tvpham / cbioportal-frontend

React Frontend of cBioPortal :tada:

cbioportal-frontend

Live demo

Development: http://cbioportal-frontend-demo.herokuapp.com/#/patient?studyId=prad_fhcrc&caseId=00-090 Master: http://cbioportal-frontend.herokuapp.com/#/patient?studyId=prad_fhcrc&caseId=00-090

Test status & Code Quality

Branch	master	integration	rc
Status

Deployment

This is the frontend code for cBioPortal using React, MobX and TypeScript. The frontend for the new patient view is now completely in this repo. The

Make sure you have the latest stable node version installed:

https://nodejs.org/en/

To install all app and dev dependencies

npm install

To build DLLs in common-dist folder (must be done prior to start of dev server)

npm run buildDLL:dev

To start dev server with hot reload enabled

npm run start

A good example page is: http://localhost:3000/?cancer_study_id=lgg_ucsf_2014&case_id=P04

To run unit/integration tests (need to have API URL defined in .env)

npm run test

To run unit/integration tests in watch mode

npm run test:watch

To run linting

npm run lint

precommit hook

There is a precommit hook installed that lint checks the typescript in this project. The hook can be viewed in package.json. You can skip it with

git commit -n

Changing the URL of API

If the version of the desired API URL is the same as the one used to generate the typescipt client, one can hange the API_ROOT variable for development in my-index.ejs. If the version is different, make sure the API endpoint works with the checked in client by changing the API URL in package.json and running:

npm run updateAPI
npm run test

Check in cBioPortal context

Go to http://cbioportal-rc.herokuapp.com/case.do?cancer_study_id=lgg_ucsf_2014&case_id=P04

In your browser console set:

localStorage.setItem("localdev",true)

This will use whatever you are running on localhost:3000 to serve the JS (i.e. you need to have the frontend repo running on port 3000). To unset do:

localStorage.setItem("localdev",false)

or clear entire local storage

localStorage.clear()

You can also use a heroku deployed cbioportal-frontend pull request for serving the JS by setting localStorage to:

localStorage.setItem("heroku", "cbioportal-frontend-pr-x")

Change x to the number of your pull request.

Run e2e tests

Install webdriver-manager, which manages standalone Selenium installation:

npm install -g webdriver-manager

Run updater to get necessary binaries

webdriver-manager update

Start the webdriver-manager

webdriver-manager start

In one terminal run frontend (this will get mounted inside whatever CBIOPORTAL_URL is pointing to)

npm run start

In another terminal run the e2e tests

# get CBIOPORTAL backend url from my-index.ejs
export CBIOPORTAL_URL=http://$(grep '__API_ROOT__' my-index.ejs | cut -d= -f2 | tr -d "'" | tr -d [:space:] | tr -d ';')
cd end-to-end-tests
npm install
npm run test-webdriver-manager