rdkitwebserver

To start development

We need multiple environments to set up first

Make sure you have python packages

Make sure you are not in a conda environment.

These commands will read in requirements.txt to download python packages for python functionality

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

docker environment

This command with go into the express backend and the python backend to start up the docker containers

docker compose up --build

to start development mode

for python service

cd python_service && uvicorn main:app --host 0.0.0.0 --port 5000 

for celery

cd python_service && celery -A lib.celery_worker worker --loglevel=info

for express

cd backend && nodemon index.js

python backend

to develop

First, you need to run redis-server

sudo systemctl start redis-server

You can see the status of the redis-server

sudo systemctl status redis-server

Then, start the fastapi app by using uvicorn

cd python_server && uvicorn main:app --reload

Also, you have to keep celery on too

cd python_service && celery -A lib.celery_worker worker --loglevel=info

if you run:

cd python_server/app/examples && curl -X POST "http://localhost:8000/v1/smi/descriptors" -F "[email protected]"

you will get a job id back. The job will run in the background, where the celery worker will do the work.

You can see the status of the job by doing:

curl "http://localhost:8000/v1/job/JOBID"

where if completed, will return results

Ensure these criteria before making changes

-[] add test cases

-[] submit benchmarking

Benchmarking

no aiofiles

444957 smiles divided up by 8 threads

time: 1358 sec (55620 chunk size)

444957 smiles all computed under 1 thread

time: 3162 sec (444958 chunk size)

444957 smiles divided up by 8 threads line by line

time: 1652 sec (55620 chunk size)

444957 smiles all computed under 1 thread line by line

time: 3247 sec (444958 chunk size)

444957 sdf mols divided up by 8 threads line by line

time: 1592 sec (5000 chunk size)

444957 sdf mols divided up by 8 threads line by line

time: n/a crashed out due to oom (444958 chunk size)