Installation with Docker on Windows 10 - Jupyter installs and runs but I get "Invalid credentials" every time I try to login... authentication token doesn't work

[Rich Lysakowski]

I installed GenePattern Notebook with the latest available Docker container (v3.9.11 build 244) on Windows 10. 

I followed the instructions for Docker installation on the page http://genepattern-notebook.org/install/

I installed and launched Kitematic, then selected the latest image "genepattern-notebook" (GenePattern Notebook server running the full Jupyter stack).

I loaded that Genepattern-Notebook image and then copied and pasted the URL with the authentication token (http://127.0.0.1:8888/?token=f583e72b50aeae22820cff2751ad49a3347a809ff9008839)   into a Chrome browser (Version 80.0.3987.122 (Official Build) (64-bit)) 

 

The authentication token doesn't work.  I get a message of "Invalid credentials" every time.  I have tried to restart Docker several times.

I tried an older Docker container and it launches okay, specifically genepattern-notebook-plus from a Docker user named "JunkDNALab".  However, it is an obsolete version of Python 2.7 that won't work with the latest Dash/Plotly packages for Python and R and many other modern packages that require Python 3.x to work.  

Is JAVA Required? 

I want to get the full GenePattern Server running so that I can use the Module designer / integrator.  We have a specialized resource-intensive permutation analysis that we need to run, so we want to modularize that part of the workflow to send to higher performance compute server if necessary.  

Does the GenePattern Notebook Docker container provide the GenePattern Server with the Module Integrator also?  

Do I need a Java runtime or SDK installed first, or any other Docker containers in addition to the GenePattern Jupyter NB Server?  

I do not have Java installed now, but the instructions for the Docker installation of GenePattern Server do not mention anywhere that Java must be installed first.  

If Java and additional docker containers are required, can someone provide a hyperlink to end-to-end instructions for installing Java, Genepattern Server, Module Integrator, Module Repository on Windows 10 ? 

Thank you.  

Best Regards, 

Rich Lysakowski

[Thorin Tabor]

Rich,

The times I have seen this error in the past, it is usually caused by accidentally running two instances of Jupyter at once. One instance binds to port 8888, then the other provides the token. When you go to authenticate using the token, it is sent to the wrong instance, and of course then the token's doesn't match.

To troubleshoot this, I would recommend two things:

1) Shut down your Docker container and then try to access http://127.0.0.1:8888. If you're still getting the authentication page and not a connection error, then it is safe to conclude that you have an extra instance of Jupyter running somewhere. You will need to figure out where the process is running and shut it down. I can help with this if you've confirmed that this is the problem. Worst case scenario, rebooting might fix things.

2) I would also double-check to make sure you have the most recently built version of the GenePattern Notebook container. It should be genepattern/genepttern-notebook:20.01.2.

Thorin Tabor

GenePattern Team

[Rich Lysakowski]

Okay.  I routinely run a local instance of Jupyter while I am developing in order to validate that I am getting the same results locally as online.   I can change the local Jupyter NB server default IP port address to something other than 8888.  That way it will start up in a different port range, and not collide with the port that Docker uses for GPNB.