FLOWViZ

FLOWViZ is an integration framework that allows you to seamlessly integrate other phylogenetic tools and frameworks, while providing workflow scheduling and execution, through the Apache Airflow workflow system.

It is composed by two components: an HTTP Express server and a React client, both written in JavaScript.

It is still a work under development! If you find a bug, please report here

With this framework, you can integrate your own phylogenetic tools, by filling a contract where you specify the tool's access, rules and guidelines.

The integrated tools can then be used to build your own customized workflows.

You can also customize each task inside the workflow.

The system architecture was also detailed into an article (page 206), which was submitted and accepted for presentation at the Inforum 2022's conference.

Setup

Configuring database

1. Install Docker

2. Download mongo image

docker pull mongo

3. Run and create mongo container, exposing port 27017

docker run --name mongodb -d -p 27017:27017 mongo

Add server's dot-env environment variables

1. Create a file called .env in server/ folder.

2. Fill it with the variables below (remove the curly brackets and change what is in between them):

PRODUCTION={true|false}
SERVER_NAME={server_name}
SERVER_PORT={server_port_number}
DATABASE_ADDRESS={database_address}
DATABASE_PORT={database_port}
AIRFLOW_ADDRESS={airflow_address}
AIRFLOW_PORT={airflow_port}
AIRFLOW_DAG_GENERATOR={airflow_dag_generator_name}
JWT_SECRET={jwt_secret}
AIRFLOW_USERNAME={airflow_username}
AIRFLOW_PASSWORD={airflow_password}

Running on localhost

1. Install dependencies:

npm i

2. To run both client and server (concurrently):

npm run dev

Running on localhost with tmux

Allows you to isolate each log in a terminal individual session, providing better log visibility than the concurrently way.

1. Install tmux

Arch distros:

sudo pacman -Sy tmux

Debian distros:

sudo apt-get update && sudo apt-get install tmux

macOS:

brew install tmux

2. Enable tmux mouse scroll (optional)

echo "set -g mouse on" >> ~/.tmux.conf && tmux source-file ~/.tmux.conf

3. Execute the start.sh script

Note: if there are no execution permissions, execute:

chmod +x start.sh

Build and start:

./start.sh

Testing

To run unit tests:

npm test