oncokb-ts-api-client v1.3.5

cbioportal-frontend

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

Branch Information

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

Run

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

Tip: We recommend that you use nvm: Node Version Manager and yvm: Yarn Version Manager to switch between versions more easily.

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 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

Example pages:

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

To run unit/integration tests

yarn run test

Windows Tip: There is a known solved hiccup running the tests on Ubuntu via Windows Subsystem for Linux (WSL): #7096

To run unit/integration tests in watch mode

yarn run test:watch

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 -- --grep=#specName#

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 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

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

First, install webdriver-manager, which manages standalone Selenium installation:

yarn global add webdriver-manager

Run updater to get necessary binaries

webdriver-manager update

Start the webdriver-manager

webdriver-manager start

Tip: To verify that your webdriver-manager is running, go to: http://127.0.0.1:4444/wd/hub/static/resource/hub.html.

Windows Tip: If you are developing on Ubuntu under Windows Subsystem for Linux (WSL), we recommend that you install and run webdriver-manager via Powershell/Windows. If you install and run webdriver-manager via Ubuntu, webdriver-manager has a hard time finding the Chrome browser, and this will cause all the end-to-end tests to fail.

In a second terminal, run the frontend

# set the environment variables for your branch
export BRANCH_ENV=master # or rc if branching from rc
# export any custom external API URLs by editing env/custom.sh
yarn run startSSL

Tip: Before going to the next step, verify that your front end code is running by going to: https://localhost:3000/.

In a third terminal, run the e2e tests

export SPEC_FILE_PATTERN=./remote/specs/**/*.spec.js
export SCREENSHOT_DIRECTORY=./remote/screenshots
export BRANCH_ENV=master # or rc if branching from rc
# export any custom external API URLs in env/custom.sh
cd end-to-end-test
yarn install
yarn run test-webdriver-manager
# use `test-webdriver-manager-debug` for debugging of tests

If all goes well, you will soon seen the end-to-end tests running via your Chrome browser.

Tip: If you want to run just one end-to-end test, you can modify SPEC_FILE_PATTERN accordingly. For example, if you want to only run the genomicEvolution.spec.js test, you can use: export SPEC_FILE_PATTERN=./remote/specs/core/genomicEvolution.spec.js.

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 local 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.

Contexts for e2e-localdb tests

E2e-tests can run in local context (workstation for software development) or CircleCI context (for continuous integration testing). On CircleCI, e2e-tests can be conducted on commits that are inside or outside the context of a pull request. These different contexts for e2e-localdb tests are refered to below as Local, CircleCi and CircleCI+PR contexts, respectively.

Running e2e-localdb tests in Local context for development

Running of e2e-localdb tests in Local context in essence follows the procedure as defined in .circleci/config.yml. In Local context the e2e-localdb tests can be run in a dockerized environment (usefull for generating screenshots) or directly on the host sytem. The end-to-end-test/local/runtime-config/run_container_screenshot_test.sh script is included to run e2e-local tests in a dockerized environment in Local context. The end-to-end-test/local/runtime-config/run_local_screenshot_test.sh is included to run e2e-local tests on the host system directly in Local context. Prior to running the script several environmental variables should be set. For local development follow these steps:

1. Add export BACKEND=cbioportal:rc (or other backend branch) to /env/custom.sh.
2. Setup a local docker container environment:

export PORTAL_SOURCE_DIR=~/git/cbioportal-frontend # change path if needed
export DB_DATA_DIR=/tmp/mysql # change path if needed
export TEST_HOME="$PORTAL_SOURCE_DIR/end-to-end-test"
source $PORTAL_SOURCE_DIR/env/custom.sh
cd $TEST_HOME/local/runtime-config
eval "$(./setup_environment.sh)"
cd $PORTAL_SOURCE_DIR

3. Running tests can be executed (a) on the local system or (b) in the docker environment;

(a) local system (best for test development)

export CBIOPORTAL_URL='http://localhost:8081'
$TEST_HOME/local/runtime-config/setup_local_context.sh -j -d -p -e # remove flags to exclude specific stages if desired (see below)
cd $PORTAL_SOURCE_DIR
./end-to-end-test/local/runtime-config/run_local_screenshot_test.sh # (repeat this step while developing)

(b) docker environment (best for making reference screenshots)

export CBIOPORTAL_URL='http://cbioportal:8080'
yarn
yarn build
cd $TEST_HOME/local/docker
./setup_docker_containers.sh -p -d -e # remove flags to exclude specific stages if desired (see below)
cd $PORTAL_SOURCE_DIR
$TEST_HOME/local/runtime-config/run_container_screenshot_test.sh

4. When finished reclaim ports by killing selenium and node servers:

lsof -n -i4TCP:3000 && lsof -n -i4TCP:3000 | grep LISTEN | awk '{ print $2 }' | xargs kill # reclaims port 3000
lsof -n -i4TCP:4444 && lsof -n -i4TCP:4444 | grep LISTEN | awk '{ print $2 }' | xargs kill # reclaims port 4444

Inclusion of specific build stages

Setup of the local context involves building of the local frontend code, building of the cbioportal database, building the cbioportal application, building the e2e service and the start of all docker containers. During rebuilding of the development environment the developer can specify which stept should be executed by providing -j (building of frontent code), -d (building of database), -p (building of cbioportal), and/or -e (building of e2e service) flags to the setup_local_context.sh script. For instance, to rebuild the database and start all containers the script can be executed as:

./end-to-end-test/local/runtime-config/setup_local_context.sh -d

When no parameters are passed, no build steps are executed (only (re)start of containers).

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:

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').

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.