migrating from XNAT 1.8.8 to 1.8.10 JupyterHub 1.1

[Nadya Shusharina]

Hello,

I have set up XNAT 1.8.10 with JupyterHub plugin 1.1.0. It all works. My data was stored in XNAT 1.8.8. When I am copying over archive and postgres-data from 1.8.8 to 1.8.10, I get an error when launching Jupyter notebook.

Thank you,

Nadya

[Andrew Lassiter]

Hi Nadya,

In JupyterHub, there's a "pre_spawn_hook" function which calls XNAT and retrieve the configuration for a user's notebook container (mounts, cpu and mem requirements, etc). The error seems to suggest the configuration JSON returned from XNAT is empty or not valid JSON, which shouldn't be the case.

After starting a notebook from XNAT could you check the response from this API endpoint: /jupyterhub/users/{username}/server/user-options. You can access this in XNAT from: Administer -> Site Administration -> Other -> Miscellaneous -> Development Utilities -> View Swagger Page -> jupyter-hub-api -> endpoint: /jupyterhub/users/{username}/server/user-options

Thanks,

Andy

[Nadya Shusharina]

Thank you Andy. In the web browser, using View Swagger Page -> jupyter-hub-api -> endpoint: /jupyterhub/users/{username}/server/user-options does return a good JSON. Nevertheless, Jupyter does not start, same error in the logs as before. I suspect that the JupyterHub cannot authenticate to XNAT which would result in a 404 or empty JSON. Is there a possibility that the 1.8.8 and 1.8.10 databases are not exactly the same? It did work with a clean install of 1.8.10, but I need to migrate my projects stored in 1.8.8.

Thank you,

Nadya

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[Andrew Lassiter]

Hi Nadya,

We did add fields to the user options JSON but you are getting a good JSON back so that seems to have updated successfully. We also moved some hibernate entites from the JupyterHub plugin to core XNAT, but I think that REST endpoint would have failed. I recently migrated a 1.8.9 XNAT + 1.0.0 JupyterHub Plugin to 1.8.10 + 1.1.0 and didn't have any issues. Do you see anything in the logs that might indicate a DB issue?

I would also verify that the JupyterHub user account is enabled.

Thank,

Andy