def make_enr_clust():
import enrichr_functions as enr_fun
enr, response_list = enr_fun.enrichr_get_request('ChEA_2015', 939279)
net = enr_fun.enrichr_clust_from_response(response_list)
net.write_json_to_file('viz','json/enr_clust_example.json')
def main():
import enrichr_functions as enr_fun
import json
import requests
gmt = 'KEA_2015'
userListId = 939279
# userListId = 939379
# userListId = 100
# define the get url
get_url = 'http://amp.pharm.mssm.edu/Enrichr/enrich'
# get parameters
params = {'backgroundType': gmt, 'userListId': userListId}
# try get request until status code is 200
inst_status_code = 400
# wait until okay status code is returned
num_try = 0
while inst_status_code == 400 and num_try < 100:
num_try = num_try + 1
try:
# make the get request to get the enrichr results
print('make-get-req-Enrichr')
try:
get_response = requests.get(get_url, params=params)
# get status_code
inst_status_code = get_response.status_code
print('inst_status_code: ' + str(inst_status_code))
except:
print('get request failed\n------------------------\n\n')
except:
pass
# load as dictionary
resp_json = json.loads(get_response.text)
# get the key
only_key = resp_json.keys()[0]
# get response_list
response_list = resp_json[only_key]
net = enr_fun.enrichr_clust_from_response(response_list)
views = net.viz['views']
net.write_json_to_file('viz', 'json/enr_clust_example.json')
def Enrichr_cluster(mongo_address, viz_id, enr_list):
import enrichr_functions as enr_fun
from bson.objectid import ObjectId
from pymongo import MongoClient
print('-----------------')
print('Enrichr_cluster function, running enrichr_clust_from_response')
print('-----------------')
# set up database connection
client = MongoClient(mongo_address)
db = client.clustergrammer
viz_id = ObjectId(viz_id)
# get placeholder viz data
found_viz = db.networks.find_one({'_id': viz_id })
# try to get enr and make clustergram
try:
# make clustergram
threshold = 0.001
num_thresh = 1
# get results from Enrichr and make clustergram netowrk object
net = enr_fun.enrichr_clust_from_response(enr_list)
# export dat to database
#!! export dat not working
export_dat = {}
export_dat['name'] = 'enrichment_vector'
export_dat['dat'] = '' # net.export_net_json('dat')
export_dat['source'] = 'Enrichr_clustergram'
dat_id = db.network_data.insert( export_dat )
update_viz = net.viz
update_dat = dat_id
# if there is an error update json with error
except:
update_viz = 'error'
update_dat = 'error'
# export viz to database
found_viz['viz'] = update_viz
found_viz['dat'] = update_dat
# update the viz data
db.networks.update_one( {"_id":viz_id}, {"$set": found_viz} )
# close database connection
client.close()
