cbioportal-frontend

This repo contains the frontend code for cBioPortal which uses React, MobX and TypeScript. Read more about the architecture of cBioPortal here.

Branch Information

	main branch	upcoming release branch	later release candidate branch
Branch name	master	--	rc
Description	All bug fixes and features not requiring database migrations go here. This code is either already in production or will be released this week	Next release that requires database migrations. Manual product review often takes place for this branch before release	Later releases with features that require database migrations. This is useful to allow merging in new features without affecting the upcoming release. Could be seen as a development branch, but note that only high quality pull requests are merged. That is the feature should be pretty much ready for release after merge.
Test Status	CircleCI master workflow	--	CircleCI rc workflow
Live instance frontend	https://frontend.cbioportal.org / https://master--cbioportalfrontend.netlify.app/	--	https://rc--cbioportalfrontend.netlify.app
Live instance backend	https://www.cbioportal.org / https://master.cbioportal.org	--	https://rc.cbioportal.org

Note: you can check the frontend version of the live instance by checking window.FRONTEND_COMMIT in the console.

Run

Make sure you have installed the node version and yarn version specified in package.json.

Tip: For node, we recommend that you use nvm: Node Version Manager to switch between versions easily.

Tip: For yarn, you can use yarn set version or npm install yarn@(version).

Windows Tip: If you are developing on Windows, we recommend that you use Ubuntu / Windows Subsystem for Linux.

Remove old compiled node_modules if it exists

rm -rf node_modules

To install all app and dev dependencies

yarn install --frozen-lockfile

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

yarn run buildDLL:dev

To build all packages the main project depends on (must be done prior to start of dev server):

yarn run buildModules

Running the Application with a Self-Signed Certificate

When running the application locally, you might encounter issues with SSL due to the self-signed certificate being used. Most browsers will block access to localhost when an untrusted certificate is detected. To bypass this and allow local development, you can start your browser in "insecure mode."

For Google Chrome:

1. Close all instances of Chrome.

2. Open a terminal or command prompt.

3. Run the following command:

   • Windows:

     chrome.exe --ignore-certificate-errors --disable-web-security

   • macOS:

     open -na "Google Chrome" --args --ignore-certificate-errors --disable-web-security

   • Linux:

     google-chrome --ignore-certificate-errors --disable-web-security

For Mozilla Firefox:

1. Open Firefox.
2. Type about:config in the address bar and press Enter.
3. Search for security.tls.version.min and set it to 1.
4. Search for security.tls.version.fallback-limit and set it to 1.
5. Confirm any warnings, and restart Firefox.

Note: Running the browser in insecure mode should only be used for local development purposes. Warning: Running your browser in insecure mode can expose you to security risks. Do this only for local development purposes and revert any changes made when done.

To start the dev server with hot reload enabled

# set the environment variables you want based on what branch you're branching
# from
export BRANCH_ENV=master # or rc if branching from rc
# export any custom external API URLs by editing env/custom.sh
yarn run start

Tip: BRANCH_ENV should be set to master or rc, and not to your local branch name. You can set this in your ~/.bashrc if you don't intend to change it often.

Example pages:

• http://localhost:3000/
• http://localhost:3000/patient?studyId=lgg_ucsf_2014&caseId=P04

Tip: If you see dependency errors, especially the error that the script cannot identify the packages managed by lerna(monorepo), you could do a yarn buildModules first before starting the project.

To run unit/integration tests

// run tests for main project
yarn run testMain

// run tests for all packages
yarn run testPackages

// run the above with grep on particular spec file
GREP=example.spec.js yarn run testMain
GREP=example.spec.js yarn run testModules

To run unit/integration tests in watch mode

yarn run test:watch

// see above for GREP

To run unit/integration tests in watch mode (where specName is a fragment of the name of the spec file (before .spec.))

yarn run test:watch 

// see above for GREP

Formatting Code with PrettierJS

When you make a git commit, PrettierJS will automatically run in write mode on all the files you changed, and make formatting adjustments to those entire files as necessary, before passing them through to the commit (i.e. this is a "pre-commit git hook"). No action from you is necessary for this. You may observe that your changes don't look exactly the same as you wrote them due to formatting adjustments.

