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#
# Copyright 2021 Martin Owens <doctormo@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>
#
"""
Access Reactome Content Services.
"""
import re
from import_sources import RemoteSource
TAG_REX = re.compile(r'<[^<]+?>')
class Reactome(RemoteSource):
name = 'Reactome (Bio)'
icon = 'sources/reactome.svg'
search_url = "https://reactome.org/ContentService/search/query"
file_url = "https://reactome.org/icon/{stId}.svg"
icon_url = "https://reactome.org/icon/{stId}.png"
all_licence = "cc-by-sa-4.0"
def search(self, query):
params = {
"query": query,
"types": "Icon",
"cluster": "true",
"Start row": 0,
"rows": 100,
}
response = {}
try:
response = self.session.get(self.search_url, params=params).json()
except Exception:
pass
if 'messages' in response and 'No entries' in response['messages'][0]:
return
for cats in response.get('results', []):
for entry in cats['entries']:
yield {
'id': entry['dbId'],
'name': TAG_REX.sub('', entry['name']),
'author': 'Reactome/'+entry.get('iconDesignerName', "Unknown"),
'summary': TAG_REX.sub('', entry.get('summation', '')),
'created': None, # No data
'popularity': 0, # No data
'thumbnail': self.icon_url.format(**entry),
'file': self.file_url.format(**entry),
'license': self.all_licence,
}
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