README.md

In genesysr: Genesys PGR Client

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

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 helpdesk\@genesys-pgr.org{.email} for assistance.

# Setup
library('genesysr')
genesysr::setup(server = "https://api.genesys-pgr.org",
  client_id = "[e-mail]",
  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)))))

genesysr documentation built on May 29, 2024, 3:42 a.m.