StABDMIN

StABDMIN Site

Currently running at: marvin.st-andrews.ac.uk on port 80.

The StABDMIN site was born of the need of a way to track the users on marvin, the PIs they're associated with, the funded and unfunded grants they hold and the data they use.

It was written by Joe in about 2 weeks in 2019 and he apologises sincerely for the lack of comments in the code, and absence of tests. It's still a damn site better than what was there before (i.e. nothing).

Keeping it running

The database is called StABDMIN, the database user is StABDMIN and the password is stored in /etc/mysql/stabdmin.cnf.

The code for the project is in /storage/home/users/StABDMIN. The site is set to store static files (css, js etc) in /var/www/StABDMIN/.

Currently static files are being server using the python package "whitenoise", but this ought to be done with nginx or apache in the long run. It's also not served over https currently as marvin can't cope with a modern apache (mod_wsgi was compiled with python 2.6).

Restarting the server

As root:

• To start the webserver navigate to /storage/home/users/StABDMIN/StABDMIN
• run module load python/3.6.4
• run sh run_webserver.sh

And this will run gunicorn using

gunicorn StABDMIN.wsgi:application  --pid StABDMIN.pid -b marvin.st-andrews.ac.uk:80 -n StABDMIN -D

Importing data into the backend

The script /storage/home/users/StABDMIN/StABDMIN/importUsageFromFiles.py is set into cron to run everyday at 5.05am. It relies on the result of the /mnt/system_usage/ scripts written by Peter Thorpe. It loads the data from the files created by this script into the system for tracking user data usage and total disk use/free space.

To add users/PIs/Grants, you need to use the ADMIN site, access from the "Admin" link on the navigation bar of the website.

If a new PI has a new Users and a new Grant, the PI must be created first.

If a new bioinformatician joins, assign them the PI "StABU" and add them to the bioinformatician table. This allows tracking of their use within the StABU PI, and also allows them to be assigned as primary bioinformaticians on grants.

How it works

The whole thing is based on the python package Django, but uses javascript for loading data into datatables (javascript package that makes the tables pretty), using JQuery (js again) ajax calls. The plots are created by D3 (javascript plotting library), again from data from ajax calls.

There are 5 tables in the database directly used by django.

Pis stores all the PI information. GrantSubmissions stores the grants information, whether it's proposals, expired, or funded. Users stores the information on users. help notes stores notes on help given, meaning we can track what we've done for people. These can be assigned to users, PIs and/or grants. Bioinformaticians is a way of highlighting user instances as bioinformaticians so we can assign them to grants.