Gromstole Dashboard

Gromstole Dashboard is a web-server and dashboard for analysis/visualization of frequency of SARS-CoV-2 genomic detected in wastewater samples.

It is based on two independant softwares

• Gromstole for the backend web-server
• Tesselo for the frontend data-visualization

Dependencies

• Backend web-server
  • Python
  • Python-dotenv
  • Flask
  • Flask-Cors
  • psycopg2
  • PostgreSQL
• Frontend dashboard
  • React >= 18.2.0
  • Node >= 16.0.0
  • npm >= 5.6

Installation

1. Clone the gromstole_dashboard Repository

git clone https://github.com/DeGrootResearchGroup/gromstole_dashboard

2. Install the required packages for the backend server

cd gromstole_dashboard/backend/
pip3 install -r requirements.txt

3. Install the required packages for the frontend

cd gromstole_dashboard/frontend/frontend_react/
npm install

Environment Variables

The backend web-server and frontend dashboard require specific environment variables to be established at runtime.

The backend environment variables are expected in a text-file at gromstole_dashboard/backend/.env.

# POSTGRES-SQL CONNECTION
POSTGRES_DB       = "gromstole_db"
POSTGRES_HOST     = "localhost"
POSTGRES_PORT     = "5432"
POSTGRES_USER     = "myuser"
POSTGRES_PASSWORD = "mypassword"

The frontend environment variables are expected in a text-file at gromstole_dashboard/frontend/frontend_react/.env.

REACT_APP_API_DEVELOPMENT_URL           = "http://localhost:8000"
REACT_APP_API_TEST_URL                  = "https://example.com:8000"
REACT_APP_API_PRODUCTION_URL            = "https://example2.com:8000"
REACT_APP_API_MUTATION_HEADERS_ENDPOINT = "/mutation_headers"
REACT_APP_API_DATE_HEADERS_ENDPOINT     = "/date_headers"
REACT_APP_API_DEFAULTS_ENDPOINT         = "/defaults"
REACT_APP_API_SPARSE_MATRIX_ENDPOINT    = "/sparse_frequencies"
REACT_APP_API_FILTER_ENDPOINT           = "/filter"
REACT_APP_API_CSV_ENDPOINT              = "/csv"
REACT_APP_REACT_ENV                     = "DEVELOPMENT"     # to be used in development environment
# REACT_APP_REACT_ENV                   = "TEST"            # to be used in testing environment
# REACT_APP_REACT_ENV                   = "PRODUCTION"      # to be used in production environment

Usage

First, start the backend server in development mode. Navigate to the backend directory and run the following command:

flask run --port 8000

Then start the React application. Navigate to the frontend/frontend_react directory and run the following command:

npm run start