Code Walkthrough

Modules

The code is split into 5 different sections:

• The Tree API simply lets users query the clades collection; it builds a tree based on a root clade and a depth).
• The User API provides the front-end with members and permissions.
• The Client hold all of the React code and serves as the client.
• The Admin Daemon is basically a transaction processor; when someone makes a change, it doesn't update the database directly. It creates a transaction that the daemon picks up and processes to then update the database.
• The Common code is included in every module above. It contains code to access AWS (for S3 which is used for storing images) as well as database models.

Technologies

This project uses:

• Git (Bitbucket)
• Node.js
• Express
• Express-jwt
• React.js
• Bluebird
• D3
• Mongoose
• Passport
• fbjs
• fixed-data-table
• isomorphic-style-loader
• Draft.js
• Classnames
• throttle-debounce
• eventemitter3
• fetch (whatwg-fetch, window.fetch polyfill)
• history
• Babel
• Fastclick
• universal-router
• compression
• pretty-error
• AWS (aws-sdk)
• MongoDB
• npm
• pm2

Code organization

General

Let's explore how the code is organized. Each of the modules contains the following:

File/Folder	Description
File package.json	The input file for the npm install command. Contains a list of all the library dependencies, with version numbers. Contains also the actions you can do on this project.
File package-lock.json	Contains a detailed description of all the actions of npm install.
node_modules	This is where the library dependencies get downloaded to.
src	Source code (more on this in next section).
test	Tests. Not used.
tools/*.js	This contains the configuration and scripts that are used to compile the project.
File README.md	Description of the repository.

src folder (back-end modules)

The content of the src folder, depends on the type of module. For the back-end modules (admin-api, admin-daemon, public-api), the structure is:

File/Folder	Description
common	A subproject that contains S3 utilities and database models. It is located in its own Git repository, and included in each other project.
File app.js	"Main" of the module.
controllers	For REST API modules (admin-api, public-api), this contains a list of controllers. Each controller is in charge of a single subset of the API, e.g. authentication, user management, clade administration.
routes	Contains the mapping between URLs and controllers. index.js is the main map, and other files each contain a single subset.
middleware	Contains adapters to external systems. For example, AuthCheck.js contains the adapter between the Passport authentication system and our database.
modules
components	Contains various utility classes.
build	Generated by the build.

src folder (font-end module)

File/Folder	Description
docs	Documentation. (Outdated.)
node_modules	Contains the library dependencies, as downloaded by the build.
components	Contains all the dynamic web pages and GUI elements.
core	Contains various utility classes.
public	Contains all the static GUI elements such as icons, robots.txt, etc.
routes	Contains the mapping between URLs and components. index.js is the main map, and other files each contain a single subset.
File server.js	Server-side "main" for the web application.
File client.js	Client-side "main" for the web application.
File config.js	Hardcoded values for port and external URLs and credentials.

Security

Users of the system are stored in the phylex-admin database in the users table.

There are two types of users: Admin and User.

• An admin can do anything including administer the users, roles, transactions, and everything that a normal user can do.
• A user can only access the clades and has a read-only access to everhthing else. Users must be vetted via a registration process. They first apply via the main page's Register section. After they are accepted, they can log in.