tests/testthat/test-taxinfo.R

In ALA4R: Atlas of Living Australia (ALA) Data and Resources in R

context("Test taxonomic information functions")

## taxinfo_download
thischeck <- function() {
    test_that("taxinfo_download generally works as expected", {
        skip_on_cran()
        tx <- taxinfo_download("rk_family:SPHENISCIDAE",
                               fields = c("guid", "rk_genus", "scientificName",
                                        "rank"))
        expect_equal(names(tx), c("guid", "genus", "scientificName", "rank"))
        expect_gte(nrow(tx), 10) ## expect at least 10 results here
        ## matching is case-sensitive, so this should return no results
        ala_config(warn_on_empty = TRUE)
        ## expect warning here
        expect_warning(tx <- taxinfo_download("rk_family:spheniscidae",
                                              fields = c("guid", "rk_genus",
                                                       "scientificName",
                                                       "rank")))
        ala_config(warn_on_empty = FALSE)
        tx <- taxinfo_download("rk_family:spheniscidae",
                               fields = c("guid", "rk_genus", "scientificName",
                                        "rank"))
        expect_equal(nrow(tx), 0) ## expect no results here
        ## but names in data.frame should be consistent even when empty
        expect_equal(names(tx), c("guid", "genus", "scientificName", "rank"))

        ## default fields
        expect_true(setequal(names(taxinfo_download("rk_genus:Heleioporus")),
                             c("guid", "rank", "scientificName",
                               "scientificNameAuthorship", "taxonomicStatus",
                               "establishmentMeans", "genus", "family", "order",
                               "class", "phylum", "kingdom", "datasetName",
                               "parentGuid", "acceptedConceptName",
                               "acceptedConceptID", "type", "title")))
    })
}
check_caching(thischeck)

thischeck <- function() {
    test_that("taxinfo_download downloads all fields", {
        skip_on_cran()
        f <- ala_fields("general")
        t <- taxinfo_download("rk_family:Spheniscidae", fields = "all")
        expect_equal(ncol(t), nrow(f))
    })
}
check_caching(thischeck)

thischeck <- function() {
  test_that("taxinfo_download uses fq as expected", {
    skip_on_cran()
    tx <- taxinfo_download("rk_family:Fabaceae",
                           fq = "taxonomicStatus:accepted",
                           fields = "all")
    f <- ala_fields("general")
    expect_equal(ncol(tx), nrow(f))
    expect_equal(unique(tx$taxonomicStatus), "accepted")
  })
}
check_caching(thischeck)

thischeck <- function() {
  test_that("taxinfo_download handles query as expected", {
    skip_on_cran()
    tx <- taxinfo_download(factor("rk_family:Fabaceae"),
                           fields = "all")
    f <- ala_fields("general")
    expect_equal(ncol(tx), nrow(f))
    expect_error(taxinfo_download(fields = "all"))
  })
}
check_caching(thischeck)

thischeck <- function() {
  test_that("taxinfo_download handles fields as expected", {
    skip_on_cran()
    expect_error(taxinfo_download("rk_family:Fabaceae", fields = "bad-field"))
  })
}
check_caching(thischeck)