GDC Frontend Framework

Installation

Prerequisites

This is a multi-workspace repo that requires npm v10.2.4. The minimum node version is set to v20.11.0.

Node can be downloaded from the official Node.js site. You may also consider using a Node version manager.

Your version of Node may not ship with npm v10.2.4. To install it, run:

npm install npm@10.2.4

If you are using a Node version manager, you can run the following to install the correct version of Node:

nvm install 20.11.0

to use the correct version of Node:

nvm use 20.11.0

Install Dependencies

From the root of the project, install dependencies by running:

npm install

Installing from the root of the repository is required to avoid multiple installations of React in the workspaces. When this happens, React will fail to render.

Adding Dependencies

Dependencies can also be installed from the root of the repository. To install a dependency for a specific workspace, you can run:

npm install --save my-package --workspace=packages/core

Since this is a TypeScript project, installing the community type definitions may also be required:

npm install --save-dev @types/my-package --workspace=packages/core

Development

Run the prototype in dev mode with auto-rebuilding:

npm run dev

By default, this will start a dev server listening to http://localhost:3000

Note: Recompiling the type definitions for core needs to be done manually:

npm run compile --w=packages/core

Linting

Run ESLint for all of the workspaces:

npm run lint

Formatting

Run prettier for all of the workspaces:

npm run format

Testing

This project uses jest for testing.

Naming Convention

Test Type	Filename
Unit	*.unit.test.ts
Integration	*.int.test.ts

Locations

Tests should live in the same directory as if a single module is under test. Since unit tests should only test a single module, they should also live in the directory. For example,

+ /src
| - monarch.ts
| - monarch.unit.ts
| - monarch.int.ts

Running tests

npm run test will run unit tests.

npm run test:int will run integration tests.

npm run test:all will run both unit and integration tests.

Running the portal in Docker

The portal has support for running in a Docker container To create a docker container:

 docker build -t GDCV2 .

to run it:

 docker run -p 3000:3000 -t GDCV2

Running Auth in Localhost (Login and other Auth related actions)

1. Open Chrome (web browser) which disables web security to suppress the CORS warning. Or, if using Safari for feature testing with a logged-in user, click Develop -> Disable Cross-Origin Restrictions.

2. Configure your machine to map localhost.gdc.cancer.gov (or a similar subdomain) to resolve to 127.0.0.1.

   In Mac or Linux, edit the file /etc/hosts (You need to give sudo access to edit this file), add the following line:

       127.0.0.1   localhost localhost.gdc.cancer.gov
   

3. Since the sessionid cookie can only be send through HTTPS, you need to add https to your localhost.

local-ssl-proxy --source 3010 --target 3000 --cert localhost.pem --key localhost-key.pem

4. After these steps, you can access the app on https://localhost.gdc.cancer.gov:3010.
5. Even after all these steps you will see SecurityError: Blocked a frame with origin "https://localhost.gdc.cancer.gov:3010" from accessing a cross-origin frame error. But you can close the error and refresh the page. This warning will be suppressed in production.
6. Now you can Login and use features that are available with Authentication.
7. For developing 3rd party tools with its own server API endpoint or URL:

• Create a ssl-proxy.json file, using the template below with example proxy names and port numbers:

{
  "GFF v2 proxy": {
    "source": 3010,
    "target": 3001,
    "key": "localhost-key.pem",
    "cert": "localhost.pem",
    "hostname": "localhost"
  },
  "MyTool proxy": {
    "source": 3011,
    "target": 3000,
    "key": "localhost-key.pem",
    "cert": "localhost.pem",
    "hostname": "localhost"
  }
}

• run the following

mkcert localhost
local-ssl-proxy --config path/to/ssl-proxy.json --cert localhost.pem --key localhost-key.pem

Version

Update the versions of all workspaces at the same time. (Replace 2.13.0 with the new version to set)

npm run version -- 2.13.0

Documentation

Run build-docs to generate documentation for "portal-proto" and "core" packages For developing applications for the GDC Portal, please review Developer Guide.

npm run build-docs

After generation documentation can be found in the docs folder

Project Structure

This project is a monorepo managed by lerna. It is composed of the following packages:

• packages/core: Contains the state management and function for accessing the APIs of the GDC.
• packages/portal-proto: The GDC Frontend Framework prototype. This is the main package for the project. It uses NextJS as the application framework and React as the UI framework. For basic components we use Mantine.dev (version 6), as the UI library as it compatiable with our design system and use of Tailwind CSS. Please note that before the final release the package will be renamed to packages/portal.
• packages/sapien: is the package that contains the Bodyplot UI used on the GDC Portal V2 home page.
• packages/lighthouse: is the package that contains the Lighthouse UI used on the GDC Portal V2 home page for testing performance.