How do I enable analysis in HistomicsUI?

[kwsp]

I don't have the "analysis" button I seen in other screenshots, like this #292

[manthey]

You need to add an analysis task to the system. This can be done from the Girder interface (not the HistomicsUI interface). Go to Collections -> Tasks -> Slicer CLI Web Tasks, you'll see an upload button that says "CLI" underneath it:

Click that and add the name of the docker image to add (e.g., "dsarchive/histomicstk:latest") and it will pull the docker image and add it to the available analyses.

[kwsp]

The mongo container restarts about every 7 seconds, so I can't really exec into the container to check the permission issue.

[manthey]

Hmm... The default deployment mounts the devops/dsa/db directory as the internal container /data/db directory, so you should be able to do ls -l devops/dsa/db and see if any mongo created files are owned by your current user. If you tried running docker compose as a different user, this could cause such a problem, in which case chown-ing the files in the db directory to your current user might fix it.

[kwsp]

Looks like the mongo container doesnt have the permission to do anything in the /data/db directory. I see its the devlops/dsa/db directory, and it is owned by the current user. I wonder if DSA_USER=$(id -u):$(id -g) is doing something funky.

[kwsp]

So the devops/dsa/db directory is owned by me, and I'm running docker-compose as my user, and I provided DSA_USER=$(id -u):$(id -g), yet mongo doesn't have permission to write to /data/db. Do you have any other ideas on what might've gone wrong?

[kwsp]

@manthey I tried docker-compose again in a clean Ubuntu install and it worked. Still not sure how to fix the problem I saw before.