# 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('| Symbol | Name | ')
for gene in out['hits']:
print('
| %s | %s |
' % (gene['_id'], gene.get('symbol', 'None'), gene.get('name', '')))
print('
')
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('')