tests/testthat/test-download_d1_data.R

In metajam: Easily Download Data and Metadata from 'DataONE'

context("download_d1_data")

test_that("accepts correct inputs", {
  expect_error(download_d1_data(7))
  expect_error(download_d1_data(c("test", "test2")))
  expect_error(download_d1_data(""))
  expect_error(download_d1_data("test", 7))
  expect_error(download_d1_data("test", c("test", "test2")))
  expect_error(download_d1_data("test", ""))
  expect_error(download_d1_data("test", "test"))
})

test_that("test Arctic Data Center data URL (fully up to date data file)", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- download_d1_data(data_url = "https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570",
                          path = temp_dir)
  files <- list.files(out)

  expect_equal(length(files), 5)
  expect_true(any(stringr::str_detect(files, "attribute_metadata.csv")))
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  # expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})

test_that("test Arctic Data Center data URL (fully up to date data file) with one data table", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- download_d1_data("https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570",
                          temp_dir)
  files <- list.files(out)

  expect_equal(length(files), 5)
  expect_true(any(stringr::str_detect(files, "attribute_metadata.csv")))
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})

test_that("test Arctic Data Center data URL (fully up to date data file) with multiple data tables", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- download_d1_data(data_url = "https://cn.dataone.org/cn/v2/resolve/urn:uuid:a4f85031-0b91-4d92-ba0a-b02f216bba64",
                          path = temp_dir)
  files <- list.files(out)

  expect_equal(length(files), 6)
  expect_true(any(stringr::str_detect(files, "attribute_metadata.csv")))
  expect_true(any(stringr::str_detect(files, "attribute_factor_metadata.csv")))
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})

test_that("Data without metadata downloads and returns summary metadata", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  expect_error(download_d1_data(data_url = "urn:uuid:7bdab6cc-8dc1-4c49-a80b-ca771c18eaa9",
                                path = temp_dir))
  # files <- list.files(out)
  #
  # expect_equal(length(files), 2)
  # expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))
  #
  # remove files
  unlink(temp_dir, recursive = TRUE)
})

#adding a test for a dataset that uses ISO metadata and is from the Alaska Ocean Observing System member node
test_that("test data URL with ISO metadata from AOOS member node and with multiple data tables", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- expect_warning(download_d1_data(data_url = "https://cn.dataone.org/cn/v2/resolve/4139539e-94e7-49cc-9c7a-5f879e438b16",
                          path = temp_dir))
  files <- list.files(out)

  expect_equal(length(files), 4)
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  # expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})

#adding a test for a dataset that uses ISO metadata from Research Workspace member node
test_that("test data URL with ISO metadata from Research Workspace member node and with multiple data tables", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- download_d1_data(data_url = "https://cn.dataone.org/cn/v2/resolve/f8e4b479-2c85-4cfd-ad69-4aa059b58a92",
                          path = temp_dir)
  files <- list.files(out)

  expect_equal(length(files), 4)
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  # expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})

# EDI data test
test_that("test EDI data URL (fully up to date data file) with multiple data tables", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- download_d1_data(data_url = "https://cn.dataone.org/cn/v2/resolve/https%3A%2F%2Fpasta.lternet.edu%2Fpackage%2Fdata%2Feml%2Fedi%2F746%2F1%2F2eac05447c1141bc8942284dfb32643c",
                          path = temp_dir)
  files <- list.files(out)

  expect_equal(length(files), 5)
  expect_true(any(stringr::str_detect(files, "attribute_metadata.csv")))
  # expect_true(any(stringr::str_detect(files, "attribute_factor_metadata.csv")))
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  # expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})

# Another EDI test
test_that("test EDI data URL (fully up to date data file, eml v2.2.0) with one data table", {
  # Takes too much time and add load on servers
  skip_if_offline()

  temp_dir <- tempdir()
  out <- download_d1_data(data_url = "https://cn.dataone.org/cn/v2/resolve/https%3A%2F%2Fpasta.lternet.edu%2Fpackage%2Fdata%2Feml%2Fedi%2F858%2F1%2F15ad768241d2eeed9f0ba159c2ab8fd5",
                          path = temp_dir)
  files <- list.files(out)

  expect_equal(length(files), 6)
  expect_true(any(stringr::str_detect(files, "attribute_metadata.csv")))
  expect_true(any(stringr::str_detect(files, "full_metadata.xml")))
  expect_true(any(stringr::str_detect(files, "summary_metadata.csv")))

  folder_name <- stringr::str_extract(out, "[^/]*$")
  # expect_true(stringr::str_detect(folder_name, "^doi")) #starts with doi

  # remove files
  unlink(temp_dir, recursive = TRUE)
})