library(taxa)
library(testthat)
context("taxon_id")
test_that("taxa_id - just ID", {
aa <- taxon_id(93036)
expect_is(aa, "TaxonId")
expect_null(aa$database)
expect_type(aa$id, "character")
expect_output(aa$print())
})
test_that("taxa_id - ID and database (TaxonDatabase)", {
aa <- taxon_id(93036, database_list$ncbi)
expect_is(aa, "TaxonId")
expect_is(aa$database, "TaxonDatabase")
expect_equal(aa$database$name, "ncbi")
expect_equal(aa$database$url, "http://www.ncbi.nlm.nih.gov/taxonomy")
expect_type(aa$id, "character")
expect_output(aa$print())
})
test_that("taxa_id - ID and database (character)", {
aa <- taxon_id(93036, "ncbi")
expect_is(aa, "TaxonId")
expect_is(aa$database, "TaxonDatabase")
expect_equal(aa$database$name, "ncbi")
expect_null(aa$database$url)
expect_type(aa$id, "character")
expect_output(aa$print())
# S3 constructor passes by value
db = taxon_database("1")
x = taxon_id(93036, db)
db$name = "2"
expect_equal(x$database$name, "1")
# R6 constructor passes by reference
db = taxon_database("1")
x = TaxonId$new(93036, db)
db$name = "2"
expect_equal(x$database$name, "2")
expect_identical(x$database, db)
# R6 constructor passes by value any non-R6 objects, since they have to
id = "1"
x = TaxonId$new(id, "db")
id = "2"
expect_equal(x$id, "1")
x$id = "3"
expect_equal(id, "2")
})
test_that("taxon_id fails well", {
expect_error(taxon_id(),
"argument \"id\" is missing")
expect_error(taxon_id(mtcars),
"must be a class that is or inherits one of the following classes")
expect_error(taxon_id("adf", 5),
"must be a class that is or inherits one of the following classes")
})
test_that("taxon_id can do null data", {
# empty taxon_id() tested in above block
x <- taxon_id(NULL)
expect_is(x, "TaxonId")
expect_null(x$name)
expect_null(x$database)
})
test_that("taxon_id: id getters and setters", {
# Can set the id with a character
x <- taxon_id(id = "12345", database = database_list$ncbi)
x$id <- "new id"
expect_equal(x$id, "new id")
# Can set the id with a factor
x <- taxon_id(id = "12345", database = database_list$ncbi)
x$id <- as.factor("new id")
expect_equal(x$id, "new id")
# Can coerce to character
x <- taxon_id(id = "12345", database = database_list$ncbi)
expect_equal(as.character(x), "12345")
# Error when given odd input
x <- taxon_id(id = "12345", database = database_list$ncbi)
expect_error(x$id <- TRUE,
"must be a class that is or inherits one of the following classes")
expect_error(x$id <- mtcars,
"must be a class that is or inherits one of the following classes")
# Error when ID does not match database id regex
db1 <- taxon_database(name = "id_regex", id_regex = "^[0-9]+$")
db2 <- taxon_database(name = "no id_regex")
expect_error(taxon_id(id = "aaa", database = db1),
"Taxon IDs must follow the database ID conventions")
expect_silent(taxon_id(id = "aaa", database = db2))
expect_silent(taxon_id(id = "aaa"))
})
test_that("taxon_id: database getters and setters", {
# Can set the database with a character
x <- taxon_id(id = "12345", database = database_list$ncbi)
x$database <- "new database"
expect_equal(x$database, taxon_database("new database"))
# Can set the database with a database object
x <- taxon_id(id = "12345", database = database_list$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_id(id = "12345", 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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