OsmoseApp

In this repository there are actually 2 projets : APLOSE software and OSmOSE team's website. The backend is shared by the 2 projects but is located in distincts Django apps.

> Read the documentation

APLOSE

APLOSE is a scalable web-based annotation tool for marine bioacoustics. It allows the annotations of audio spectrograms. It is currently used for marine bioacoustics studies but its usage can be extended to all kind of acousitc studies.

APLOSE is composed of a React frontend, located in "frontend" folder, and a Django backend, located in the "backend" folder ("api" app).

OSmOSE team's website

OSmOSE team's website is composed of a React frontend, located in "website" folder, and a Django backend, located in the "backend" folder ("osmosewebsite" app).

Deployment

For Ifremer infrastructure follow the comments in the .gitlab-ci.yml file, otherwise use the docker-compose.yml file (you should create a .env file with the required variables, see possible variables).

Development

This project uses poetry (pip install poetry) for Python dev and npm for Javascript dev.

Setup

Backend:

```bash

Initial setup

poetry install docker run --name devdb -e POSTGRES_PASSWORD=postgres -p 127.0.0.1:5432:5432 -d postgis/postgis docker start devdb poetry run ./manage.py migrate poetry run ./manage.py seed

Run

docker start devdb poetry run ./manage.py runserver ```

Frontend:

```bash

Initial setup

cd frontend npm install

Run

npm run dev ```

Testing

```bash

Run backend & frontend tests

docker start devdb poetry run ./manage.py test cd frontend; npm test

Run backend coverage

coverage run ./manage.py test && coverage report

You can also get an html report in the htmlcov folder

coverage html ```

Cypress testing

We use Cypress for end to end testing. Examples of cypress tests are kept in frontend/cypress/examples, they should be deleted once we have a solid E2E test base.

```bash cd frontend

Run Cypress test runner

./node_modules/.bin/cypress open ```

Before pushing to github

```bash

Be sure not to forget any migrations

poetry run ./manage.py makemigrations

You should run Pylint regularly when coding to get tips and avoid bad patterns

poetry run pylint backend

Also don't forget to use black in order to unify code style

poetry run black backend ```

Tooling & maintenance

To update a package to a specific version do not directly edit the pyproject.toml file but rather use the following command: bash poetry add --group dev "pylint==2.14.5" Here --group dev because this is a dev tool, if it's a library to also be used in production you can drop that option.

If you want to changes pylint rules, the configuration options are in the pyproject.toml file.

Formatting :

If you use VSCode, you can add "python.formatting.provider": "black" to your .vscode/settings.json

Possible .env variable

ENV= # either "development" or "production", used for backend.api.settings STAGING= # "true" if we are in staging, used in backend/start.sh to install dev libraries SECRET_KEY= # see https://docs.djangoproject.com/en/3.2/ref/settings/#secret-key OSMOSE_HOST= # "osmose.ifremer.fr" for production, use what you want for staging and localhost OSMOSE_DB_USER= # database username OSMOSE_DB_PWD= # database password HTTPS_PORTAL_STAGE= # see https://github.com/SteveLTN/https-portal, use "local" to test on your machine OSMOSE_SENTRY_URL= # if you use https://sentry.io (more for staging and production)