Last updated: 23-Sep-2019
diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R
index 3becb18c..8e646623 100644
--- a/tests/testthat/test-mo.R
+++ b/tests/testthat/test-mo.R
@@ -24,15 +24,15 @@ context("mo.R")
test_that("as.mo works", {
clear_mo_history(force = TRUE)
-
+
library(dplyr)
MOs <- AMR::microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
-
+
expect_identical(
as.character(as.mo(c("E. coli", "H. influenzae"))),
c("B_ESCHR_COLI", "B_HMPHL_INFL"))
-
+
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(22242416)), "B_ESCHR_COLI")
@@ -53,14 +53,14 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
expect_equal(as.character(suppressWarnings(as.mo("B_STRPTC"))), "B_STRPT") # old MO code (<=v0.5.0)
expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
-
+
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRPA", "B_STRPT_GRPB"))
-
+
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
-
+
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
-
+
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_ARGN")
@@ -68,7 +68,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
-
+
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
@@ -76,9 +76,9 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
-
+
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
-
+
# prevalent MO
expect_identical(
suppressWarnings(as.character(
@@ -104,15 +104,15 @@ test_that("as.mo works", {
"B nodosa",
"Burkholderia nodosa"))),
rep("B_BRKHL_NODS", 4))
-
+
# empty values
expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
# too few characters
expect_warning(as.mo("ab"))
-
- expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRS", "K. pneu rhino", "esco")))),
+
+ expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))),
c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
-
+
# check for Becker classification
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
@@ -125,7 +125,7 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
-
+
# check for Lancefield classification
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
@@ -145,9 +145,9 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
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
-
+
library(dplyr)
-
+
# select with one column
expect_identical(
example_isolates[1:10,] %>%
@@ -157,7 +157,7 @@ test_that("as.mo works", {
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,] %>%
@@ -166,28 +166,28 @@ test_that("as.mo works", {
left_join_microorganisms() %>%
select(genus, species) %>%
as.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"))),
1)
-
+
# check empty values
expect_equal(as.character(suppressWarnings(as.mo(""))),
NA_character_)
-
+
# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
@@ -197,11 +197,11 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
-
+
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
print(mo_renamed())
-
+
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
@@ -209,7 +209,7 @@ test_that("as.mo works", {
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
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_AURS")
-
+
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
@@ -219,21 +219,16 @@ test_that("as.mo works", {
c("B_ESCHR_COLI", "B_ESCHR_COLI"))
expect_warning(as.mo("TestingOwnID", reference_df = NULL))
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
-
+
# combination of existing mo and other code
- expect_identical(suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
+ expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COLI", "B_ESCHR_COLI"))
-
- # expect_equal(mo_fullname(c("E. spp.",
- # "E. spp",
- # "E. species")),
- # rep("Escherichia species", 3))
-
+
# from different sources
expect_equal(as.character(as.mo(
c("PRTMIR", "bclcer", "B_ESCHR_COLI"))),
c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI"))
-
+
# hard to find
expect_equal(as.character(suppressWarnings(as.mo(
c("Microbacterium paraoxidans",
@@ -241,43 +236,43 @@ test_that("as.mo works", {
"Raoultella (here some text) terrigena")))),
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG"))
expect_output(print(mo_uncertainties()))
-
+
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressWarnings(as.mo("Salmonella Goettingen"))),
"B_SLMNL_ENTR")
expect_equal(as.character(as.mo("Salmonella Group A")), "B_SLMNL")
-
+
# no virusses
expect_equal(as.character(as.mo("Virus")), NA_character_)
-
+
# summary
expect_equal(length(summary(example_isolates$mo)), 6)
-
+
# WHONET codes and NA/NaN
expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
rep(NA_character_, 3))
expect_equal(as.character(as.mo("con")), "UNKNOWN")
expect_equal(as.character(as.mo("xxx")), NA_character_)
expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI"))
- expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
+ expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
rep("UNKNOWN", 3))
-
+
expect_null(mo_failures())
expect_true(example_isolates %>% 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))
-
+
# very old MO codes (<= v0.5.0)
expect_equal(suppressWarnings(as.character(as.mo("F_CCCCS_NEO"))), "F_CRYPT_NFRM")
expect_equal(suppressWarnings(as.character(as.mo("F_CANDD_GLB"))), "F_CANDD_GLBR")
# debug mode
expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
-
+
# ..coccus
expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN"))
diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R
index 777f922a..4682b157 100644
--- a/tests/testthat/test-mo_property.R
+++ b/tests/testthat/test-mo_property.R
@@ -90,7 +90,9 @@ test_that("mo_property works", {
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
-
+ # old codes must throw a warning in mo_* family
+ expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
+
# outcome of mo_fullname must always return the fullname from the data set
library(dplyr)
x <- microorganisms %>%