tests/testthat/test-metadata.R

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

message(paste0(capture.output(Rlabkey:::labkey.curlOptions()), collapse = "\n"))
test_that("special case is handled correctly", {
  study <- "SDY1529"
  gef <- readRDS("test_data/sdy1529/SDY1529_day0_gef.rds")
  fas_id <- 54
  meta_data <- get_meta_data(
    study,
    gef,
    fas_id,
    labkey.url.base
  )
  expect_equal(meta_data$file_location, "custom")
  expect_failure(expect_null(meta_data$custom_file_info))
  expect_equal(meta_data$custom_file_info$directory, "author_data")
  expect_equal(meta_data$custom_file_info$file_identifier_regex, "GA")
})

test_that("file location is identified correctly", {
  study <- "SDY1328"
  meta_data <- get_meta_data(study,
    baseUrl = labkey.url.base
  )
  expect_equal("gsm_supp_files", meta_data$file_location)

  study <- "SDY1324"
  meta_data <- get_meta_data(study,
    baseUrl = labkey.url.base
  )
  expect_equal("custom", meta_data$file_location)
})

test_that("custom_file_info is identified correctly", {
  study <- "SDY1324"
  meta_data <- get_meta_data(study,
    baseUrl = labkey.url.base
  )
  expect_failure(expect_null(meta_data$custom_file_info))
  expect_equal(meta_data$custom_file_info$directory, "raw_counts")
  expect_equal(meta_data$custom_file_info$file_identifier_regex, "RawCounts")
})