Error logging in to XNAT from Jupyter notebook on neurodeskapp with netrc file

[juan-d]

Hello,

I'm working on Neurodeskapp v 1.14.

I am using the XNAT client for python Version: 0.7.2, to connect to an xnat server (on a MacBook Pro with M5 chip and macOS Tahoe). I have no trouble connecting via the basic command, e.g., (on a Jupyter notbook):

import xnat
session = xnat.connect('https://central.xnat.org', user='myusername', password='mypassword')

(central.xnat.org is just an example, not my actual xnat).

After connecting, I can list all contents from different projects/subjects and download data with no issues.

However, when I use the .netrc file to connect, I get the following error:

XNATAuthError: Could not determine if login was successful!

I then try to list my projects or the subjects of specific projects, and I get the error:

NameError: name 'session' is not defined

My netrc file has the following structure:

machine central.xnat.org
login myusername
password mypassword

To connect to the server from the Jupyter notebook, after saving the netrc file in my home directory as ~/.netrc and after running chmod 600 ~/.netrc, I have tried the following command:

session = xnat.connect('https://central.xnat.org')

After running import os, I have also tried:

netrc_path = os.path.expanduser('~/.netrc')
session = xnat.connect('https://central.xnat.org', netrc_file=netrc_path)

I have also tried

session = xnat.connect('https://central.xnat.org', netrc_file='~/.netrc')

Finally, I have also tried to place the netrc file in the neurodesktop-storage folder and point netrc_file there, e.g.:

session = xnat.connect('https://central.xnat.org', netrc_file='/path/neurodesktop-storage/.netrc')

All of the above results in the same XNATAuthError as above.

I would greatly appreciate your help with this.

[stebo85]

Dear @juan-d - we have a look if we can reproduce this problem and then see how to fix it!

@akshitbeniwal - any ideas?

[aswinnarayanan]

Hi @juan-d

import module
await module.load('xnat/1.9.2.1')

The module version of xnat is actually the full xnat installation (which we're using for some development work)
Not the xnat client. We'll make sure to make this clear

You'll need to use the pip install xnat package version

[juan-d]

Thanks for that @aswinnarayanan.

I was able to connect to xnat using pip install xnat but the problem with the .netrc file persists.

Cheers

[aswinnarayanan]

Hi @juan-d

I couldn't reproduce the issue, but have seen netrc errors in the past. We might need to troubleshoot this a bit

We'll first confirm that python can parse your netrc files. Can you run this, and let us know if it works:

import netrc
print(netrc.netrc('/Users/juand/.netrc').authenticators('central.xnat.org'))"

[juan-d]

Hi @aswinnarayanan,

Many thanks for that. I ran the command you suggested and got the message No such file or directory. I then tried to access my home directory !ls /Users/juand/ but I got the message cannot access '/Users/juand: No such file or directory

I then did a search for "get neurodeskapp to see my home directory." I found that within Neurodesk I need to look for data in /home/jovyan/data

So, I tried,

session = xnat.connect('https://central.xnat.org', netrc_file='/home/jovyan/data/.netrc')

And that did the trick. I was able to connect.

To sum up, the solution is

!pip install xnat
import xnat
session = xnat.connect('https://central.xnat.org', netrc_file='/home/jovyan/data/.netrc')

Thank you so much @stebo85 and @aswinnarayanan for all your help.