The genesysr R package provides functions for
authentication with Genesys and functions to fetch accession data from
https://www.genesys-pgr.org database.
Note: See NEWS.md
devtools::install_git('https://gitlab.croptrust.org/genesys-pgr/genesysr')genesysrlibrary('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 = "...")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()Accessing Genesys without user interaction requires that a client is registered on Genesys with client credentials grant. Contact helpdesk@genesys-pgr.org for assistance.
# Setup
library('genesysr')
genesysr::setup(server = "https://api.genesys-pgr.org",
client_id = "someId.....@www.genesys-pgr.org",
client_secret = "your-private-secret")
# Obtain access tokens
genesysr::client_login()filters <- mcpd_filter(ORIGCTY = c("DEU", "SVN"))
accessions <- genesysr::get_accessions(filters)
# Sort columns, hand-pick first few columns
require(data.table)
setcolorder(accessions, unique(c("id", "instituteCode", "accessionNumber", "taxonomy.genus", sort(names(accessions)))))