Introduction

The PAML Editor (PAMLED) is a web application that supports the authoring and sharing of PAML protocols. PAMLED consists of two components: frontend and backend. The frontend is a React-based server for handling the graphical interface. The backend is a Django REST server that handles persistent storage (protocols, user accounts, and primitives), and access to the pyPAML library.

User Guide

See the user guide at: User Guide

Running the PAML Editor in Development

Pre-requisites

• Backend
  • Python 3.9
  • Pipenv
• Frontend
  • Node & Npm

Backend Instructions

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1. On your development system install backend dependencies

2. Get PAMLED:

git clone https://github.com/Bioprotocols/pamled.git

3. Initialize the pamled pipenv environment:

cd pamled
pipenv install
pipenv shell

4. Set the secret key in backend/.env:

python -c "import secrets; print(f'SECRET_KEY=\"{secrets.token_urlsafe()}\"')"  > backend/.env

5. Initialize the backend

# from within the pipenv shell
cd backend
python manage.py makemigrations accounts editor
python manage.py migrate

# optionally create a admin user
python manage.py createsuperuser

6. Start the backend

# from within the pipenv shell, in backend/
python manage.py runserver

The backend server should now be running. You will see some output in the terminal like this:

Performing system checks...

System check identified no issues (0 silenced).
January 24, 2022 - 18:52:36
Django version 3.2.9, using settings 'pamled.settings'
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.

Frontend Instructions

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1. On your development system install:

• node & npm

2. Initialize the frontend

# while in backend/ from above
cd ../frontend/web
npm install

3. Start the frontend

# while in frontend/web/
npm run start

If npm does not open a browser automatically then you can connect to the frontend at http://localhost:3000 from your preferred browser.

4. Once connected you should be greeted by a login page. If you made a superuser account then you can login with that. Otherwise you can navigate to the sign up page and register a new account with your development database.

5. Once logged in you will see the editor.

Development using Visual Studio Code

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For those familiar with VSCode the backand and frontend instructions have mostly been encapsulated within a VSCode workspace. See the pamled.code-workspace in the root of the repo.

Note that this workspace does still require pipenv and npm to be installed.

Tasks

The workspace provides a set of tasks available via command palette (Ctrl+Shift+P) under Tasks: Run Task.

These make initialization of the backend and frontend a bit easier to manage.

Tasks:

• Make Migrations
• Migrate
• Create Superuser
• Nuke DB & Migrations

Launchers

It also provides a set of launch commands available from the Run and Debug panel (Ctrl+Shift+D).

These make it easier to launch all of the editor parts at once.

Launchers

• Django
• React
• Firefox
• Chrome

Compound Launchers

• Django & React & Firefox
• Django & React & Chrome