In [ ]:
# Initialize PYTHONPATH for pyopencga
import sys
import os
from pprint import pprint
cwd = os.getcwd()
print("current_dir: ...."+cwd[-10:])
base_modules_dir = os.path.dirname(cwd)
print("base_modules_dir: ...."+base_modules_dir[-10:])
sys.path.append(base_modules_dir)
In [ ]:
from pyopencga.opencga_config import ConfigClient
from pyopencga.opencga_client import OpenCGAClient
import json
Credentials
Plese add the credentials for opencga login into a file in json format and read them from there.
i.e: file: __user_config.json flie_content: {"user":"xxx","pwd":"yyy"}
In [ ]:
## Reading user config/credentials to connect to server
user_config_json = "./__user_config.json"
with open(user_config_json,"r") as f:
user_credentials = json.loads(f.read())
print('User: {}***'.format(user_credentials["user"][:3]))
In [ ]:
user = user_credentials["user"]
passwd = user_credentials["pwd"]
In [ ]:
## Creating ConfigClient
host = 'http://bioinfodev.hpc.cam.ac.uk/opencga-test'
cc = ConfigClient()
config_dict = cc.get_basic_config_dict(host)
print("Config information:\n",config_dict)
In [ ]:
oc = OpenCGAClient(configuration=config_dict,
user=user,
pwd=passwd)
In [ ]:
## Getting the session id / token
token = oc.session_id
print("Session token:\n{}...".format(token[:10]))
In [ ]:
oc = OpenCGAClient(configuration=config_dict,
session_id=token)
You are now connected to OpenCGA
[TODO]