commit: 3d50b0288dc2ba42baf550353f3fb5bee6462754
parent: 6d28e9d6945b5510b3d861e20521554435a10f63
Author: Adam Tauber <asciimoo@gmail.com>
Date: Wed, 1 Nov 2017 21:27:57 +0100
Merge pull request #1075 from kvch/finish-jibe-b-engines
Finish PRs of @jibe-b: pubmed, oa_doi_rewrite, openaire, arxiv
Diffstat:
13 files changed, 373 insertions(+), 40 deletions(-)
diff --git a/searx/engines/arxiv.py b/searx/engines/arxiv.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+"""
+ ArXiV (Scientific preprints)
+ @website https://arxiv.org
+ @provide-api yes (export.arxiv.org/api/query)
+ @using-api yes
+ @results XML-RSS
+ @stable yes
+ @parse url, title, publishedDate, content
+ More info on api: https://arxiv.org/help/api/user-manual
+"""
+
+from lxml import html
+from datetime import datetime
+from searx.url_utils import urlencode
+
+
+categories = ['science']
+
+base_url = 'http://export.arxiv.org/api/query?search_query=all:'\
+ + '{query}&start={offset}&max_results={number_of_results}'
+
+# engine dependent config
+number_of_results = 10
+
+
+def request(query, params):
+ # basic search
+ offset = (params['pageno'] - 1) * number_of_results
+
+ string_args = dict(query=query,
+ offset=offset,
+ number_of_results=number_of_results)
+
+ params['url'] = base_url.format(**string_args)
+
+ return params
+
+
+def response(resp):
+ results = []
+
+ dom = html.fromstring(resp.content)
+ search_results = dom.xpath('//entry')
+
+ for entry in search_results:
+ title = entry.xpath('.//title')[0].text
+
+ url = entry.xpath('.//id')[0].text
+
+ content_string = '{doi_content}{abstract_content}'
+
+ abstract = entry.xpath('.//summary')[0].text
+
+ # If a doi is available, add it to the snipppet
+ try:
+ doi_content = entry.xpath('.//link[@title="doi"]')[0].text
+ content = content_string.format(doi_content=doi_content, abstract_content=abstract)
+ except:
+ content = content_string.format(doi_content="", abstract_content=abstract)
+
+ if len(content) > 300:
+ content = content[0:300] + "..."
+ # TODO: center snippet on query term
+
+ publishedDate = datetime.strptime(entry.xpath('.//published')[0].text, '%Y-%m-%dT%H:%M:%SZ')
+
+ res_dict = {'url': url,
+ 'title': title,
+ 'publishedDate': publishedDate,
+ 'content': content}
+
+ results.append(res_dict)
+
+ return results
diff --git a/searx/engines/base.py b/searx/engines/base.py
@@ -73,7 +73,7 @@ def request(query, params):
def response(resp):
results = []
- search_results = etree.XML(resp.text)
+ search_results = etree.XML(resp.content)
for entry in search_results.xpath('./result/doc'):
content = "No description available"
diff --git a/searx/engines/pubmed.py b/searx/engines/pubmed.py
@@ -0,0 +1,98 @@
+#!/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
diff --git a/searx/plugins/__init__.py b/searx/plugins/__init__.py
@@ -22,7 +22,7 @@ if version_info[0] == 3:
logger = logger.getChild('plugins')
-from searx.plugins import (doai_rewrite,
+from searx.plugins import (oa_doi_rewrite,
https_rewrite,
infinite_scroll,
open_results_on_new_tab,
@@ -78,7 +78,7 @@ class PluginStore():
plugins = PluginStore()
-plugins.register(doai_rewrite)
+plugins.register(oa_doi_rewrite)
plugins.register(https_rewrite)
plugins.register(infinite_scroll)
plugins.register(open_results_on_new_tab)
diff --git a/searx/plugins/doai_rewrite.py b/searx/plugins/doai_rewrite.py
@@ -1,32 +0,0 @@
-from flask_babel import gettext
-import re
-from searx.url_utils import urlparse, parse_qsl
-
-regex = re.compile(r'10\.\d{4,9}/[^\s]+')
-
-name = gettext('DOAI rewrite')
-description = gettext('Avoid paywalls by redirecting to open-access versions of publications when available')
-default_on = False
-preference_section = 'privacy'
-
-
-def extract_doi(url):
- match = regex.search(url.path)
- if match:
- return match.group(0)
- for _, v in parse_qsl(url.query):
- match = regex.search(v)
- if match:
- return match.group(0)
- return None
-
-
-def on_result(request, search, result):
- doi = extract_doi(result['parsed_url'])
- if doi and len(doi) < 50:
- for suffix in ('/', '.pdf', '/full', '/meta', '/abstract'):
- if doi.endswith(suffix):
- doi = doi[:-len(suffix)]
- result['url'] = 'http://doai.io/' + doi
- result['parsed_url'] = urlparse(result['url'])
- return True
diff --git a/searx/plugins/oa_doi_rewrite.py b/searx/plugins/oa_doi_rewrite.py
@@ -0,0 +1,44 @@
+from flask_babel import gettext
+import re
+from searx.url_utils import urlparse, parse_qsl
+from searx import settings
+
+
+regex = re.compile(r'10\.\d{4,9}/[^\s]+')
+
+name = gettext('Open Access DOI rewrite')
+description = gettext('Avoid paywalls by redirecting to open-access versions of publications when available')
+default_on = False
+preference_section = 'privacy'
+
+doi_resolvers = settings['doi_resolvers']
+
+
+def extract_doi(url):
+ match = regex.search(url.path)
+ if match:
+ return match.group(0)
+ for _, v in parse_qsl(url.query):
+ match = regex.search(v)
+ if match:
+ return match.group(0)
