repromon 1.0

Overview

ReproNim/repromon monitoring project. The goal is to provide a core software solution to be deployed at Dartmouth Brain Imaging Center (DBIC) as a pilot location, to provide “online” feedback about ongoing data entry and acquisition (videos, MRI) as is planned to be captured and provided by the ReproNim projects such as ReproIn, ReproStim, ReproEvents and con/noisseur which have being developed separately.

System Setup

SSL Certificates

For development purposes should be created self-signed SSL certificate to be used for HTTPS/WSS communications under ./certs/ directory and named as '${WEB_HOST}.key' and '${WEB_HOST}.pem'. Below listed script to generate these files for "localhost" domain:

WEB_HOST=localhost && mkdir -p ./certs && openssl req -x509 -nodes -newkey rsa:4096 -keyout ./certs/$WEB_HOST.key -out ./certs/$WEB_HOST.crt -days 3650 -subj "/CN=$WEB_HOST" && openssl x509 -in ./certs/$WEB_HOST.crt -out ./certs/$WEB_HOST.pem -outform PEM

In DEV/QA/UAT and other environments WEB_HOST should be specified to real DNS or IP address value end-user and backend clients will use to communicate with the repromon server. Also this value should be the same as WEB_HOST variable in '.env.*' file.

For production deployment should be used SSL certificate from trusted authorities.

Podman / Docker Environment

There is a template.env.dev file with a configuration for a typical setup, but it has fields to fill in. To expedite generation of the local .env.dev, you can use following command

sed -e "s,TODO_apikey_secret,$(openssl rand -hex 32),g" \
    -e "s,TODO_apikey_salt,$RANDOM,g" \
    -e "s,TODO_token_secret_key,$(openssl rand -hex 32),g" \
    -e "s,TODO_initial_admin_password,$(openssl rand -base64 32 | tr -d /=+ | cut -c -12),g" \
    -e "s,TODO_postgres_user,repromon,g" \
    -e "s,TODO_postgres_password,$(openssl rand -base64 32 | tr -d /=+ | cut -c -12),g" template.env.dev > .env.dev

To build and start the instance for the first time execute it in a subshell (so that we do not leak those variables in the current env) and use:

( set -a &&  source ./.env.dev && podman-compose  -f docker-compose.dev.yml up -d --build  ; )

To start container instances use:

( set -a &&  source ./.env.dev && podman-compose  -f docker-compose.dev.yml up -d  ; )

Then you can check that all services started using:

podman ps

which should have repromon_db_1 and repromon_web_1 services by default.

You can see the logs using these commands:

podman logs --since "2023-09-01T00:00:00Z" repromon_web_1
podman logs repromon_db_1

To open shell on web server container use:

podman exec -it repromon_web_1 bash

To stop instances use:

( set -a &&  source ./.env.dev && podman-compose  -f docker-compose.dev.yml down  ; )

Local Development Environment

Local Python development can be used on project 'as is' with any editors, e.g. PyCharm. Default local configuration specified in '.env.local' file and uses project built-in SQLite3 DB.

Testing

Repromon testing based on pytest and integrated into project 'repromon_app' package. Unit tests can be executed with 'pytest' directly. It's recommended to turn on live logging for more detailed logs from repromon_app:

pytest --pyargs repromon_app -o log_cli=true -o log_cli_level=DEBUG

or via poetry:

 ./venv/bin/poetry run pytest

 ./venv/bin/poetry run pytest --cov=. --cov-report=xml -s