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(v0.7.0.9010) mo_synonyms, plot/barplot fixes
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@ -22,34 +22,37 @@
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context("mo_property.R")
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test_that("mo_property works", {
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expect_equal(mo_kingdom("E. coli"), "Bacteria")
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expect_equal(mo_phylum("E. coli"), "Proteobacteria")
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expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
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expect_equal(mo_order("E. coli"), "Enterobacteriales")
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expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
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expect_equal(mo_genus("E. coli"), "Escherichia")
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expect_equal(mo_species("E. coli"), "coli")
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expect_equal(mo_subspecies("E. coli"), "")
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expect_equal(mo_fullname("E. coli"), "Escherichia coli")
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expect_equal(mo_name("E. coli"), "Escherichia coli")
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expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
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expect_equal(mo_gramstain("E. coli", language = "en"), "Gram-negative")
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expect_equal(class(mo_taxonomy("E. coli")), "list")
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expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
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expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
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expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
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expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
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expect_equal(mo_order("Escherichia coli"), "Enterobacteriales")
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expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
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expect_equal(mo_genus("Escherichia coli"), "Escherichia")
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expect_equal(mo_species("Escherichia coli"), "coli")
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expect_equal(mo_subspecies("Escherichia coli"), "")
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expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
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expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
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expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
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expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
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expect_equal(class(mo_taxonomy("Escherichia coli")), "list")
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expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies"))
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expect_equal(names(mo_info("E. coli")), c("kingdom", "phylum", "class", "order",
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expect_equal(mo_synonyms("Escherichia coli"), NULL)
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expect_gt(length(mo_synonyms("C. albicans")), 1)
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expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies",
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"url", "ref"))
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"synonyms", "url", "ref"))
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expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
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expect_equal(mo_authors("E. coli"), "Castellani et al.")
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expect_equal(mo_year("E. coli"), 1919)
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expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
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expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
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expect_equal(mo_year("Escherichia coli"), 1919)
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expect_equal(mo_shortname("MRSA"), "S. aureus")
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expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
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expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
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expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
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expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
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expect_equal(mo_shortname("Escherichia coli"), "E. coli")
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expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
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expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
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expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
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expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
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expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
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expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
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@ -58,28 +61,28 @@ test_that("mo_property works", {
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expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
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# check languages
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expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
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expect_equal(mo_gramstain("E. coli", language = "nl"), "Gram-negatief")
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expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
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expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
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expect_output(print(mo_gramstain("E. coli", language = "en")))
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expect_output(print(mo_gramstain("E. coli", language = "de")))
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expect_output(print(mo_gramstain("E. coli", language = "nl")))
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expect_output(print(mo_gramstain("E. coli", language = "es")))
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expect_output(print(mo_gramstain("E. coli", language = "pt")))
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expect_output(print(mo_gramstain("E. coli", language = "it")))
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expect_output(print(mo_gramstain("E. coli", language = "fr")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "en")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "de")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "nl")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "es")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "pt")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "it")))
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expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
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expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))
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expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
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# manual property function
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expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
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expect_error(mo_property("E. coli", property = "UNKNOWN"))
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expect_identical(mo_property("E. coli", property = "fullname"),
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mo_fullname("E. coli"))
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expect_identical(mo_property("E. coli", property = "genus"),
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mo_genus("E. coli"))
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expect_identical(mo_property("E. coli", property = "species"),
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mo_species("E. coli"))
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expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
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expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
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expect_identical(mo_property("Escherichia coli", property = "fullname"),
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mo_fullname("Escherichia coli"))
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expect_identical(mo_property("Escherichia coli", property = "genus"),
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mo_genus("Escherichia coli"))
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expect_identical(mo_property("Escherichia coli", property = "species"),
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mo_species("Escherichia coli"))
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expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
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expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
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@ -87,14 +90,13 @@ test_that("mo_property works", {
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# outcome of mo_fullname must always return the fullname from the data set
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library(dplyr)
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a <- microorganisms %>%
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x <- microorganisms %>%
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transmute(mo,
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# fullname from the original data:
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f1 = fullname,
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# newly created fullname based on MO code:
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f2 = mo_fullname(mo, language = "en")) %>%
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filter(f1 != f2)
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expect_equal(nrow(a), 0)
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expect_equal(nrow(x), 0)
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})
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