Development Documentation

[inodb]

Project name: cBioPortal Development Documentation

Description: Improve the cBioPortal Documentation for new developers. cBioPortal uses a Java REST backend that exposes data from a MySQL database. The frontend is a React Single Page App. Often one only needs to edit a component of this system e.g. only the frontend or only the backend. The current documentation doesn't clearly mention for new developers how to set up a development environment.

We should have one or more recommended ways to deploy the portal for development. Docker could be useful for this. Right now we don't provide easy documentation to get people started on the backend project. For frontend development there is some decent documentation available: https://github.com/cBioPortal/cbioportal-frontend/blob/master/README.md.

It would furthermore be good to have one page where all developers can go that points them to the various locations where one can read more about how to make changes to backend, frontend, data importing, etc.

Our current technical documentation is written as markdown files in our GitHub repo and displayed using GitBook

Possible mentors: @inodb @alisman @lemccarthy

For more information about cBioPortal GSoD: See our wiki page

[lemccarthy]

In the backend setup documents, I think there are a few deficiencies:

• It tells you how to set up your own local sample database, but not how to connect to our public one which is often easier and more practical for local development.
• Too much of the process is setting up small config files, some kind of script that would just do all that would be very nice.
• It doesn't explicitly explain how to start the project with the JPDA option which is required if you want to attach a debugger.
• mvn clean install will fail. The docs tell you to pass in -DskipTests, but I think the explanation of why should be made clear (the integration tests can't run locally). And at some point we should restructure the tests so that the full suite of unit tests can be run by that command, while still allowing Travis to run the integration tests.
• No mention of the quicksearch setting in the portal.properties file. We need to add a section to the docs explaining how to enable it.

In the frontend setup documentation:

• Explain more clearly the process for regenerating the TypeScript definitions to reflect changes in the backend API
• This includes telling them not to manually edit the generated files.