library(taxa)
library(testthat)
context("taxon_rank")
test_that("taxa_rank - just rank", {
aa <- taxon_rank("species")
expect_is(aa, "TaxonRank")
expect_null(aa$database)
expect_type(aa$name, "character")
expect_output(print(aa$print()), "<TaxonRank>")
})
test_that("taxa_rank - name and database (TaxonRank)", {
aa <- taxon_rank("species", database_list$ncbi)
expect_is(aa, "TaxonRank")
expect_is(aa$database, "TaxonDatabase")
expect_equal(aa$database$name, "ncbi")
expect_equal(aa$database$url, "http://www.ncbi.nlm.nih.gov/taxonomy")
expect_type(aa$name, "character")
})
test_that("taxa_rank - name and database (character)", {
aa <- taxon_rank("genus", "ncbi")
expect_is(aa, "TaxonRank")
expect_is(aa$database, "TaxonDatabase")
expect_equal(aa$database$name, "ncbi")
expect_null(aa$database$url)
expect_type(aa$name, "character")
# S3 constructor passes by value
db <- taxon_database("1")
x <- taxon_rank("species", db)
db$name <- "2"
expect_equal(x$database$name, "1")
x$database$name <- "3"
expect_equal(db$name, "2")
# R6 constructor passes by reference
db <- taxon_database("1")
x <- TaxonRank$new("species", db)
db$name <- "2"
expect_equal(x$database$name, "2")
expect_identical(x$database, db)
x$database$name <- "3"
expect_equal(db$name, "3")
})
test_that("taxon_rank fails well", {
expect_error(taxon_rank(),
"argument \"name\" is missing")
expect_error(taxon_rank(mtcars),
"must be a class that is or inherits one of the following classes")
expect_error(taxon_rank("adf", 5),
"must be a class that is or inherits one of the following classes")
})
test_that("taxon_rank can do null data", {
# empty taxon_rank() tested in above block
x <- taxon_rank(NULL)
expect_is(x, "TaxonRank")
expect_null(x$name)
expect_null(x$database)
})
test_that("taxon_rank: name getters and setters", {
# Can set the name with a character
x <- taxon_rank(name = "species", database = database_list$ncbi)
x$name <- "genus"
expect_equal(x$name, "genus")
# Can set the name with a factor
x <- taxon_rank(name = "species", database = database_list$ncbi)
x$name <- as.factor("genus")
expect_equal(x$name, "genus")
# Can coerce to character
x <- taxon_rank(name = "species", database = database_list$ncbi)
expect_equal(as.character(x), "species")
# Error when given odd input
x <- taxon_rank(name = "species", database = database_list$ncbi)
expect_error(x$name <- TRUE,
"must be a class that is or inherits one of the following classes")
expect_error(x$name <- mtcars,
"must be a class that is or inherits one of the following classes")
})
test_that("taxon_rank: database getters and setters", {
# Can set the database with a character
x <- taxon_rank(name = "species", database = database_list$ncbi)
x$database <- "new database"
expect_equal(x$database, taxon_database("new database"))
# Can set the database with a database object
x <- taxon_rank(name = "species", database = database_list$ncbi)
database_obj <- taxon_database("new database")
x$database <- database_obj
expect_identical(x$database, database_obj) # "expect_identical" since R6 setters pass by reference
# Error when given odd input
x <- taxon_rank(name = "species", database = database_list$ncbi)
expect_error(x$database <- 1,
"must be a class that is or inherits one of the following classes")
expect_error(x$database <- mtcars,
"must be a class that is or inherits one of the following classes")
})
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