Genesys PGR Client

Access data on plant genetic resources from genebanks around the world published on Genesys (< https://www.genesys-pgr.org>). Your use of data is subject to terms and conditions available at < https://www.genesys-pgr.org/content/legal/terms>.

The genesysr R package provides functions for authentication with Genesys and functions to fetch accession data from https://www.genesys-pgr.org database.

Installing the development version

devtools::install_git('https://gitlab.croptrust.org/genesys-pgr/genesysr')

Using genesysr

1. Setup and configure
2. Authenticate
3. User authentication
4. Client authentication
5. Query

Setup and configuration

library('genesysr')
 
# www.genesys-pgr.org
genesysr::setup_production()
 
# or sandbox.genesys-pgr.org
genesysr::setup_sandbox()
 
# or custom
genesysr::setup(server = "http://localhost:8080",
  client_id = "...", client_secret = "...")

User authentication

The package is configured with default Genesys R client credentials that require user authentication:

# Setup
genesysr::setup_production()
 
# Open Genesys web page in browser and get verifier code
genesysr::user_login()

Client authentication

Accessing Genesys without user interaction requires that a client is registered on Genesys with client credentials grant. Contact [email protected] for assistance.

# Setup
library('genesysr')
genesysr::setup(server = "https://www.genesys-pgr.org",
  client_id = "[email protected]",
  client_secret = "your-private-secret")
 
# Obtain access tokens
genesysr::client_login()

Query Genesys

filters <- mcpd_filter(ORIGCTY = c("DEU", "SVN"))
accessions <- genesysr::fetch_accessions(filters)