ceesem/neuvue-app

MICrONS Proofreading App

Neuvue

A Proofreading web-app and task management system

What is Proofreading?

Installation

Clone this repository recursively so that the neuvue-client submodule will also be included.

git clone https://github.com/aplbrain/neuvue-app.git --recursive

Create a python3 virtual environment and install the requirements in neuvue_project/requirements.txt.

python3 -m venv venv
source  venv/bin/activate
cd neuvue_project
pip install -r requirements.txt

Development Installation

Install developer python requirements and set up pre-commit enviroment.

source  venv/bin/activate
pip install -r requirements-dev.txt
pre-commit install

Once changes are staged. Run pre-commit to automatically remove trailing whitespaces, check YAML files, and run black formatting on all python files.

pre-commit

(Optional) Compiling the neuroglancer project

A working neuroglancer compilation is included under neuvue_project/workspace/static/workspace/. However, if the underlying neuroglancer client needs to change,it must be compiled and linked.

Requirements: nvm

1. Clone the neuroglancer repo, and build it

   git clone https://github.com/aplbrain/neuroglancer
   nvm install --lts
   cd neuroglancer
   npm i
   npm run build
   npm link
   

2. Build the NG wrapper

   cd neuvue_project/workspace/static/ts/wrapper
   ln -s <absolute-path-to-neuroglancer>/src/neuroglancer ./third_party/neuroglancer
   npm i
   npm link neuroglancer
   npm run build
   

3. Copy the built files to static

   cd neuvue_project/workspace/static/ts/wrapper
   cp -r dist/workspace ../../
   

Running a development environment

There is an included neuvueDB.sqlite3 database file containing the tables needed to run the Django app. By default, the settings are configured for production which uses a cloud-enabled MySQL database server. To enable development mode:

Run the following convenience script:

python run-dev-server.py

Or perform each step individually:

1. Open neuvue_project/neuvue/settings.py and set DEBUG=True

2. In the same file, modify NEUVUE_QUEUE_ADDR variable to the Nuevue-Queue endpoint you would like to use.

3. Get the recent migrations to the database by running

   python manage.py migrate

4. (OPTIONAL) Create a superuser to modify the app in your development environment.

   python manage.py createsuperuser

5. Collect all static files into /static:

   python manage.py collectstatic --no-input

6. Run the app with the runserver command to start a development instance. Run on the localhost:8000 address and port to allow OAuth client to properly authenticate user.

   python manage.py runserver localhost:8000

7. Open your app on http://localhost:8000

OAuth Set-up

The included development database is preconfigured to allow OAuth to authetnticate user accounts from localhost:8000. Here is a more complete guide on how this was done.

We use django-allauth to connect Google OAuth to the Django environment. Users also have the option to log in through the base allauth login/signup page:

http://localhost:8000/accounts/login/

Django users, OAuth settings, and site configuration can be modified in the admin console.

http://localhost:8000/admin

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