library(testthat)
library(NACHO)

# setwd("tests")

if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  rcc_files_directory <- "testthat/plexset_data"
  plexset_files <- list.files(rcc_files_directory, full.names = TRUE, pattern = "\\.RCC")
  plexset_tidy <- data.frame(stringsAsFactors = FALSE,
    name = basename(plexset_files),
    datapath = plexset_files,
    IDFILE = basename(plexset_files),
    plexset_id = rep(paste0("S", seq_len(8)), each = length(plexset_files))
  )
  plexset_nacho <- load_rcc(
    data_directory = rcc_files_directory,
    ssheet_csv = plexset_tidy,
    id_colname = "IDFILE"
  )

  rcc_files_directory <- "testthat/salmon_data"
  salmon_files <- list.files(rcc_files_directory, full.names = TRUE, pattern = "\\.RCC")
  salmon_tidy <- data.frame(stringsAsFactors = FALSE,
    name = basename(salmon_files),
    datapath = salmon_files,
    IDFILE = basename(salmon_files),
    plexset_id = rep(paste0("S", seq_len(8)), each = length(salmon_files))
  )
  salmon_nacho <- load_rcc(
    data_directory = rcc_files_directory,
    ssheet_csv = salmon_tidy,
    id_colname = "IDFILE"
  )

  rcc_files_directory <- "testthat"
  plexset_salmon_tidy <- data.frame(stringsAsFactors = FALSE,
    name = list.files(rcc_files_directory, pattern = "\\.RCC", recursive = TRUE),
    datapath = list.files(rcc_files_directory, full.names = TRUE, pattern = "\\.RCC", recursive = TRUE),
    IDFILE = basename(list.files(rcc_files_directory, full.names = TRUE, pattern = "\\.RCC", recursive = TRUE)),
    plexset_id = rep(paste0("S", seq_len(8)), each = length(list.files(rcc_files_directory, pattern = "\\.RCC", recursive = TRUE)))
  )

  test_check("NACHO")
}