])
+
+    def test_response(self):
+        self.assertRaises(AttributeError, pubmed.response, None)
+        self.assertRaises(AttributeError, pubmed.response, [])
+        self.assertRaises(AttributeError, pubmed.response, '')
+        self.assertRaises(AttributeError, pubmed.response, '[]')
+
+        response = mock.Mock(text='<PubmedArticleSet></PubmedArticleSet>')
+        self.assertEqual(pubmed.response(response), [])
+
+        xml_mock = """<eSearchResult><Count>1</Count><RetMax>1</RetMax><RetStart>0</RetStart><IdList>
+<Id>1</Id>
+</IdList></eSearchResult>
+"""
+
+        response = mock.Mock(text=xml_mock.encode('utf-8'))
+        results = pubmed.response(response)
+        self.assertEqual(type(results), list)
+        self.assertEqual(len(results), 1)
+        self.assertEqual(results[0]['content'], 'No abstract is available for this publication.')