(v1.4.0.9036) more unit tests

tests/testthat/test-eucast_rules.R

@@ -116,6 +116,6 @@ test_that("EUCAST rules work", {
   expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
   
   # check verbose output
-  expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, info = TRUE)))
+  expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
   
 })

tests/testthat/test-mo.R

@@ -57,8 +57,10 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
   expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
   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("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
   
-  expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRPA", "B_STRPT_GRPB"))
+  expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
+
   
   expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
   
@@ -110,7 +112,8 @@ test_that("as.mo works", {
     rep("B_PRBRK_NODS", 4))
   
   # empty values
-  expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
+  expect_identical(as.character(as.mo(c("", "  ", NA, NaN))), rep(NA_character_, 4))
+  expect_identical(as.character(as.mo("  ")), NA_character_)
   # too few characters
   expect_warning(as.mo("ab"))
   
@@ -203,6 +206,7 @@ test_that("as.mo works", {
   # check old names
   expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
   print(mo_renamed())
+  expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
   
   # check uncertain names
   expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
@@ -210,7 +214,7 @@ test_that("as.mo works", {
   expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
   expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
   expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
-  expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS_ANRB")
+  expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB"))
   
   # predefined reference_df
   expect_equal(as.character(as.mo("TestingOwnID",
@@ -238,6 +242,9 @@ 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()))
+  x <- as.mo("S. aur")
+  # many hits
+  expect_output(print(mo_uncertainties()))
 
   # Salmonella (City) are all actually Salmonella enterica spp (City)
   expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
@@ -285,4 +292,11 @@ test_that("as.mo works", {
   expect_warning(x[[1]] <- "invalid code")
   expect_warning(c(x[1], "test"))
   
+  # ignoring patterns
+  
+  # frequency tables
+  if (require("cleaner")) {
+    expect_s3_class(cleaner::freq(example_isolates$mo), "freq")
+  }
+  
 })

tests/testthat/test-mo_property.R

@@ -122,6 +122,10 @@ test_that("mo_property works", {
                                          "vanco"),
                c(TRUE, FALSE, FALSE))
   
+  # with reference data
+  expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")), 
+               "Escherichia coli")
+  
   library(dplyr)
   expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
                730)