When you make a pull request, CircleCI will run PrettierJS in check mode on all of the files that have changed between your pull request and the base branch of your pull request. If all of the files are formatted correctly, then the CircleCI prettier job will pass and you'll see a green check on Github. But if, for whatever reason, this check fails, you must run the following command in your cbioportal home directory:

yarn run prettierFixLocal

This will make PrettierJS run through the same files that CircleCI checks (i.e. all files changed since the base branch) but in write mode and thus adjust those files to have correct formatting. When you make this update, the CircleCI prettier job should pass. To check if it will pass, you can also run the same command that CircleCI will run:

yarn run prettierCheckCircleCI

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 change 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:

# set the environment variables you want based on what branch you're branching
# from
export BRANCH_ENV=master # or rc if branching from rc
# export any custom external API URLs by editing env/custom.sh
yarn run updateAPI
yarn run test

Check in cBioPortal context

Go to https://cbioportal.org (master branch) or https://rc.cbioportal.org/ (rc branch)

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 add a bookmarklet to quickly switch to your local frontend server. Set the URL to the following:

javascript:(function()%7BlocalStorage.setItem%28%60localdev%60,true%29%3Bwindow.location.reload()%3B %7D)()

You can also use a netlify deployed cbioportal-frontend pull request for serving the JS:

1. Create the following bookmarklet:

javascript:(function()%7Bvar pr %3D prompt("Please enter PR%23")%3Bif (pr %26%26 Number(pr)) %7B localStorage.netlify %3D %60deploy-preview-%24%7Bpr%7D--cbioportalfrontend%60%3Bwindow.location.reload()%3B %7D%7D)()

2. Navigate to the cBioPortal installation that you want to test.
3. Click the bookmarklet and enter your pull request number.

Run e2e-tests

End-to-end tests can be run against public cbioportal instances or against a local dockerized backend. These two e2e-tests types are referred to as remote and local types of e2e-tests.

Run of remote e2e-tests

Follow instructions to boot up frontend dev server. This is the frontend that will be under test in the e2e tests (running against production backend/api)

cd end-to-end-test

// install deps
yarn --ignore-engines

cd ..

yarn run e2e:remote --grep=some.spec* 

Mount of frontend onto HTTPS backend

A custom frontend can be tested against any backend in the web browser using a local node server (command yarn run start) and the localdev flag passed to th e browser (see section 'Check in cBioPortal context'). For remote backends that communicate over a HTTP over SSL (https) connection (e.g., cbioportal.org or rc.cbioportal.org), the frontend has to be served over SSL as well. In this case run yarn run startSSL in stead of yarn run start.

Run of localdb e2e-tests

To enable e2e-tests on for features that depend on data that are not included in studies served by the public cBioPortal instance, cbioportal-frontend provides the e2e local database (refered to as e2e-localdb or local e2e in this text) facility that allows developers to load custom studies in any backend version used for e2e-tests. CircleCI runs the e2e-localdb tests as a separate job.

Files for the local database e2e-tests are located in the ./end-to-end-test/local directory of cbioportal-frontend. The directory structure of ./end-to-end-test/local is comparable to that of the ./end-to-end-test/remote directory used for e2e-tests against remote public cBioPortal instances.

Running localdb e2e-tests for development

1. You need to have Docker installed and running.

2. You need to have the jq package installed on your system. E.g. using brew: brew install jq

3. You need to have a global version of Maven installed.

In a terminal, start the frontend dev server

export BRANCH_ENV=custom
yarn install --frozen-lockfile // only necessary first time
yarn buildDLL:dev // only necessary first tiem
yarn start

3. Install dev dependencies:

cd end-to-end-test
yarn

5. In a second terminal at project root, spinup the backend (api) instance:

// if you are running for first time, you will need to build the docker containers.
// Answer yes when it prompts you to do so. This will take at least 20 minutes depending
// on your system speed.
// Once you have done this, you can answer no on subsequent attempts

yarn run e2e:spinup

6. When backend instance is operational, you can run tests. Upon executing the command below, a browser should open and you should see your tests execute.

//grep accepts fragments of file name, 
//but you MUST using trailing *
//you need only match the file name, not path

yarn run e2e:local --grep=some.spec*   

Running e2e-localdb tests CircleCI or CircleCI+PR context

E2e-tests on CircleCI and CircleCI+PR context are triggered via hooks configured on GitHub. Configuration of hooks falls beyond the scope of this manual.

cBioPortal-backend version

E2e-testing against a local database removes dependence on data provided by public cbioportal instances for testing. This makes it possible to test features for data types that are not provided by public cbioportal instances or test features that depend on a backend feature not yet integrated in public cbioportal instances. E2e-localdb tests make use of the BACKEND environmental variable to test against a specific backend version. Depending on the running context (see section above) setting the BACKEND environmental variable is required or optional (see table below).

