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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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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))
})