brapi-proxy 0.9.0

A BRAPI server instance that functions as a proxy to merge and combine endpoints from existing BRAPI services

BrAPI proxy solution

A BrAPI server instance that functions as a proxy to merge and combine endpoints from existing BrAPI services.

Installation

• Step 1: Install BrAPI Proxy
  • To install the BrAPI Proxy, run the following command:

    pip install brapi_proxy
    

• Step 2: Test the Installation (Optional)
  • To ensure that the installation was successful, you can run the BrAPI Proxy in demo mode with the following command:

    brapi_proxy --demo
    

    This will start a service on port 8080 from a configuration based on the BrAPI Test Server

Usage

• Step 1: Create Configuration File

  • Create a file named config.ini.
  • Populate this file with the necessary configuration settings.

• Step 2: Start the Service

  • Start the service by running the command:

    brapi_proxy
    

  • If the config.ini file is located outside the working directory, use the --config option to specify its location. For example:

    brapi_proxy --config /path/to/config.ini
    

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Currently Supported

BrAPI Versions

• version 2.1

Endpoints

• BrAPI-Core
  • /commoncropnames
  • /lists
  • /lists/{listDbId}
  • /locations
  • /locations/{locationDbId}
  • /people
  • /people/{personDbId}
  • /programs
  • /programs/{programDbId}
  • /seasons
  • /seasons/{seasonDbId}
  • /studies
  • /studies/{studyDbId}
  • /trials
  • /trials/{trialDbId}
• BrAPI-Phenotyping
  • /methods
  • /methods/{methodDbId}
  • /observations
  • /observations/{observationDbId}
  • /observationunits
  • /observationunits/{observationUnitDbId}
  • /ontologies
  • /ontologies/{ontologyDbId}
  • /scales
  • /scales/{scaleDbId}
  • /traits
  • /traits/{traitDbId}
  • /variables
  • /variables{observationVariableDbId}
• BrAPI-Genotyping
  • /allelematrix
  • /callsets
  • /callsets/{callSetDbId}
  • /plates
  • /plates/{plateDbId}
  • /references
  • /references/{referenceDbId}
  • /referencesets
  • /referencesets/{referenceSetDbId}
  • /samples
  • /samples/{sampleDbId}
  • /variants
  • /variants/{variantDbId}
  • /variantsets
  • /variantsets/{variantSetDbId}
• BrAPI-Germplasm
  • /attributes
  • /attributes/{attributeDbId}
  • /attributevalues
  • /attributevalues/{attributeValueDbId}
  • /breedingmethods
  • /breedingmethods/{breedingMethodDbId}
  • /germplasm
  • /germplasm/{germplasmDbId}

ToDo

• Implement additional endpoints

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Structure Configuration File

Create a config.ini file with the necessary configuration settings.

Basic Configuration

Include at least the brapi section:

[brapi]
port=8080
host=0.0.0.0
location=/
threads=4
debug=False
version=1.2.3

Optional: Serverinfo

Optionally, provide serverinfo entries:

contactEmail=[e-mail]
documentationURL=https://github.com/matthijsbrouwer/brapi-proxy/
location=Wageningen
organizationName=Wageningen University and Research
organizationURL=https://www.plantbreeding.wur.nl/
serverDescription=Demo-version proxy to combine multiple BrAPI services
serverName=BrAPI-Proxy

Optional: Authorization

Optionally, provide authentication tokens to restrict access in the authorization section:

[authorization]
john=tokenjohn123abc
mary=tokenmary456def

Server Definitions

Within sections prefixed with server., define the underlying servers:

[server.test1]
url=https://test-server.brapi.org/brapi/v2
calls=commoncropnames,variants,allelematrix
authorization=XXXX
prefix.variants=barley:
prefix.variantsets=barley:
prefix.references=barley:
prefix.referencesets=barley:
prefix.callsets=barley:

[server.test2]
url=https://test-server.brapi.org/brapi/v2
calls=commoncropnames,variants,allelematrix
prefix.variants=wheat:
prefix.variantsets=wheat:
prefix.references=wheat:
prefix.referencesets=wheat:
prefix.callsets=wheat:

[server.test3]
url=https://test-server.brapi.org/brapi/v2
calls=samples,studies,plates,callsets,variantsets,referencesets,references

To include all available and supported calls from a namespace:

[server.test3]
url=https://test-server.brapi.org/brapi/v2
calls=core.*

To include all available and supported calls:

[server.test3]
url=https://test-server.brapi.org/brapi/v2
calls=*

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This software has been developed for the AGENT project