Requirement for setting the BACKEND variable depends on the context of the job:

context	BACKEND var	comments
Local	mandatory
CircleCI	mandatory for feature branches	not for master or rc builds
CircleCI+PR	optional	1. When specified, GitHub PR must be of 'draft' state. 2. When not-specified, backend branch will mirror frontend branch (rc frontend vs. rc backend)

The value of the BACKEND variable must be formatted as <BACKEND_GITHUB_USER>:<BACKEND_BRANCH>. For example, when the /env/custom.sh file contains export BACKEND=thehyve:uwe7872A this is interpreted as a requirement for the commit uwe7872A of the github.com/thehyve/cbioportal repository.

BACKEND environmental variable in CircleCI+PR context

Using the BACKEND variable e2e-localdb tests can be conducted against any backend version. This poses a risk when testing in CircleCI+PR context, i.e., tests show up as succesful but should have failed against the backend version that compatible with the target cbioportal-frontend branch. To guard against this and prevent merging of incompatible branches into cbioportal-frontend the e2e-localdb tests enforce the use of draft pull requests (see here for more info). When a cBioPortal backend version is specified (i.e., may require a not yet merged backend branch) and the branch is part of a pull request, the pull request must be in state draft. Only when the BACKEND variable is not defined a (non-draft) e2e-localdb tests will be conducted on branches that are part of pull requests. Needles to say, pull request should for this and other reasons only be merged when the e2e-localdb tests succeed!

When the BACKEND variable is not set, the backend version will be set to the target branch of the pull request, i.e. a pull request to 'rc' branch will be tested against the 'rc' branch of the backend.

Writing e2e tests

Some random remarks on e2e-test development

• Screenshot tests and DOM-based tests are contained in files that end with *.screenshot.spec.js or *.spec.js, respectively.
• Screenshot tests should only be used to test components that cannot be accessed via the DOM.
• Screenshots should cover as little of the page possible to test behavior. Larger screenshots will make it more likely the screenshot will need to be updated when an unrelated feature is modified.
• For DOM selection webdriverio selectors are used. Although overlapping with jQuery selectors and both using the '$' notation these methods are not equivalent. See this link for more information on webdriverio selectors.
• At the moment of this writing webdriverio v4 is used. Selectors for this version are not fully compatible with webdriverio v5. For instance, selecting of a element with id test $('id=test') does not work; this should be $([id=test]). I was not able to find documentation of v4 selectors.
• e2e tests use the node.js assert library for assertions. It has an API that is different API from chai assertion library used in unit tests of cbioportal-frontend! See the assert documentation for information on assert API.
• Screenshots for failing tests are placed in the screenshots/diff and screenshots/error folders. These are a valuable asset to debug tests on when developing in Local context.
• A great tool for test development is the ability of webdriverio to pause execution with browser.debug(). When placing this command in the test code and using the run_local_screenshot_test.sh facility, a prompt becomes available on the command line that allows testing of DOM selectors in the webbrowser. In addition, the browser window is available on screen; opening of DevTools allows to explore the DOM and observe the effects of webdriverio commands on the command line.
• Although webdriverio takes asynchronous behavor of webbrosers into account it does not defend against asynchronous behavior of specific web components (e.g., database access). Not taking this asynchronicity into account will result in flaky tests. Typically, flaky test run well on the local system used for development (that has plenty of free resources at moment of test), but fail often on a CI system. Often this is the result of longer times needed page/component update causing tests to fail because the test evaluates a condition before it is loaded. In webdriverio the waitForExist(), waitForVisible() and waitFor() method should be used to pause test execution until the page has been updated. Sometimes it is needed to wait for the appearance of a DOM element which presence is tested.

browser.waitForExist('id=button');
assert($('id=button'));

• Reference screenshosts that are created on host system directly (not in dockerized process) differ from screenshots produced by the dockerized setup (e.g., on CircleCI) and cannot be used as references

Create new e2e-test

Making e2e-tests follows the current procedure for the e2e-tests:

1. Create junit test file and place in the ./end-to-end-test/local/specs or ./end-to-end-test/remote/specs directory.
2. [Optional] Add a folder with an uncompressed custom study in the ./end-to-end-test/local/studies directory.

