## ----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())