clinical-logging

Clinical logging platform to scan, digitize and store information from handwritten case records from Flowleaflets clinical logbooks.

Our app will have the following components:

• Frontend
  • Pages:
    • Login
    • Signup
    • Home
    • Logs
    • Add photo
• Backend
• Database
• Transcription

Project Structure

├── assets                # assets such as logos, marketing materials, transcription pages, provided to us by Flowleaflets. Please keep them here instead of the `public` folder in frontend
├── backend                  
│   ├── routes             # most of the backend code for API routes should be here
│   ├── ├── ...
│   ├── index.js           # Code for running the server and some basic routes
│   ├── package.json             
│   ├── package_lock.json
│   ├── .env.example         #example env file          
│   └── .gitignore             
└──
├── frontend             
│   ├── src
│   ├── ├── assets
│   ├── ├── ├── ...
│   ├── ├── pages         # frontend code for each page should go here
│   ├── ├── ├── ...
│   ├── ├── utils         # put util or helper functions that are shared across multiple files here (eg: protectedRoutes)
│   ├── ├── ├── ...
│   ├── ├── App.jsx         # Main component of the app, likely do not need to modify this
│   ├── ├── App.css         # Styles for App.jsx, likely do not need to modify this
│   ├── ├── index.css         # global css styles go here
│   ├── ├── main.jsx         # root layout of app, wrap all pages inside it
│   ├── public             # Use assets folder instead of this one for logos and visual assets
│   ├── ├── ...
│   ├── package.json             
│   ├── package_lock.json
│   ├── other config files
│   ├── .env.example         #example env file
│   └── .gitignore  
└──
├── transcription         # All code related to the transcription models should be here
│   ├── requirements.txt         # list of required python packages
│   └── testing.py         # run Microsoft Florence 2 model on a test file
└──

Setup

• Install Node.js and npm
• Install Python version 3.12 or later
• Clone the repository

Backend - Node.js

1. 'cd backend' to change directory to backend folder
2. 'npm install' to install dependencies
3. 'npm run dev' to run local development server

.env file

1. Create a new .env file in the backend directory, where the .env.example file is located.
2. Copy the contents of the .env.example file
3. Fill in with the correct credentials

Frontend - React + Vite

1. 'cd frontend' to change directory to frontend folder
2. 'npm install' to install dependencies
3. 'npm run dev' to run local development server

.env file

1. Create a new .env file in the frontend directory, where the .env.example file is located.
2. Copy the contents of the .env.example file
3. Fill in with the correct credentials

Transcription - Python

1. cd transcription to change directory to transcription folder
2. pip install -r "requirements.txt" to install required packages
3. python testing.py or python3 testing.py to run the script

NOTE: These packages are in the requirements.txt file, but if you get an error telling you to install einops or timm, use pip install einops timm to install einops and timm seperately.