## ----setup, include = FALSE---------------------------------------------------
library(rirods)
library(httptest2)
start_vignette("local-irods")

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

root_dir <- tempdir()

knitr::opts_knit$set(
  root.dir = root_dir
)

## ----setup2, include=FALSE----------------------------------------------------
# # set user config directory to temporary location
# withr::local_envvar(
#   R_USER_CONFIG_DIR = root_dir
# )
# eval(substitute(create_irods(x, overwrite = TRUE), list(x = rirods:::.irods_host)))
# iauth("rods", "rods")
# 
# if (length(ils())> 0) {
#   for (file in ils()$logical_path) {
#     irm(file, recursive = TRUE, force=TRUE)
#   }
# }
# 
# dir.create(file.path(root_dir, "data"))
# imkdir("data")

## -----------------------------------------------------------------------------
# getwd()
# ipwd()

## -----------------------------------------------------------------------------
# dir()
# ils()

## ----include=FALSE------------------------------------------------------------
# change_state()

## -----------------------------------------------------------------------------
# old_local <- setwd("data")
# dir()
# old_irods <- icd("data")
# ils()

## ----include=FALSE------------------------------------------------------------
# change_state()

## -----------------------------------------------------------------------------
# setwd(old_local)
# getwd()
# 
# icd(old_irods)
# ipwd()

## ----include=FALSE------------------------------------------------------------
# change_state()

## -----------------------------------------------------------------------------
# dir.create("analysis")
# dir()
# 
# imkdir("analysis")
# ils()

## -----------------------------------------------------------------------------
# set.seed(1234)
# fake_data <- data.frame(x = rnorm(20, mean = 1))
# fake_data$y <- fake_data$x * 2 + 3 - rnorm(20, sd = 0.6)
# write.csv(fake_data, file.path("data", "data.csv"), row.names = FALSE)
# dir("data")

## ----include=FALSE------------------------------------------------------------
# change_state()

## -----------------------------------------------------------------------------
# iput("data/data.csv", "data/data_from_local.csv")
# ils("data")

## -----------------------------------------------------------------------------
# m <- lm(y ~ x, data = fake_data)
# m

## ----include=FALSE------------------------------------------------------------
# change_state()

## -----------------------------------------------------------------------------
# isaveRDS(m, "analysis/linear_model.rds")
# ils("analysis")
# dir("analysis") # nothing was saved locally

## -----------------------------------------------------------------------------
# iget("data/data_from_local.csv", "data/data_from_irods.csv")
# dir("data")
# read.csv("data/data_from_irods.csv") # same as fake_data

## -----------------------------------------------------------------------------
# # copy locally first
# iget("analysis/linear_model.rds", "analysis/linear_model_in_local.rds")
# dir("analysis")
# readRDS("analysis/linear_model_in_local.rds")
# 
# # or read directly from iRODS
# ireadRDS("analysis/linear_model.rds")

## ----include=FALSE------------------------------------------------------------
# change_state()

## -----------------------------------------------------------------------------
# unlink("analysis", recursive = TRUE)
# dir()
# 
# irm("data", recursive = TRUE, force = TRUE)
# ils()

## ----cleanup, include=FALSE---------------------------------------------------
# change_state()
# for (file in ils()$logical_path) {
#   irm(file, recursive = TRUE, force=TRUE)
# }
# unlink(file.path(root_dir, "data"), recursive=TRUE)
# unlink(file.path(root_dir, "analysis"), recursive=TRUE)
# end_vignette()
# unlink(rirods:::path_to_irods_conf())