This textbook was written for the clinical research community at Johns Hopkins leveraging the precision medicine analytics platform (PMAP). These notebooks are available in html form on the Precision Medicine portal as well as in computational form in the CAMP-share folder on Crunchr (Crunchr.pm.jh.edu).

• Platform Tool : Jupyter/Crunchr on PMAP using
• Programming Language : Python 3
• Author(s) : Brandon Smith
• License : The notebook is released under the Apache 2.0 License
• Last Updated : May 12th, 2020

How to access files from your SAFE Desktop (S:) drive

Setup: Import dependencies

import subprocess
import getpass
import os
from SciServer import Authentication

Get JHED ID and enter JHED Password

myUserName = Authentication.getKeystoneUserWithToken(Authentication.getToken()).userName
passwd = getpass.getpass('Password for ' + myUserName + ': ')

Set up paths and enter SAFE Project folder name

userstring = "username=" + myUserName + ",workgroup=win,uid=idies,password=" + passwd
projectname = input("Please enter the name of your SAFE Desktop project folder : ") 
dir = "//cloud.nas.jh.edu/sddesktop$/" + projectname

Create SAFE folder at the top of the directory and mount contents of your SAFE Project folder

devnull = open(os.devnull, 'w')
subprocess.run(["sudo", "mkdir", "-p" "/home/idies/workspace/SAFE/"], capture_output=False)
subprocess.run(["sudo", "chown", "idies:idies", "/home/idies/workspace/SAFE/"], capture_output=False)
try:
    subprocess.run(["sudo", "mount", "-t", "cifs", dir, "/home/idies/workspace/SAFE/", "-o", userstring], stdout=devnull, stderr=devnull)
except FileNotFoundError as e:
    print(e)