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bryan-brancotte / ktyper_deploy

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Deploy

There are four primary components involved in deployment of this web application:

  1. the application code base,
  2. nginx web server,
  3. the web server gateway interface, and
  4. systemd unit files

This guide has been dividing into sections representing these four components. The target system for this deployment guide is debian stable.

There are several assumptions made herein:

  • application codebase install directory: /opt/ktyper/
  • application virtual environment directory: /opt/ktyper/venv/
  • domain name: ktyper.pasteur.fr
  • ssl certificate path: /etc/letsencrypt/live/pasteur.fr/fullchain.pem
  • ssl certificate key path: /etc/letsencrypt/live/pasteur.fr/privkey.pem
  • ssh dhparam path: /etc/ssl/certs/dhparam.pem
  • software: Python3 is installed and is the system default
  • current user: user is not root, has sudo access, is in www-data group

Application codebase

The web application requires npm for frontend compilation, sqlite3 for the database, and git to retrieve the source:

sudo apt-get install git sqlite3 npm

Clone repo and temporarily change owner so we can easily configure:

# NOTE: this is assumed to be cloned into /opt/
sudo git clone https://github.com/scwatts/ktyper.git -b deploy_pasteur && cd ktyper/
sudo chown $(whoami) -R ./

Create secret:

SECRET=$(tr -dc '[:alnum:]' < /dev/urandom | head -c${1:-64})
echo -e "{\n  \"SECRET_KEY\": \"${SECRET}\"\n}" > config/secrets.json

Compile the frontend:

cd frontend/
npm install
npm run build
cd ../

Create upload directory and venv:

mkdir -p uploads/
python3 -m venv venv/
. venv/bin/activate

Install necessary packages into virtual environment:

pip3 install \
    git+https://github.com/scwatts/spectracl.git \
    numpy \
    pandas \
    scipy \
    scikit_learn \
    django \
    djangorestframework \
    huey

Create database from migrations (ensuring virtual environment is still activate):

./manage.py makemigrations backend
./manage.py migrate

Deactivate virtual environment:

deactivate

Set permissions for codebase:

sudo chown root:www-data -R ./
sudo chmod ug+r-w,o-rwx -R ./
sudo chmod ug+w uploads/ huey.db* db.sqlite3 ./

nginx server

Install nginx if not already present:

sudo apt-get install nginx

Copy configuration from ./config/etc/nginx/ to /etc/nginx/. Check that appropriate ports are open:

# List current rules in INPUT chain
sudo iptables -L INPUT

# Add new rules if required
sudo iptables -A INPUT -p tcp -m tcp --dport 80 -m state --state NEW -j ACCEPT
sudo iptables -A INPUT -p tcp -m tcp --dport 443 -m state --state NEW -j ACCEPT

Restart nginx server to load new config:

sudo systemctl restart nginx

uWSGI

Install uWSGI and required plugins if needed:

sudo apt-get install uwsgi uwsgi-plugin-python3 python3-django-uwsgi

Copy configuration from ./config/etc/uwsgi/ to /etc/uwsgi/.

systemd

Copy configuration from ./config/etc/systemd/ to /etc/systemd/. Next, load the new unit files into memory:

sudo systemctl daemon-reload

Enable and start unit files:

sudo systemctl enable --now ktyper-uwsgi ktyper-queuer

Other

When deviating from assumptions layed out in the this section ensure that:

  • the configs for nginx, uwsgi, and/or systemd unit files are updated appropriately,
  • ALLOWED_HOSTS in ktyper/config/settings.py is set to contain the correct domain, and
  • the spectracl executable called in ktyper/backend/tasks.py points to the correct location

Updating model

Currently the most robust way to update a model is to do so through spectracl. Specifically, update the model in the spectracl GitHub repo and then reinstall spectracl into the virtual environment:

. /opt/ktyper/venv/bin/activate
pip3 install --force-reinstall git+https://github.com/scwatts/ktyper.git

Following this all services should be restarted to ensure the update is propogated:

sudo systemctl restart nginx ktyper-uwsgi ktyper-queuer

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