more unit tests

R/mo.R

@@ -182,7 +182,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
   # defined df to check for
   if (!is.null(reference_df)) {
     if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
-      stop('`reference_df` must be a data.frame with at least two columns.')
+      stop('`reference_df` must be a data.frame with at least two columns.', call. = FALSE)
     }
     # remove factors, just keep characters
     suppressWarnings(

R/mo_property.R

@@ -231,16 +231,7 @@ mo_property <- function(x, property = 'fullname', language = NULL, ...) {
     stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
   }
 
-  # this will give a warning if x cannot be coerced
+  mo_translate(mo_validate(x = x, property = property, ...), language = language)
-  res <- exec_as.mo(x = x, Becker = Becker, Lancefield = Lancefield, property = property)
-
-  if (property != "tsn") {
-    res[x %in% c("", NA) | res %in% c("", NA, "(no MO)")] <- ""
-    if (property %in% c("fullname", "shortname", "genus", "species", "subspecies", "type", "gramstain")) {
-      res <- mo_translate(res, language = language)
-    }
-  }
-  res
 }
 
 #' @rdname mo_property

tests/testthat/test-mo.R

@@ -165,7 +165,15 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
                                   reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))),
                c("B_ESCHR_COL", "B_ESCHR_COL"))
-  expect_warning(as.character(as.mo("TestingOwnID",
+  expect_warning(as.mo("TestingOwnID", reference_df = NULL))
-                                  reference_df = NULL)))
+  expect_error(as.mo("E. coli", reference_df = data.frame(a = "TestingOwnID")))
+
+  # combination of existing mo and certe
+  expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
+                   c("B_ESCHR_COL", "B_ESCHR_COL"))
+
+  # TSN of prevalent and non prevalent ones
+  expect_equal(mo_TSN(c("Gomphosphaeria aponina delicatula", "Escherichia coli")),
+                   c(717, 285))
 
 })

tests/testthat/test-mo_property.R

@@ -12,6 +12,7 @@ test_that("mo_property works", {
   expect_equal(mo_fullname("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(mo_TSN("E. coli"), 285)
   expect_equal(class(mo_taxonomy("E. coli")), "list")
   expect_equal(names(mo_taxonomy("E. coli")), c("subkingdom", "phylum", "class", "order",
                                                 "family", "genus", "species", "subspecies"))
@@ -42,4 +43,14 @@ test_that("mo_property works", {
 
   expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))
 
+  # manual property function
+  expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
+  expect_error(mo_property("E. coli", property = "UNKNOWN"))
+  expect_identical(mo_property("E. coli", property = "fullname"),
+                   mo_fullname("E. coli"))
+  expect_identical(mo_property("E. coli", property = "genus"),
+                   mo_genus("E. coli"))
+  expect_identical(mo_property("E. coli", property = "species"),
+                   mo_species("E. coli"))
+
 })