TORCH Hub

This repository has a flask app that triggers and manages a prefect workflow

Requirements

Requires Python 3.10*

Installation

All dependencies are listed in requirements.txt:

pip install -r requirements.txt

Configuration

App specific configs: The current version needs a .env file inside the src/torch folder. Use .env.sample as a template.

Workflow specific configs: Workflow configs should be added inside the src/torch/prefect_flows/configs folder, example: workflow_name_config.json, this file should be loaded from the workflow function as necessary check flow_template_config.json and flow_template.py. There is a process_specimen workflow on this solution, use the process_specimen_config_example.json as template.

How to create a new workflow

1. Add a new flow file inside src/torch/prefect_flows/ folder following the flow template
2. Register the new flow on the run_workflow function at workflow.py

How to run

Once the dependencies are installed, run the app as follows: Navigate to the src folder and run

python3 app.py

or you can also run at Visual Studio Code, make sure the launch.json file is at the same directory as the app.py, open the app.py and select the Run and Debug menu

Prefect server

Observe your flow runs in the Prefect UI Fire up the Prefect UI locally by entering this command in your terminal:

prefect orion start

Follow the link in your terminal to see the dashboard.

Adding an admin user

After running the web app for the first time, the database and admin role are created automatically, and you should be able to Sign Up and create a new user from the Sign-Up page.

To assign the admin role to your user navigate to src/torch and access the database sqlite3 torch-hub.db and then execute the command INSERT INTO roles_users (your_user_id, 1)