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PHGv2 - Ktor Specifications

In this document, we will discuss the BrAPI endpoints provided by the Ktor server implemented in the start-server command.

Overview

As stated in the "Export data" documentation, start-server is a command that allows users to start a "RESTful" web service. This service can provide access to a centralized PHG database, allowing multiple individuals in a team to simultaneously retrieve PHG-relevant information. This service relies on two components: the Ktor framework and BrAPI-compliant endpoints.

Ktor is an asynchronous framework for building web applications and microservices in Kotlin. It is designed for creating connected systems, focusing on scalability, high performance, and ease of use. Ktor supports both server and client-side development, allowing developers to create RESTful APIs, web sockets, and various other server applications. It provides a DSL (Domain-Specific Language) to define routing, request handling, and response production, making it highly customizable and flexible for a wide range of use cases.

This framework aids in the deployment of BrAPI-compliant data endpoints. BrAPI is a standardized RESTful web service API specification for plant breeding data. It ensures interoperability among breeding databases and tools by providing a common framework. Additionally (and most importantly), BrAPI is developed by a global community of contributors and is intended to be an open and accessible standard for anyone involved in plant breeding data management.

Relevant endpoints

While BrAPI comprises several "modules", PHGv2 leverages data endpoints found within the core and genotyping modules:

  • serverinfo
  • Usage: <host-url>:<port>/brapi/v2/serverinfo
  • Find all available BrAPI calls implemented for the server
  • samples
  • Usage: <host-url>:<port>/brapi/v2/samples
  • List all samples available in the PHG database
  • variants
  • Usage: <host-url>:<port>/brapi/v2/variants
  • List all reference ranges available in the PHG database
  • variantsets
  • Usage: <host-url>:<port>/brapi/v2/variantsets
  • Downloadable link for a composite hVCF file. (Currently for all data)

Response fields

Each of the prior BrAPI calls will contain "key-value" response fields which contain the actual data:

  • serverinfo
  • calls - array of available calls to the server
    • dataTypes - possible data formats returned by the available call (e.g., "APPLICATION_JSON")
    • methods - HTTP methods to be used for each call (e.g., GET)
    • service - name of the call (e.g., samples)
    • version - supported versions for a given call (e.g., "_2")
  • samples
  • additionalInfo - "free" space for further information (not bound by any data type)
  • sampleDbId - internal ID value for given sample
  • sampleDescription - description of sample
  • sampleName - name of sample in PHG database
  • variants
  • additionalInfo - an object for additional information
  • alternateBases - an array of alternate base sequences
  • ciend - an array of confidence interval end positions
  • cipos - an array of confidence interval start positions
  • created - the creation timestamp of the variant
  • end - the end position of the variant
  • filtersApplied - a boolean indicating if filters were applied
  • filtersFailed - an array of failed filters
  • filtersPassed - a boolean indicating if the variant passed filters
  • referenceBases - the reference base sequence
  • referenceName - the reference chromosome or scaffold name
  • start - the start position of the variant
  • svlen - the structural variant length
  • updated - the last update timestamp of the variant
  • variantDbId - the unique identifier of the variant
  • variantNames - an array of variant names
  • variantSetDbId - an array of associated variant set IDs
  • variantType - the type of variant (e.g., "REF_RANGE")
  • variantsets
  • additionalInfo - an object for additional information
  • analysis - an array of analysis related to the variant set
  • availableFormats - a list of available formats with details
    • dataFormat - the data format (e.g., "VCF")
    • fileFormat - the file format (e.g., "TEXT_TSV")
    • fileURL - the URL to access the file
  • callSetCount - the count of call sets
  • referenceSetDbId - the unique identifier of the reference set
  • studyDbId - the unique identifier of the study
  • variantCount - the count of variants
  • variantSetDbId - the unique identifier of the variant set
  • variantSetName - the name of the variant set