+ return None
+
+
+def get_doi_resolver(args, preference_doi_resolver):
+ doi_resolvers = settings['doi_resolvers']
+ doi_resolver = args.get('doi_resolver', preference_doi_resolver)[0]
+ if doi_resolver not in doi_resolvers:
+ doi_resolvers = settings['default_doi_resolver']
+ return doi_resolver
+
+
+def on_result(request, search, result):
+ doi = extract_doi(result['parsed_url'])
+ if doi and len(doi) < 50:
+ for suffix in ('/', '.pdf', '/full', '/meta', '/abstract'):
+ if doi.endswith(suffix):
+ doi = doi[:-len(suffix)]
+ result['url'] = get_doi_resolver(request.args, request.preferences.get_value('doi_resolver')) + doi
+ result['parsed_url'] = urlparse(result['url'])
+ return True
diff --git a/searx/preferences.py b/searx/preferences.py
@@ -15,6 +15,7 @@ LANGUAGE_CODES = [l[0] for l in languages]
LANGUAGE_CODES.append('all')
DISABLED = 0
ENABLED = 1
+DOI_RESOLVERS = list(settings['doi_resolvers'])
class MissingArgumentException(Exception):
@@ -266,7 +267,9 @@ class Preferences(object):
'results_on_new_tab': MapSetting(False, map={'0': False,
'1': True,
'False': False,
- 'True': True})}
+ 'True': True}),
+ 'doi_resolver': MultipleChoiceSetting(['oadoi.org'], choices=DOI_RESOLVERS),
+ }
self.engines = EnginesSetting('engines', choices=engines)
self.plugins = PluginsSetting('plugins', choices=plugins)
diff --git a/searx/settings.yml b/searx/settings.yml
@@ -60,6 +60,12 @@ engines:
disabled : True
shortcut : ai
+ - name : arxiv
+ engine : arxiv
+ shortcut : arx
+ categories : science
+ timeout : 4.0
+
- name : base
engine : base
shortcut : bs
@@ -409,6 +415,18 @@ engines:
shortcut : nt
disabled : True
+ - name : openaire
+ engine : json_engine
+ paging : True
+ search_url : http://api.openaire.eu/search/datasets?format=json&page={pageno}&size=10&title={query}
+ results_query : response/results/result
+ url_query : metadata/oaf:entity/oaf:result/children/instance/webresource/url/$
+ title_query : metadata/oaf:entity/oaf:result/title/$
+ content_query : metadata/oaf:entity/oaf:result/description/$
+ categories : science
+ shortcut : oa
+ timeout: 5.0
+
- name : openstreetmap
engine : openstreetmap
shortcut : osm
@@ -442,6 +460,12 @@ engines:
url: https://pirateproxy.red/
timeout : 3.0
+ - name : pubmed
+ engine : pubmed
+ shortcut : pub
+ categories: science
+ timeout : 3.0
+
- name : qwant
engine : qwant
shortcut : qw
@@ -694,3 +718,10 @@ locales:
tr : Türkçe (Turkish)
uk : українська мова (Ukrainian)
zh : 中文 (Chinese)
+
+doi_resolvers :
+ oadoi.org : 'https://oadoi.org/'
+ doi.org : 'https://doi.org/'
+ doai.io : 'http://doai.io/'
+
+default_doi_resolver : 'oadoi.org'
diff --git a/searx/templates/oscar/preferences.html b/searx/templates/oscar/preferences.html
@@ -118,6 +118,18 @@
<option value="0" {% if not results_on_new_tab %}selected="selected"{% endif %}>{{ _('Off')}}</option>
</select>
{{ preferences_item_footer(info, label, rtl) }}
+
+ {% set label = _('Open Access DOI resolver') %}
+ {% set info = _('Redirect to open-access versions of publications when available (plugin required)') %}
+ {{ preferences_item_header(info, label, rtl) }}
+ <select class="form-control" id='doi_resolver' name='doi_resolver'>
+ {% for doi_resolver_name,doi_resolver_url in doi_resolvers.items() %}
+ <option value="{{ doi_resolver_name }}" {% if doi_resolver_name == current_doi_resolver %}selected="selected"{% endif %}>
+ {{ doi_resolver_name }} - {{ doi_resolver_url }}
+ </option>
+ {% endfor %}
+ </select>
+ {{ preferences_item_footer(info, label, rtl) }}
</div>
</fieldset>
</div>
diff --git a/searx/webapp.py b/searx/webapp.py
@@ -66,6 +66,7 @@ from searx.search import SearchWithPlugins, get_search_query_from_webapp
from searx.query import RawTextQuery
from searx.autocomplete import searx_bang, backends as autocomplete_backends
from searx.plugins import plugins
+from searx.plugins.oa_doi_rewrite import get_doi_resolver
from searx.preferences import Preferences, ValidationException
from searx.answerers import answerers
from searx.url_utils import urlencode, urlparse, urljoin
@@ -695,6 +696,8 @@ def preferences():
shortcuts={y: x for x, y in engine_shortcuts.items()},
themes=themes,
plugins=plugins,
+ doi_resolvers=settings['doi_resolvers'],
+ current_doi_resolver=get_doi_resolver(request.args, request.preferences.get_value('doi_resolver')),
allowed_plugins=allowed_plugins,
theme=get_current_theme_name(),
preferences_url_params=request.preferences.get_as_url_params(),
@@ -839,7 +842,10 @@ def config():
'autocomplete': settings['search']['autocomplete'],
'safe_search': settings['search']['safe_search'],
'default_theme': settings['ui']['default_theme'],
- 'version': VERSION_STRING})
+ 'version': VERSION_STRING,
+ 'doi_resolvers': [r for r in search['doi_resolvers']],
+ 'default_doi_resolver': settings['default_doi_resolver'],
+ })
@app.errorhandler(404)
diff --git a/tests/unit/engines/pubmed.py b/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.')
