tests/testthat/test-phylomatic.R

In ropensci/brranching: Fetch 'Phylogenies' from Many Sources

# context("phylomatic")
#
# taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
#
# test_that("phylomatic - GET (default) method works", {
#   skip_on_cran()
#
#   tree <- phylomatic(taxa = taxa)
#
#   expect_is(taxa, "character")
#   expect_is(tree, "phylo")
#   expect_is(tree, "phylomatic")
# })
#
#
# test_that("phylomatic - POST method works", {
#   skip_on_cran()
#
#   tree <- phylomatic(taxa = taxa, get = 'POST')
#
# 	expect_is(tree, "phylo")
# 	expect_is(tree, "phylomatic")
# })
#
# test_that("phylomatic - stored tree", {
#   skip_on_cran()
#
#   tree <- phylomatic(taxa, storedtree = 'smith2011')
#
#   expect_is(tree, "phylo")
#   expect_is(tree, "phylomatic")
# })
#
# test_that("phylomatic - nexml output format", {
#   skip_on_cran()
#
#   out <- phylomatic(taxa, outformat = "nexml")
#
#   expect_is(out, "phylomatic")
#   expect_is(out[1], "character")
#   expect_true(grepl("nexml", out))
# })
#
# # FIXME: dryad url is broken, can't find new url
# # test_that("phylomatic - treeuri param", {
# #   skip_on_cran()
#
# #   spp <- c("Abies_nordmanniana", "Abies_bornmuelleriana", "Abies_cilicica", "Abies_cephalonica",
# #     "Abies_numidica", "Abies_pinsapo", "Abies_alba")
# #   url <- "http://datadryad.org/bitstream/handle/10255/dryad.8791/final_tree.tre?sequence=1"
# #   tree <- phylomatic(taxa = spp, treeuri = url)
#
# #   expect_is(tree, "phylo")
# #   expect_is(tree, "phylomatic")
# #   expect_equal(tree$tip.label, spp)
# # })
#
#
# test_that("phylomatic fails as expected", {
#   skip_on_cran()
# 
#   # fails when no taxa given
# 	expect_error(phylomatic(), "argument \"taxa\" is missing")
#
# 	# fails when no taxnames FALSE and improper name strings passed
# 	expect_error(phylomatic(taxa, taxnames = FALSE), "No taxa in common")
#
# 	# fails when get isn't in allowed set
# 	expect_error(phylomatic(taxa, get = "STUFF"), "get must be one of 'POST' or 'GET'")
#
# 	# fails when too many taxa passed and get='GET'
# 	library("taxize")
# 	spp <- taxize::names_list("species", 200)
# 	expect_error(phylomatic(spp, get = "GET"), "\\(414\\) Request-URI Too Long")
# })