Add Pagination Sorting to Discrete Copy Number Alterations API Endpoint

[jagnathan]

Background:
cBioPortal is an open-source platform designed to provide a web interface for exploring, visualizing, and analyzing cancer genomics data, and has grown to be widely used by researchers and clinicians worldwide. The current interface provides comprehensive tools for individual patient data exploration, including mutations, copy number variations, and clinical information as well as cohort exploration, analytics, and cohort comparisons.

APIs that support cBioPortal have Pagination and Sorting. However the API endpoints for Discrete Copy Number Alterations, Copy Number Segments (POST only, GET already supports it) dont support them.

Goal:
Develop Pagination and Sorting to API endpoints such as Discrete Copy Number Alterations, Copy Number Segments (POST only, GET already supports it)

Approach:
Currently API end points such as Clincial Data, Samples, Mutation support pagination.
Discrete Copy Number Alterations API Endpoint can support Pagination similar to other end points.

The API has a page number and page size parameters to reduce the load on server and manage the result set to a manageable level at the client side.

It also can support Sorting with SortBy and Sort Direction parameters

If a study has a large number of CNV data, then this end point can return a large amount of data.

Parameters for Pagination:

PageNumber -

PageSize

SortBy - Fields in CNA table - standardized list available

Sort Direction - ASC, DESC

Additional Parameter:
In addition, it is possible to add HugoGene as an additional parameter similar to Mutation end point.

URLs:

POST URL - /api/molecular-profiles/{molecularProfileId}/discrete-copy-number/fetch

GET URL- /api/molecular-profiles/{molecularProfileId}/discrete-copy-number

https://www.cbioportal.org/api/swagger-ui/index.html#/Copy%20Number%20Segments/fetchCopyNumberSegmentsUsingPOST