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(v1.7.1.9012) update unit tests

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dr. M.S. (Matthijs) Berends
2021-07-04 20:25:30 +02:00
parent 5b5741f681
commit 350dbe6a11
15 changed files with 34 additions and 31 deletions
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33
inst/tinytest/test-mo_property.R
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@ -28,12 +28,23 @@ expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
expect_equal(mo_genus("Escherichia coli"), "Escherichia")
# S3 class for taxonomic names
expect_inherits(mo_family("Escherichia coli"), "taxonomic_name")
expect_equal(as.character(mo_family("Escherichia coli")), "Enterobacteriaceae")
expect_equal(as.character(mo_fullname("Escherichia coli")), "Escherichia coli")
expect_equal(as.character(mo_genus("Escherichia coli")), "Escherichia")
expect_equal(as.character(mo_name("Escherichia coli")), "Escherichia coli")
expect_equal(as.character(mo_shortname("Escherichia coli")), "E. coli")
expect_equal(as.character(mo_shortname("Escherichia")), "Escherichia")
expect_equal(as.character(mo_shortname("Staphylococcus aureus")), "S. aureus")
expect_equal(as.character(mo_shortname("Staphylococcus aureus", Becker = TRUE)), "S. aureus")
expect_equal(as.character(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en")), "CoPS")
expect_equal(as.character(mo_shortname("Streptococcus agalactiae")), "S. agalactiae")
expect_equal(as.character(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE)), "GBS")
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_inherits(mo_taxonomy("Escherichia coli"), "list")
@ -52,20 +63,12 @@ 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("Escherichia"), "Escherichia")
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("Candida albicans") %like% "catalogueoflife.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity
MOs <- microorganisms
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
expect_identical(MOs$fullname, as.character(mo_fullname(MOs$fullname, language = "en")))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
@ -81,7 +84,7 @@ expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
expect_identical(as.character(mo_name(dutch, language = NULL)), microorganisms$fullname) # gigantic test - will run ALL names
# manual property function
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
@ -117,7 +120,7 @@ expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aur
"vanco"),
c(TRUE, FALSE, FALSE))
# with reference data
expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
expect_equal(as.character(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI"))),
"Escherichia coli")
if (AMR:::pkg_is_available("dplyr")) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),