CATHAI

Notes

• Need to write your own config.py! See the sample config.py included
• Uses shiny server to serve the R shiny apps that are proxied through the authenication dashboard portal
• Make sure that the shiny server is only bound on 127.0.0.1 or that the host has a firewall (either local system or NeCTAR security group e.g.) to block shiny server ports to outside sources

Docker

Build

docker image build --file ./docker/Dockerfile --tag cathai ./docker

Process data

docker run -p 8080:5000 --mount type=bind,source="./shiny/data/",target="/opt/cathai/shiny/data" cathai 1000 1000 process

Run webapp

docker run -p 8080:5000 --mount type=bind,source="./shiny/data/",target="/opt/cathai/shiny/data" cathai 1000 1000 run

Setup and running

Setup conda and python modules:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
conda create -n cathai -c conda-forge python=3.9 uwsgi=2.0 redis=5.0
conda activate cathai
pip install -r requirements-freeze.txt

System libraries (bash):

apt-get update && apt-get install build-essential libtiff-dev --yes

In R:

install.packages(c('flexdashboard','visNetwork','rjson','DT','shinyjs','igraph','stringr','readr','dplyr','ggplot2','ISOweek','EpiCurve','RColorBrewer','gghighlight','imager','bslib','shinydashboard','fresh','tibble','cowplot','parsedate'), repos='https://cran.rstudio.com/')

Run standalone (no user accounts):

./standalone.sh

Run dev:

./local.sh

Run prod:

./prod.sh

Setup app database and init admin user defined in config.py:

flask shell
import manager
manager.recreate_db()
manager.setup_prod()

Setup nginx reverse proxy for python app, setup LE for prod:

apt update && apt install nginx
cp cathai.fordelab.com.conf /etc/nginx/sites-available
ln -s /etc/nginx/sites-available/cathai.fordelab.com.conf /etc/nginx/sites-enabled/cathai.fordelab.com.conf
nginx -t && systemctl reload nginx
add-apt-repository ppa:certbot/certbot
apt install python-certbot-nginx
certbot -d cathai.fordelab.com

Setup systemctl service for prod:

cp cathai.service /etc/systemd/system/
systemctl enable cathai.service
systemctl start cathai.service

Setup Shiny Server:

cp shiny-server.conf /etc/shiny-server/
systemctl restart shiny-server.service

• env files and examples
• docker launch script
• move this to wiki and expand