Central job coordination server for quarantineAtHome project.

You can obtain a full SQL dump from the production server at these two links. It is missing a few extra-large tables, and has the IP addresses trimmed from the jobs table. (See createDB.sh in this repo)

See the flatfiles at https://quarantine.infino.me/static/

To import the sql database into your own private MySQL server :

wget https://quarantine.infino.me/static/quarantineJobs.sql.bz2
wget https://quarantine.infino.me/static/quarantine.sql.bz2
bunzip *.bz2
mysql -u root -p[yourpass] -e 'create schema quarantine;'
mysql -u root -p[yourpass] quarantine < quarantineJobs.sql
mysql -u root -p[yourpass] quarantine < quarantine.sql

To fetch the docked poses, we have prepared a tar archive

cd quarantineServer # or wherever else you pulled this repository
wget https://quarantine.infino.me/static/poses.tar.gz
tar -xvzf poses.tar.gz

This repo is only useful for developers. Also see the Client codebase

After cloning, create a secrets.py file at app/initializers/secrets.py

MYSQL_PASSWORD='its a secret'
SECRET_KEY='somerandom1oi3n10i81203fi82eifn'

To run :

./runserver -debug

• import subset'ed tranches into sql and assign them preferrentially

• expose ligand metadata in frontend

• results viz improvements - template and JS configs

• SMILES rendering

• query caching https://flask-caching.readthedocs.io/en/latest/

• stats page with common queries and caching

• work on data exports - need to find best way to remove ip address column : https://stackoverflow.com/questions/15264597/how-to-take-mysql-dump-of-selected-columns-of-a-table

• more indexes for sql schema

• create a docker-compose file to orchestrate this along with a containerized mysql, as well as a sentry server for remote error collection

python2.7 runserver.py

for production use, you must install the relevant mysql libraries

sudo apt-get install libmysqlclient-dev
pip2.7 install mysqlclient

then create a secrets.py file in app/initializers/secrets.py with the relevant MYSQL_PASSWORD = 'password'

To run the server, pass the production flag

python2.7 runserver.py -production

This webserver also contains a "client" controller that serves up a page at '/client/' - including demo ligans and receptors. This page, and associated coffeescript, serves as a place to develop the frontend that runs on the users client computer. Hosting it on the main server like this permits more rapid development with coffeescript and jade/pug templates, and these are dependencies I'd rather not push onto the client stack.

Regarding the interface, this is what Im thinking.....

• Slow clients will run 1 ligand at a time, against multiple receptors
• Fast clients will download batches of several ligands at a time, and run them against multiple receptors

It's easy to use NGL to display a running queue of ligands as they come in. Could implement it as a deque.

Displaying multiple receptors is more intensive on the graphics. A client probably shouldn't display more than a handful of receptors at a time. I can either limit the set of receptors a client works on, or I can implement a selector whereby the user chooses which receptor result to see.

• implementing a selector like this would require a /results/ subdirectory that fills with ligand structures, poses
• a list of jobs would need to be stored somewhere, storing ligand names, receptor names, energies. Could throw into sqlite, for now, JSON or txt

Endpoints :

• status.json : main polling endpoint, will have a jobID that the frontend could compare -> triggers client insert of rows to top of results table
• results.json : endpoint that returns last N jobs completed to pre-populate table