AMR/tests/testthat/test-mo_property.R

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# 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("Escherichia coli"), "Bacteria")
  expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
  expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
  expect_equal(mo_order("Escherichia coli"), "Enterobacteriales")
  expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
  expect_equal(mo_genus("Escherichia coli"), "Escherichia")
  expect_equal(mo_species("Escherichia coli"), "coli")
  expect_equal(mo_subspecies("Escherichia coli"), "")
  expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
  expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
  expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
  expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
  expect_equal(class(mo_taxonomy("Escherichia coli")), "list")
  expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
                                                "family", "genus", "species", "subspecies"))
  expect_equal(mo_synonyms("Escherichia coli"), NULL)
  expect_gt(length(mo_synonyms("Candida albicans")), 1)
  expect_equal(class(mo_synonyms(c("Candida albicans", "Escherichia coli"))), "list")
  expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
                                            "family", "genus", "species", "subspecies",
                                            "synonyms", "url", "ref"))
  expect_equal(class(mo_info(c("Escherichia coli", "Staphylococcus aureus"))), "list")

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

  expect_equal(mo_shortname("Escherichia coli"), "E. coli")
  expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
  expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
  expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
  expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
  expect_equal(mo_shortname("Streptococcus agalactiae", 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("Escherichia coli", language = "de"), "Bakterien")
  expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")

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

  expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))

  # manual property function
  expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
  expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
  expect_identical(mo_property("Escherichia coli", property = "fullname"),
                   mo_fullname("Escherichia coli"))
  expect_identical(mo_property("Escherichia coli", property = "genus"),
                   mo_genus("Escherichia coli"))
  expect_identical(mo_property("Escherichia coli", property = "species"),
                   mo_species("Escherichia 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)
  x <- 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(x), 0)

})