diff --git a/tests/unit/engines/test_arxiv.py b/tests/unit/engines/test_arxiv.py
@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+from collections import defaultdict
+import mock
+from searx.engines import arxiv
+from searx.testing import SearxTestCase
+
+
+class TestBaseEngine(SearxTestCase):
+
+ def test_request(self):
+ query = 'test_query'
+ dicto = defaultdict(dict)
+ dicto['pageno'] = 1
+ params = arxiv.request(query, dicto)
+ self.assertIn('url', params)
+ self.assertIn('export.arxiv.org/api/', params['url'])
+
+ def test_response(self):
+ self.assertRaises(AttributeError, arxiv.response, None)
+ self.assertRaises(AttributeError, arxiv.response, [])
+ self.assertRaises(AttributeError, arxiv.response, '')
+ self.assertRaises(AttributeError, arxiv.response, '[]')
+
+ response = mock.Mock(content=b'''<?xml version="1.0" encoding="UTF-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom"></feed>''')
+ self.assertEqual(arxiv.response(response), [])
+
+ xml_mock = b'''<?xml version="1.0" encoding="UTF-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom">
+ <title type="html">ArXiv Query: search_query=all:test_query&id_list=&start=0&max_results=1</title>
+ <id>http://arxiv.org/api/1</id>
+ <updated>2000-01-21T00:00:00-01:00</updated>
+ <opensearch:totalResults xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">1</opensearch:totalResults>
+ <opensearch:startIndex xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">0</opensearch:startIndex>
+ <opensearch:itemsPerPage xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">1</opensearch:itemsPerPage>
+ <entry>
+ <id>http://arxiv.org/1</id>
+ <updated>2000-01-01T00:00:01Z</updated>
+ <published>2000-01-01T00:00:01Z</published>
+ <title>Mathematical proof.</title>
+ <summary>Mathematical formula.</summary>
+ <author>
+ <name>A. B.</name>
+ </author>
+ <link href="http://arxiv.org/1" rel="alternate" type="text/html"/>
+ <link title="pdf" href="http://arxiv.org/1" rel="related" type="application/pdf"/>
+ <category term="math.QA" scheme="http://arxiv.org/schemas/atom"/>
+ <category term="1" scheme="http://arxiv.org/schemas/atom"/>
+ </entry>
+</feed>
+'''
+
+ response = mock.Mock(content=xml_mock)
+ results = arxiv.response(response)
+ self.assertEqual(type(results), list)
+ self.assertEqual(len(results), 1)
+ self.assertEqual(results[0]['title'], 'Mathematical proof.')
+ self.assertEqual(results[0]['content'], 'Mathematical formula.')
diff --git a/tests/unit/engines/test_base.py b/tests/unit/engines/test_base.py
@@ -21,10 +21,10 @@ class TestBaseEngine(SearxTestCase):
self.assertRaises(AttributeError, base.response, '')
self.assertRaises(AttributeError, base.response, '[]')
- response = mock.Mock(text='<response></response>')
+ response = mock.Mock(content=b'<response></response>')
self.assertEqual(base.response(response), [])
- xml_mock = """<?xml version="1.0"?>
+ xml_mock = b"""<?xml version="1.0"?>
<response>
<lst name="responseHeader">
<int name="status">0</int>
@@ -83,7 +83,7 @@ class TestBaseEngine(SearxTestCase):
</result>
</response>"""
- response = mock.Mock(text=xml_mock.encode('utf-8'))
+ response = mock.Mock(content=xml_mock)
results = base.response(response)
self.assertEqual(type(results), list)
self.assertEqual(len(results), 1)
