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(v1.6.0.9023) new unit test flow

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dr. M.S. (Matthijs) Berends
2021-05-13 19:31:47 +02:00
parent 655b813e99
commit aeea00881e
34 changed files with 408 additions and 355 deletions
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61
tests/testthat/test-mo.R
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@ -28,10 +28,8 @@ context("mo.R")
test_that("as.mo works", {
skip_on_cran()
library(dplyr, warn.conflicts = FALSE)
MOs <- microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
expect_identical(
@ -152,37 +150,43 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
# select with one column
expect_identical(
example_isolates[1:10, ] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
as.character(),
c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
"B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"))
# select with two columns
expect_identical(
example_isolates[1:10, ] %>%
pull(mo),
example_isolates[1:10, ] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo())
if (require("dplyr")) {
# select with one column
expect_identical(
example_isolates[1:10, ] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
as.character(),
c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
"B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"))
# select with two columns
expect_identical(
example_isolates[1:10, ] %>%
pull(mo),
example_isolates[1:10, ] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo())
# too many columns
expect_error(example_isolates %>% select(1:3) %>% as.mo())
# test pull
expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
2000)
expect_true(example_isolates %>% pull(mo) %>% is.mo())
}
# unknown results
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
# too many columns
expect_error(example_isolates %>% select(1:3) %>% as.mo())
# print
expect_output(print(as.mo(c("B_ESCHR_COLI", NA))))
# test pull
expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
2000)
# test data.frame
expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
@ -265,7 +269,6 @@ test_that("as.mo works", {
rep("UNKNOWN", 3))
expect_null(mo_failures())
expect_true(example_isolates %>% pull(mo) %>% is.mo())
expect_error(translate_allow_uncertain(5))