mirror of
https://github.com/searxng/searxng.git
synced 2024-11-14 00:30:15 +01:00
110 lines
3.5 KiB
Python
110 lines
3.5 KiB
Python
"""
|
|
PDBe (Protein Data Bank in Europe)
|
|
|
|
@website https://www.ebi.ac.uk/pdbe
|
|
@provide-api yes (https://www.ebi.ac.uk/pdbe/api/doc/search.html),
|
|
unlimited
|
|
@using-api yes
|
|
@results python dictionary (from json)
|
|
@stable yes
|
|
@parse url, title, content, img_src
|
|
"""
|
|
|
|
from json import loads
|
|
from flask_babel import gettext
|
|
|
|
categories = ['science']
|
|
|
|
hide_obsolete = False
|
|
|
|
# status codes of unpublished entries
|
|
pdb_unpublished_codes = ['HPUB', 'HOLD', 'PROC', 'WAIT', 'AUTH', 'AUCO', 'REPL', 'POLC', 'REFI', 'TRSF', 'WDRN']
|
|
# url for api query
|
|
pdbe_solr_url = 'https://www.ebi.ac.uk/pdbe/search/pdb/select?'
|
|
# base url for results
|
|
pdbe_entry_url = 'https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}'
|
|
# link to preview image of structure
|
|
pdbe_preview_url = 'https://www.ebi.ac.uk/pdbe/static/entry/{pdb_id}_deposited_chain_front_image-200x200.png'
|
|
|
|
|
|
def request(query, params):
|
|
|
|
params['url'] = pdbe_solr_url
|
|
params['method'] = 'POST'
|
|
params['data'] = {
|
|
'q': query,
|
|
'wt': "json" # request response in parsable format
|
|
}
|
|
return params
|
|
|
|
|
|
def construct_body(result):
|
|
# set title
|
|
title = result['title']
|
|
|
|
# construct content body
|
|
content = """{title}<br />{authors} {journal} <strong>{volume}</strong> {page} ({year})"""
|
|
|
|
# replace placeholders with actual content
|
|
try:
|
|
if result['journal']:
|
|
content = content.format(
|
|
title=result['citation_title'],
|
|
authors=result['entry_author_list'][0], journal=result['journal'], volume=result['journal_volume'],
|
|
page=result['journal_page'], year=result['citation_year'])
|
|
else:
|
|
content = content.format(
|
|
title=result['citation_title'],
|
|
authors=result['entry_author_list'][0], journal='', volume='', page='', year=result['release_year'])
|
|
img_src = pdbe_preview_url.format(pdb_id=result['pdb_id'])
|
|
except (KeyError):
|
|
content = None
|
|
img_src = None
|
|
|
|
# construct url for preview image
|
|
try:
|
|
img_src = pdbe_preview_url.format(pdb_id=result['pdb_id'])
|
|
except (KeyError):
|
|
img_src = None
|
|
|
|
return [title, content, img_src]
|
|
|
|
|
|
def response(resp):
|
|
|
|
results = []
|
|
json = loads(resp.text)['response']['docs']
|
|
|
|
# parse results
|
|
for result in json:
|
|
# catch obsolete entries and mark them accordingly
|
|
if result['status'] in pdb_unpublished_codes:
|
|
continue
|
|
if hide_obsolete:
|
|
continue
|
|
if result['status'] == 'OBS':
|
|
# expand title to add some sort of warning message
|
|
title = gettext('{title} (OBSOLETE)').format(title=result['title'])
|
|
superseded_url = pdbe_entry_url.format(pdb_id=result['superseded_by'])
|
|
|
|
# since we can't construct a proper body from the response, we'll make up our own
|
|
msg_superseded = gettext("This entry has been superseded by")
|
|
content = '<em>{msg_superseded} \<a href="{url}">{pdb_id}</a></em>'.format(
|
|
msg_superseded=msg_superseded,
|
|
url=superseded_url,
|
|
pdb_id=result['superseded_by'], )
|
|
|
|
# obsoleted entries don't have preview images
|
|
img_src = None
|
|
else:
|
|
title, content, img_src = construct_body(result)
|
|
|
|
results.append({
|
|
'url': pdbe_entry_url.format(pdb_id=result['pdb_id']),
|
|
'title': title,
|
|
'content': content,
|
|
'img_src': img_src
|
|
})
|
|
|
|
return results
|