## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  eval     = FALSE
)

## ----renviron-----------------------------------------------------------------
# usethis::edit_r_environ()
# # Add the following line, then save and restart R:
# # DX_API_TOKEN=your_token_here

## ----auth-login---------------------------------------------------------------
# library(ukbflow)
# 
# auth_login()  # reads DX_API_TOKEN from environment

## ----auth-login-direct--------------------------------------------------------
# auth_login("your_token_here")

## ----auth-rap-----------------------------------------------------------------
# library(ukbflow)
# 
# auth_status()  # verify the current session

## ----auth-status--------------------------------------------------------------
# auth_status()
# #> • User:    "user-XXXXXXXXXXXX"
# #> • Project: "project-XXXXXXXXXXXX"

## ----list-projects------------------------------------------------------------
# auth_list_projects()
# #> project-XXXXXXXXXXXX : My UKB Project (CONTRIBUTOR)
# #> project-YYYYYYYYYYYY : Shared Analysis Project (VIEW)

## ----select-project-----------------------------------------------------------
# auth_select_project("project-XXXXXXXXXXXX")
# #> ✔ Project selected: "project-XXXXXXXXXXXX"

## ----auth-logout--------------------------------------------------------------
# auth_logout()
# #> ✔ Logged out from DNAnexus.

## ----reauth-------------------------------------------------------------------
# auth_login("your_new_token_here")

## ----full-workflow------------------------------------------------------------
# library(ukbflow)
# 
# auth_login()                                 # authenticate
# auth_status()                                # verify session
# auth_list_projects()                         # find your project ID
# auth_select_project("project-XXXXXXXXXXXX")  # set active project
# 
# # ... run your analysis ...
# 
# auth_logout()                                # optional: clear session