# Copyright [2013-2014] [Chunlei Wu] # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. #!/usr/bin/python print("Content-Type: text/html") import os import cgi try: import urlparse import urllib import httplib PY3=False except ImportError: import urllib.parse import urllib.request, urllib.parse, urllib.error import http.client PY3=True import types import json #turn it on when debugging #import cgitb #cgitb.enable() def call_service(url): if PY3: h = http.client.HTTPConnection('mygene.info') else: h = httplib.HTTPConnection('mygene.info') h.request('GET', url) res = h.getresponse() con = res.read() if res.status == 200: out = json.loads(con) return out else: print(con) form_html = '''

''' print(form_html) qs = os.environ.get("QUERY_STRING", '') if PY3: params = urllib.parse.parse_qs(qs) else: params = urlparse.parse_qs(qs) query = params.get('q', [''])[0] if query: #do the query if PY3: out = call_service('/v2/query?' + urllib.parse.urlencode(dict(q=query, species='mouse', limit=1000))) else: out = call_service('/v2/query?' + urllib.urlencode(dict(q=query, species='mouse', limit=1000))) if 'total' in out: #render the gene list print("

Found %d matched mouse gene(s)

" % out['total']) if out['total']>0: print('') print('') for gene in out['hits']: print('' % (gene['_id'], gene.get('symbol', 'None'), gene.get('name', ''))) print('
SymbolName
%s%s
') else: #something wrong, show the error err = out.get('error', out.get('reason', 'Invalid query!')) print('

Error:

 %s

' % err) else: geneid = params.get('showgene',[''])[0] if geneid: #show gene page gene = call_service('/v2/gene/%s?fields=reporter' % geneid) ps_list = [] if gene and 'reporter' in gene: ps_list = gene['reporter'].get('Mouse430_2',[]) if PY3: if type(ps_list) is not list: ps_list = [ps_list] else: if type(ps_list) is not types.ListType: # if only one probeset available, it's returned as a string, so we need to convert it to a list ps_list = [ps_list] if ps_list: for ps in ps_list: print('' % ps) else: print('

No data available for this gene.

') print('')