OncoKB Public Website

OncoKB is a precision oncology knowledge base and contains information about the effects and treatment implications of specific cancer gene alterations. Please cite Suehnholz et al., Cancer Discovery 2023 and Chakravarty et al., JCO PO 2017.

This application was generated using JHipster 6.10.3, you can find documentation and help at https://www.jhipster.tech/documentation-archive/v6.10.3.

Status

Info

Development

Running environment

Make sure your running environment is the following:

• Java version: 8
• MySQL version: 5.7.28
• Redis

Setup Redis (optional)

The following steps is one way to set up the redis. As long as you have redis setup and ready to connect, then that would work.

• Install Docker
• Install Kubernetes(k8s) (In Mac versin, you can enable k8s in Docker Preference)
• Install helm
• Install redis helm install oncokb-public-redis bitnami/redis --set auth.password=oncokb-public-redis-password --set replica.replicaCount=1
• Follow the instructions after installing redis. Then you need to proxy the redis out, command looks like kubectl port-forward --namespace default svc/oncokb-public-redis-master 6379:6379

Modify config

/src/main/resources/config/application-dev.yml

1. Confirm database name, username, password under datasource config.
2. Change api-proxy-url to the URL where oncokb running. For example, http://localhost:8888/oncokb
3. Make sure the password for your Redis as same as the password for Redis defined in this file

Building

Before you can build this project, you must install and configure the following dependencies on your machine:

1. Node.js: We use Node to run a development web server and build the project. Depending on your system, you can install Node either from source or as a pre-packaged bundle.

After installing Node, you should be able to run the following command to install development tools. You will only need to run this command when dependencies change in package.json.

yarn install

We use yarn scripts and Webpack as our build system.

Run the following commands in two separate terminals to create a blissful development experience where your browser auto-refreshes when files change on your hard drive.

./mvnw
yarn start

yarn is also used to manage CSS and JavaScript dependencies used in this application. You can upgrade dependencies by specifying a newer version in package.json. You can also run yarn update and yarn install to manage dependencies. Add the help flag on any command to see how you can use it. For example, yarn help update.

The yarn run command will list all of the scripts available to run for this project.

Connect with server side locally

After starting project up locally, you should type the following command in your browser console

localStorage.setItem("localdev", true)

To unset do:

localStorage.removeItem("localdev")

or

localStorage.setItem("localdev", false)

Managing dependencies

For example, to add Leaflet library as a runtime dependency of your application, you would run following command:

yarn add --exact leaflet

To benefit from TypeScript type definitions from DefinitelyTyped repository in development, you would run following command:

yarn add --dev --exact @types/leaflet

Then you would import the JS and CSS files specified in library's installation instructions so that Webpack knows about them: Note: There are still a few other things remaining to do for Leaflet that we won't detail here.

For further instructions on how to develop with JHipster, have a look at Using JHipster in development.

Building for production

Packaging as jar

To build the final jar and optimize the oncokb application for production, run:

./mvnw -Pprod clean verify

This will concatenate and minify the client CSS and JavaScript files. It will also modify index.html so it references these new files. To ensure everything worked, run:

java -jar target/*.jar

Then navigate to http://localhost:9090 in your browser.

Refer to Using JHipster in production for more details.

Packaging as war

To package your application as a war in order to deploy it to an application server, run:

./mvnw -Pprod,war clean verify

Packaging with a docker image ready

./mvnw package -Pprod verify jib:dockerBuild -DskipTests

Testing

To launch your application's tests, run:

./mvnw verify

Screenshot tests

Screenshot tests are run by Jest, Puppeteer. They're located in screenshot-test/. Because different dev environments have different systems, which may cause the resulting image doesn’t quite match the expected one from the __baseline_snapshots__ directory saved in source control, we dockerized the test process and can be run with:

yarn run screenshot-test-in-docker

You can also run screenshot-test locally using yarn run screenshot-test

Update screenshot tests

After running the command above, you will see __diff_output__ and __latest_snapshots__ folders created under screenshot-test. These new images indicate potential changes. If these changes are expected, please follow the below steps to update the images under __baseline_snapshots__.

1. Send a pull request to the intended branch
2. The PR will trigger the Screenshot Test GitHub action
3. Using this example, the action will generate two folders(visual-regression-diff-report and visual-regression-screenshots) under the Artifacts section.
4. visual-regression-diff-report folder includes the files should be updated. You can copy over the ones with the same name under visual-regression-screenshots to your pull request.

Using Docker to simplify development (optional)

You can use Docker to improve your JHipster development experience. A number of docker-compose configuration are available in the src/main/docker folder to launch required third party services.

For example, to start a mysql database in a docker container, run:

docker-compose -f src/main/docker/mysql.yml up -d

To stop it and remove the container, run:

docker-compose -f src/main/docker/mysql.yml down

You can also fully dockerize your application and all the services that it depends on. To achieve this, first build a docker image of your app by running:

./mvnw -Pprod verify jib:dockerBuild

Then run:

docker-compose -f src/main/docker/app.yml up -d

For more information refer to Using Docker and Docker-Compose, this page also contains information on the docker-compose sub-generator (jhipster docker-compose), which is able to generate docker configurations for one or several JHipster applications.

Testing Slack Integration

1. Ensure you can access the MSK secret server

2. Ensure you can access the Slack API Manager

3. Install ngrok

4. Update the /src/main/resources/config/application-dev.yml file

   • Change spring.mail.username to [email protected]
   • Change spring.mail.password to the password for [email protected] found in the secret server
   • Change application.slack.user-registration-webhook to the slack hook.
   • Change application.slack.slack-base-url to https://oncokb.slack.com
   • Change application.slack.user-registration-channel-id to C03EASPQ8AZ
   • If you need to use a slack endpoint that requires a token, update application.slack.slack-bot-oauth-token with the token get from this page.

5. Start up ngrok

   ngrok http http://localhost:9090

6. Copy the forwarding URL generated by ngrok.

   • Should be something like https://xxxx-xxx-xxx-xx-xx.ngrok-free.app

7. Update the Request URL in the slack message configuration in the Request URL to https://xxxx-xxx-xxx-xx-xx.ngrok-free.app/api/slack

   • Replace the base URL with the URL generated by ngrok for forwarding

8. Register an account in your local instance of OncoKB public

   • Ensure the email you use is one you have access to

9. Check the slack-app-dev channel for a message and approve it