mirror of
https://github.com/searxng/searxng.git
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Merge branch 'master' into opensearch_shortname
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commit
5b21a7fb65
@ -59,3 +59,4 @@ generally made searx better:
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- Harry Wood @harry-wood
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- Thomas Renard @threnard
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- Pydo `<https://github.com/pydo>`_
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- Athemis `<https://github.com/Athemis>`_
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109
searx/engines/pdbe.py
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109
searx/engines/pdbe.py
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@ -0,0 +1,109 @@
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"""
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PDBe (Protein Data Bank in Europe)
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@website https://www.ebi.ac.uk/pdbe
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@provide-api yes (https://www.ebi.ac.uk/pdbe/api/doc/search.html),
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unlimited
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@using-api yes
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@results python dictionary (from json)
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@stable yes
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@parse url, title, content, img_src
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"""
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from json import loads
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from flask_babel import gettext
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categories = ['science']
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hide_obsolete = False
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# status codes of unpublished entries
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pdb_unpublished_codes = ['HPUB', 'HOLD', 'PROC', 'WAIT', 'AUTH', 'AUCO', 'REPL', 'POLC', 'REFI', 'TRSF', 'WDRN']
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# url for api query
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pdbe_solr_url = 'https://www.ebi.ac.uk/pdbe/search/pdb/select?'
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# base url for results
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pdbe_entry_url = 'https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}'
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# link to preview image of structure
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pdbe_preview_url = 'https://www.ebi.ac.uk/pdbe/static/entry/{pdb_id}_deposited_chain_front_image-200x200.png'
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def request(query, params):
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params['url'] = pdbe_solr_url
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params['method'] = 'POST'
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params['data'] = {
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'q': query,
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'wt': "json" # request response in parsable format
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}
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return params
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def construct_body(result):
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# set title
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title = result['title']
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# construct content body
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content = """{title}<br />{authors} {journal} <strong>{volume}</strong> {page} ({year})"""
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# replace placeholders with actual content
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try:
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if result['journal']:
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content = content.format(
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title=result['citation_title'],
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authors=result['entry_author_list'][0], journal=result['journal'], volume=result['journal_volume'],
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page=result['journal_page'], year=result['citation_year'])
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else:
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content = content.format(
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title=result['citation_title'],
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authors=result['entry_author_list'][0], journal='', volume='', page='', year=result['release_year'])
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img_src = pdbe_preview_url.format(pdb_id=result['pdb_id'])
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except (KeyError):
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content = None
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img_src = None
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# construct url for preview image
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try:
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img_src = pdbe_preview_url.format(pdb_id=result['pdb_id'])
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except (KeyError):
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img_src = None
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return [title, content, img_src]
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def response(resp):
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results = []
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json = loads(resp.text)['response']['docs']
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# parse results
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for result in json:
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# catch obsolete entries and mark them accordingly
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if result['status'] in pdb_unpublished_codes:
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continue
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if hide_obsolete:
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continue
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if result['status'] == 'OBS':
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# expand title to add some sort of warning message
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title = gettext('{title} (OBSOLETE)').format(title=result['title'])
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superseded_url = pdbe_entry_url.format(pdb_id=result['superseded_by'])
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# since we can't construct a proper body from the response, we'll make up our own
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msg_superseded = gettext("This entry has been superseded by")
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content = '<em>{msg_superseded} \<a href="{url}">{pdb_id}</a></em>'.format(
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msg_superseded=msg_superseded,
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url=superseded_url,
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pdb_id=result['superseded_by'], )
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# obsoleted entries don't have preview images
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img_src = None
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else:
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title, content, img_src = construct_body(result)
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results.append({
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'url': pdbe_entry_url.format(pdb_id=result['pdb_id']),
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'title': title,
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'content': content,
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'img_src': img_src
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})
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return results
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@ -339,6 +339,13 @@ engines:
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disabled : True
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shortcut : or
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- name : pdbe
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engine : pdbe
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shortcut : pdb
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# Hide obsolete PDB entries.
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# Default is not to hide obsolete structures
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# hide_obsolete : False
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- name : photon
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engine : photon
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shortcut : ph
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109
tests/unit/engines/test_pdbe.py
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109
tests/unit/engines/test_pdbe.py
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@ -0,0 +1,109 @@
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import mock
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from collections import defaultdict
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from searx.engines import pdbe
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from searx.testing import SearxTestCase
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class TestPdbeEngine(SearxTestCase):
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def test_request(self):
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query = 'test_query'
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dicto = defaultdict(dict)
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params = pdbe.request(query, dicto)
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self.assertTrue('url' in params)
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self.assertTrue('ebi.ac.uk' in params['url'])
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self.assertTrue('data' in params)
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self.assertTrue('q' in params['data'])
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self.assertTrue(query in params['data']['q'])
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self.assertTrue('wt' in params['data'])
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self.assertTrue('json' in params['data']['wt'])
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self.assertTrue('method' in params)
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self.assertTrue(params['method'] == 'POST')
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def test_response(self):
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self.assertRaises(AttributeError, pdbe.response, None)
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self.assertRaises(AttributeError, pdbe.response, [])
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self.assertRaises(AttributeError, pdbe.response, '')
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self.assertRaises(AttributeError, pdbe.response, '[]')
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json = """
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{
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"response": {
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"docs": [
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{
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"citation_title": "X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.",
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"citation_year": 1993,
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"entry_author_list": [
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"Conti E, Moser C, Rizzi M, Mattevi A, Lionetti C, Coda A, Ascenzi P, Brunori M, Bolognesi M"
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],
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"journal": "J. Mol. Biol.",
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"journal_page": "498-508",
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"journal_volume": "233",
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"pdb_id": "2fal",
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"status": "REL",
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"title": "X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES"
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}
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],
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"numFound": 1,
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"start": 0
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},
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"responseHeader": {
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"QTime": 0,
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"params": {
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"q": "2fal",
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"wt": "json"
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},
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"status": 0
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}
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}
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"""
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response = mock.Mock(text=json)
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results = pdbe.response(response)
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self.assertEqual(type(results), list)
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self.assertEqual(len(results), 1)
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self.assertEqual(results[0]['title'],
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'X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES')
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self.assertEqual(results[0]['url'], pdbe.pdbe_entry_url.format(pdb_id='2fal'))
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self.assertEqual(results[0]['img_src'], pdbe.pdbe_preview_url.format(pdb_id='2fal'))
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self.assertTrue('Conti E' in results[0]['content'])
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self.assertTrue('X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.' in
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results[0]['content'])
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self.assertTrue('1993' in results[0]['content'])
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# Testing proper handling of PDB entries marked as obsolete
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json = """
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{
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"response": {
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"docs": [
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{
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"citation_title": "Obsolete entry test",
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"citation_year": 2016,
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"entry_author_list": ["Doe J"],
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"journal": "J. Obs.",
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"journal_page": "1-2",
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"journal_volume": "1",
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"pdb_id": "xxxx",
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"status": "OBS",
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"title": "OBSOLETE ENTRY TEST",
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"superseded_by": "yyyy"
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}
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],
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"numFound": 1,
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"start": 0
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},
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"responseHeader": {
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"QTime": 0,
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"params": {
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"q": "xxxx",
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"wt": "json"
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},
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"status": 0
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}
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}
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"""
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response = mock.Mock(text=json)
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results = pdbe.response(response)
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self.assertEqual(type(results), list)
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self.assertEqual(len(results), 1)
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self.assertEqual(results[0]['title'], 'OBSOLETE ENTRY TEST (OBSOLETE)')
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self.assertTrue(results[0]['content'].startswith('<em>This entry has been superseded by'))
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