Issue running "Identify a set of cases with expression, mutation, and imaging data" notebook locally via docker

[n1zea144]

Hello,

I'm trying to run this notebook on my laptop via docker as per instructions on your github page, but having problems. I'm seeing multiple python "NameError" and also permission issues like the following:

How do I get this notebook to run? I'm specifically interested in how I go from using cdapython to query cases/specimen metadata to fetching genomic data for the sample, which is why this notebook sounds interesting.

Thank you!

[ACharbonneau]

Hi there! That notebook isn't running correctly because it is one for our testers to run and wasn't necessarily meant to be used by researchers. In cells 2 and 3 you'll see it's redirecting you to query at an internal server. If you run the notebook but skip those two cells, you won't get the permission error anymore.

That said, since it's a testing file, not all the code will actually work. It was set up so we could make sure new functionality did work, and that old code stopped working. So in several rows you'll need to edit the code a bit because it's purposely not right Q :) I just went through and made the required updates, and am attaching a notebook here that should run without issues and does the same thing.

If you explore more, the notebooks that are meant for researchers are all in the documentation website under Examples. The cohort building one in particular does the same sort of search as this one, but it reliably works, and uses the newest functionality. https://cda.readthedocs.io/en/latest/Examples/BuildingACohort/ I'll add my updated version of this one to the site on our next release so others don't have the same issue.

[ACharbonneau]

https://gist.github.com/ACharbonneau/4772de299eabb30f0151e33b7cc90782