Skip to main content

Development of Chemotion ELN

Welcome to the development documentation of the Chemotion ELN.

Repositories​

Setting up a development environment​

We recommend setting up a development environment in a Visual Studio Code devcontainer. You can find more information here.

Learning resources​

To learn more about the technologies we're using on the project, have a look at the following resources.

Technologies​

The project is built with Ruby on Rails, version 6.1. It uses the Model-View-Controller (MVC) architectural pattern. However, this project differs from a typical Rails project:

  • It is using a JSON API.
  • Rails comes with built-in support for an SQLite database, but the project is using PostgreSQL.
  • The front-end is built using the React and alt frameworks. The main page is a single-page application (SPA) along with a few other pages.

Directory structure​

app​

app is the main directory in a Rails application. It contains the MVC structure in the subdirectories models, views, and controllers. However, because the project doesn't adhere to the default Rails architecture, the controllers are mostly empty. Instead of controllers, a JSON API is used which lives in the api directory. Also, there are not many pages in the views directory.

The assets are compiled with Webpacker. There are currently multiple directories containing assets (e.g., under app, public, vendor, tmp). The app/assets directory was the main directory for storing assets in the previous version with Rails 4. With the implementation of Webpacker the assets moved to app/packs. For example, the JavaScript files with all React components formerly lived in app/assets/javascripts and now moved to app/packs/src. app/packs/src contains a directory for each single-page application (SPA). For example, the user-facing SPA lives in is the app/packs/src/components. The stylesheets directory is still located under app/assets.

config​

Contains the configuration of the application. For example, database.yml contains the configuration of the database. The environments subdirectory contains the three environments provided by Rails by default (i.e., development, production, and test). The initializers subdirectory contains the configuration of extensions. For instance, in the devise subdirectory, we configure a package for authentication which takes care of the mail sender and passwords.

lib​

Modules related to the application are added to this directory, such as PubChem, DataCite, OpenBabel. It also has the storage directory where the files are uploaded.

node_modules​

Contains node modules which are installed with yarn.

public​

Contains static files, such as images of molecules. It is difficult to query them as they have hexadecimal identifiers. When creating, e.g., a new reaction, the application will create an image for it and store it in the images/reactions directory.

spec​

Contains Ruby and JavaScript unit test, as well as feature/acceptance tests.

uploads​

Contains attachments uploaded by the user.

.rubocop.yml and .eslintrc​

.eslintrc and .rubocop.yml contain the linter configurations for JavaScript and Ruby respectively. Visit the linting chapter for more details.