tests/testthat/test-GBIFtableCleanup.R

In hannahlowens/occCite: Querying and Managing Large Biodiversity Occurrence Datasets

context("Testing GBIFtableCleanup")

library(occCite)

test_that("behaves as expected when given a stored GBIF table", {
  skip_on_cran()
  oldwd <- getwd()
  on.exit(setwd(oldwd))

  test <- try(rgbif::occ_count(country = "DK"),
              silent = T
  )
  skip_if(class(test) != "numeric", "GBIF connection unsuccessful")

  setwd(dir = system.file("extdata/", package = "occCite"))
  taxon <- "Protea cynaroides"
  testResult <- occCite:::gbifRetriever(taxon)[[1]]

  expect_equal(class(testResult), "data.frame")
  expect_true("gbifID" %in% colnames(testResult))
  expect_true("name" %in% colnames(testResult))
  expect_true("longitude" %in% colnames(testResult))
  expect_true("latitude" %in% colnames(testResult))
  expect_true("day" %in% colnames(testResult))
  expect_true("month" %in% colnames(testResult))
  expect_true("year" %in% colnames(testResult))
  expect_true("datasetName" %in% colnames(testResult))
  expect_true("datasetKey" %in% colnames(testResult))
  expect_true("dataService" %in% colnames(testResult))

  testResult1 <- occCite:::GBIFtableCleanup(testResult)
  expect_equal(class(testResult1$name), "factor")
  expect_equal(class(testResult1$longitude), "numeric")
  expect_equal(class(testResult1$latitude), "numeric")
  expect_equal(class(testResult1$coordinateUncertaintyInMeters), "numeric")
  expect_equal(class(testResult1$day), "integer")
  expect_equal(class(testResult1$month), "integer")
  expect_equal(class(testResult1$year), "integer")
  expect_equal(class(testResult1$datasetName), "factor")
  expect_equal(class(testResult1$datasetKey), "factor")
  expect_equal(class(testResult1$dataService), "factor")
})

test_that("behaves as expected when given an empty GBIF table", {
  test <- occCite:::GBIFtableCleanup(NULL)
  expect_equal(nrow(test), 1)
  expect_equal(ncol(test), 10)
  expect_true(all(is.na(test)))

  test <- occCite:::GBIFtableCleanup(NA)
  expect_equal(nrow(test), 1)
  expect_equal(ncol(test), 10)
  expect_true(all(is.na(test)))

  test <- occCite:::GBIFtableCleanup(data.frame())
  expect_equal(nrow(test), 1)
  expect_equal(ncol(test), 10)
  expect_true(all(is.na(test)))
})