# cBioPortal Backend Code Organization

# Maven Project

The backend code is structured as a Maven project. Included in the repository are pom.xml files which define the code components and modules which make up the backend. The pom.xml files also list dependencies on external open source libraries, and dependencies between cBioPortal Maven modules. They also give instructions for how to build and package code components into a deployable format.

# Refactoring

The code base is undergoing a long term refactoring effort which is nearing completion.

# Web service refactoring

The original data distribution service (still in operation) was a custom servlet called webservice.do This servlet takes a "cmd" argument which selects the category of data requested. More details can be seen on the cBioPortal webAPI tab.

An example request: curl -X GET "https://www.cbioportal.org/webservice.do?cmd=getGeneticProfiles&cancer_study_id=brca_tcga"

The new data distribution approach follows a RESTful approach, mapping various URL paths to data services, allowing the specification of database entities within the path as helpful.

An example request: curl -X GET "https://www.cbioportal.org/api/studies/brca_tcga/molecular-profiles"

# Presentation / frontend refactoring

The original presentation code was written as a set of java service pages (JSP), connected to servlets which populated needed data for page rendering into request attributes within the backend server. You can see examples of the setting of these request attributes in this example servlet

This has largely been superceded and expanded on by a new React javascript application located in a separate GitHub repository, which maintains a browser data store populated from the new RESTful Web API. Although the new frontend project is not dependent on the original custom servlets for data delivery, we may continue to use the servlet / JSP delivery path to embed configuration data in the initial HTML page in order to allow us to optimize loading times. Some of this logic has already been migrated out of the core module and moved to the portal module.

# Current Maven Modules

# The core module

The core module contains the oldest code in the code base. Much of the backend web data services logic has been re-implemented and expanded in other backend maven modules, such as model, persistence-mybatis, service, and web. We plan to discontinue the legacy webservice.do data servlet and fully transition to the new data services API in the near future. The core module will then be purged of much of the legacy code. Any surviving functionality (such as the handling of global configuration properties) may be relocated into new modules. It is therefore important that no new code features be introduced which are dependent on the core module functionality.

# The central stack modules : web, service, persistence

Three maven modules make up the central stack of the new web API implementation.

• web : define Web API request handlers, map endpoints, select services
• service : call persistence module or utils, apply business logic
• persistence : retrieve data from database. Two submodules:
  • persistence-api : declaration of repository classes / functions, caching markup
  • persistence-mybatis : implementation of persistence-api using MyBatis mappers

# Other modules

• model : data model POJO classes (used throughout the stack)
• security : user authentication methods and authorization, request filters
• business : a legacy refactor of webservice.do, has active dataSource definition
• portal : web application packaging and launch
• scripts : data import tool packaging (from core module scripts package)
• db_scripts : installation and migration scripts for the database

# External code modules

• cbioportal-frontend : a React application using MobX and TypeScript
• session-service : an external session key/query specifier storage system

cbioportal-frontend is packaged in the web application as a default frontend implementation, but the source of the frontend code can also be directed to an external source host and be deployed independently of the backend web application. See details

session-service is imported into the web module in order to set up a proxy service which receives and forwards requests for saved cBioPortal sessions to a separate system providing this storage (using a document based database) The code is needed for handling modeled types such as VirtualStudy and Session

# cBioPortal Module Dependencies

A module is directly dependent on all modules which touch it from below (touching only at a corner does not count). Dependencies are transitive : web is dependent on service, service is dependent on persistence-mybatis, therefore web is also dependent on persistence-mybatis. During packaging, all dependencies are made available to the dependent package for use. Avoid creating new dependencies between modules. cyclical dependencies will cause errors during build