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Genesys R client

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

Installing the development version

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

Using `genesysr`

Setup and configure
Authenticate
User authentication
Client authentication
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 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()

Query Genesys

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)))))

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.