Frontend application

This frontend is part of a bigger application, before going further, please go to the main project README, where you can find an introduction.

A hosted version of this application can be found at https://shareyourcloning.org/.

Getting started

If you want to quickly set up a local instance of the frontend and backend of the application using Docker, check getting started in 5 minutes in the main repository.

Running the site locally

We use node 18.8, to manage different versions of node, we use nvm. Installation instructions here.

# Install node 18.8 (first time only)
nvm install 18.8
# Activate node 18.8
nvm use 18.8

To handle dependencies and build the site, yarn 3 is used.

# Enable yarn 3 in the project (first time only)
corepack enable

# Install dependencies (every time you pull changes)
yarn install

# If you want to serve the development site locally at http://localhost:3000/
yarn start
# If you want to build the statics assets of the production site in the folder ./build
yarn build

Connecting to the backend

For the application to work, you must have a running backend. For that, see the backend installation instructions.

By default, if you run the dev server with uvicorn main:app --reload --reload-exclude='.venv', the backend will be running at http://localhost:8000/. That's where the dev server of the frontend (ran with yarn start) will send the requests to by default.

The backend URL can be changed by setting a different value in the config.json (see next section).

See also connecting to the frontend section in the backend repo.

Configuration

The configuration of the frontend is done in the file that will be served from /config.json. In the dev server, this file is served from public/config.json. That file is not included in the repository, and is generated from public/config.dev.json when you run yarn start. For the production site, config.prod.json is used. The things you can configure are:

backendUrl: The URL of the backend. By default, it is http://localhost:8000/.

For production: when building the site with yarn build, simply replace build/config.json with your settings. This is what is done in this docker-compose file.

Running with docker 🐳

If you want to serve the full site (backend and frontend) with docker, check getting started in 5 minutes in the main repository.

If you want to serve only the frontend from a docker container, an image is available at manulera/shareyourcloningfrontend. The image is built from the Dockerfile in the root of this repository and exposes the port 3000. To run it:

docker pull manulera/shareyourcloningfrontend
docker run -p 3000:3000 manulera/shareyourcloningfrontend

Contributing :hammer_and_wrench:

Check contribution guidelines in the main repository.

Settings for vscode :desktop_computer:

For the eslint to work, you will need the eslint module

Tests

To run the tests, first run the dev server with yarn start.

To run most tests, you will need the backend to be running at http://localhost:8000/. You can see how to do run it in the backend repo. For the github actions tests, a submodule is used (see below).

To run the tests:

# Open cypress UI
yarn cypress open

# Run a particular test in the command line
yarn cypress run --spec cypress/e2e/source_genome_region.cy.js

# Run a few tests in parallel from the command line (edit file if needed)
bash run_tests_in_parallel.sh
# If the tests fail, you can see screenshots of the failed tests in the folder cypress/screenshots

Actions and submodule

The tests run with cypress in github actions require the submodule ShareYourCloning_backend to be included. If you want to include it locally:

git submodule update --init

If you want to change the commit of the submodule:

cd ShareYourCloning_backend
git checkout -b the-branch
git pull origin the-branch
cd ..
# commit the frontend repo normally

Misc

Web analytics

You can configure website analytics using umami by setting the env var VITE_UMAMI_WEBSITE_ID to the website id. When building the site, the analytics script will be included in the build. See index.html and vite.config.js to see how this is done (using ejs templating).

Recording video with cypress

Settings (they can also be set as env vars or passed with flags).

module.exports = defineConfig({
  video: true,
  viewportWidth: 1000,
  viewportHeight: 1000,
  ...

Then, when running the video.

CYPRESS_NO_COMMAND_LOG=1 yarn cypress run --spec cypress/e2e/source_genome_region.cy.js

eLabFTW

The API keys should be in the ignored file .env.development.local

manulera / ShareYourCloning_frontend

readme