Random notes

• Study_es_0 is imported by default.
• Gene panel and gene set matrix data of custom studies must comply with gene panel/sets imported as part of study_es_0.
• Imports of custom seed data for gene panels and gene sets are not implemented at the moment of this writing.
• In order to minimize time of local database e2e-tests the size of custom studies should be kept as small as possible.
• When developing in Local context port 8081 can be used to access the cbioportal instance ('http://localhost:8081/cbioportal').

Debugging help

Here are some errors that have been encountered and are hard to debug.

"boundingRects.reduce is not a function"

This error occurs when an e2e test tries to take a screenshot of an element that doesn't exist.

"There are some read requests waitng on finished stream"

This error occurs in CircleCI when the reference screenshot file is somehow corrupted. It can be fixed by deleting and updating the reference screenshot.

Workspaces

We are utilizing yarn workspaces to maintain multiple packages in a single repo (monorepo). The monorepo approach is an efficient way of working on libraries in the same project as the application that is their primary consumer.

The cbioportal-frontend is the main web application workspace. It is used to build and deploy the cBioPortal frontend webapp. Workspaces under packages directory are separate modules (npm packages) designed to be imported by cbioportal-frontend workspace as well as by external projects. Please note: config and typings directories under the packages directory are NOT workspaces or packages. They are intended to share common settings among all packages under the packages directory.

Adding a new workspace

To add a new workspace, create a new directory under packages and add a package.json file. (See cbioportal-frontend-commons workspace for example configuration).

The recommended way to add a new dependency to an existing workspace is to run yarn workspace <workspace name> add <package name> instead of just yarn add <package name>. For example, run yarn workspace cbioportal-frontend add lodash instead of yarn add lodash. Similarly, to remove a package, run yarn workspace <workspace name> remove <package name>.

Tips for dependency management

Please abide by the following rules for importing dependencies in a monorepo:

1. If you are working on cbioportal-frontend repository, import modules from packages using the package's alias:

// CORRECT, uses alias:
import {something} from 'cbioportal-frontend-commons'

// INCORRECT, uses relative paths:
`import {something} from ../../packages/cbioportal-frontend-commons/src/lib/someLib`

2. When working on a package, never import custom code from outside that package unless you really intend for that package to be a dependency. For example, commons packages should not import from the main cbioportal project.

3. Avoid circular dependencies at all costs. For example, while it is okay to import a module from cbioportal-frontend-commons in react-mutation-mapper, there should not be any imports from react-mutation-mapper in cbioportal-frontend-commons. If you happen to need some component from from react-mutation-mapper in cbioportal-frontend-commons, consider moving that component into cbioportal-frontend-commons package.

Updating existing packages

Remember that the packages are used by other projects and compatibility needs to be carefully managed.

When you update code under packages a new version of changed packages automatically published once the code is merged to master. However, in a rare case when you would like to set a custom package version, you can run

yarn run updatePackageVersion

Alternatively you can manually set a custom version. When updating manually you should update the version number in the corresponding package.json as well as the dependencies of other packages depending on the package you update. For example if you update the cbioportal-frontend-commons version from 0.1.1 to 0.1.2-beta.0, corresponding cbioportal-frontend-commons dependency in the package.json for react-mutation-mapper and cbioportal-frontend should also be updated to the new version.

Note that when setting a custom version if you want the next published package version to be, for example, 1.0.6, then you should set the new version to 1.0.6-beta.1 or a similar prerelease version. If you set the custom version to 1.0.6, the next published version will be 1.0.7 not 1.0.6. This is because the auto publish script runs in any case to detect changes in all packages including custom versioned packages.

Update API clients

yarn run updateAPI

Components

Components under packages should only depend on either external node modules or workspaces under packages. Please make sure to not introduce any dependencies from cbioportal-frontend workspace when updating or adding new files under packages.

cbioportal-frontend-commons

cbioportal-frontend-commons is a separate public npm library which contains basic utility functions and components.

react-mutation-mapper

react-mutation-mapper is a separate public npm library that contains the Mutation Mapper and related components.

WSL Tips

When running on a Windows environment, use WSL: Windows Subsystem for Linux. You will be able to run a linux shell, which is necessary for many of the scripts used. You will also be able to use it concurrently with Windows applications.

Make sure the git repo is cloned under the WSL file system (under your home directory). If you instead clone it to the Windows file system (e.g. /mnt/c/... from WSL), then all scripts will be extremely slow.

If you may be working with the git repo via the Windows system, then make sure your line returns are set to lf as opposed to the Windows default crlf.

# from the repo folder
git config core.autocrlf false