AMR/tests/testthat/test-mo_property.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
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# https://gitlab.com/msberends/AMR                                     #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
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context("mo_property.R")

test_that("mo_property works", {
  expect_equal(mo_kingdom("E. coli"), "Bacteria")
  expect_equal(mo_phylum("E. coli"), "Proteobacteria")
  expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
  expect_equal(mo_order("E. coli"), "Enterobacteriales")
  expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
  expect_equal(mo_genus("E. coli"), "Escherichia")
  expect_equal(mo_species("E. coli"), "coli")
  expect_equal(mo_subspecies("E. coli"), "")
  expect_equal(mo_fullname("E. coli"), "Escherichia coli")
  expect_equal(mo_name("E. coli"), "Escherichia coli")
  expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
  expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
  expect_equal(class(mo_taxonomy("E. coli")), "list")
  expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
                                                "family", "genus", "species", "subspecies"))

  expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
  expect_equal(mo_authors("E. coli"), "Castellani et al.")
  expect_equal(mo_year("E. coli"), 1919)

  expect_equal(mo_shortname("MRSA"), "S. aureus")
  expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
  expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
  expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
  expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")

  expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")

  # test integrity
  MOs <- AMR::microorganisms
  expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))

  # check languages
  expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
  expect_equal(mo_gramstain("E. coli", language = "nl"), "Gram-negatief")

  expect_output(print(mo_gramstain("E. coli", language = "en")))
  expect_output(print(mo_gramstain("E. coli", language = "de")))
  expect_output(print(mo_gramstain("E. coli", language = "nl")))
  expect_output(print(mo_gramstain("E. coli", language = "es")))
  expect_output(print(mo_gramstain("E. coli", language = "pt")))
  expect_output(print(mo_gramstain("E. coli", language = "it")))
  expect_output(print(mo_gramstain("E. coli", language = "fr")))

  expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))

  # manual property function
  expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
  expect_error(mo_property("E. coli", property = "UNKNOWN"))
  expect_identical(mo_property("E. coli", property = "fullname"),
                   mo_fullname("E. coli"))
  expect_identical(mo_property("E. coli", property = "genus"),
                   mo_genus("E. coli"))
  expect_identical(mo_property("E. coli", property = "species"),
                   mo_species("E. coli"))

  expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
  expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")


  # outcome of mo_fullname must always return the fullname from the data set
  library(dplyr)
  a <- microorganisms %>%
    transmute(mo,
              # fullname from the original data:
              f1 = fullname,
              # newly created fullname based on MO code:
              f2 = mo_fullname(mo, language = "en")) %>%
    filter(f1 != f2)

  expect_equal(nrow(a), 0)

})