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CI tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-13 12:21:57 +02:00
parent 38a4421450
commit 0dc0715dc6
21 changed files with 137 additions and 68 deletions
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3
tests/testthat/test-eucast_rules.R
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@ -33,6 +33,9 @@ test_that("EUCAST rules work", {
"reference.rule", "reference.rule_group"))
expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text"))
expect_error(eucast_rules(data.frame(a = "test")))
expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(eucast_rules(septic_patients))))

7
tests/testthat/test-misc.R
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@ -42,3 +42,10 @@ test_that("functions missing in older R versions work", {
expect_equal(trimws(" test ", "l"), "test ")
expect_equal(trimws(" test ", "r"), " test")
})
test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
expect_warning(get_column_abx(septic_patients, soft_dependencies = "FUS"))
})

19
tests/testthat/test-mo.R
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@ -200,6 +200,9 @@ test_that("as.mo works", {
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY")
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",
@ -244,4 +247,20 @@ test_that("as.mo works", {
# summary
expect_equal(length(summary(septic_patients$mo)), 6)
# other
expect_equal(as.character(as.mo(c("xxx", "con", "na", "nan"), debug = TRUE)),
rep(NA_character_, 4))
expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
rep("UNKNOWN", 3))
expect_null(mo_failures())
expect_true(septic_patients %>% pull(mo) %>% is.mo())
expect_equal(get_mo_code("test", "mo"), "test")
expect_equal(length(get_mo_code("Escherichia", "genus")),
nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
expect_error(translate_allow_uncertain(5))
})

3
tests/testthat/test-mo_property.R
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@ -31,6 +31,7 @@ test_that("mo_property works", {
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")
@ -47,6 +48,8 @@ test_that("mo_property works", {
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"))