# LIBS
library(phylotaR)
library(testthat)
# DATA
raw_recs <- readRDS(phylotaR:::datadir_get("raw_txrecs.rda"))
wd <- tempdir()
ps <- parameters(wd = wd)
# RUNNING
context("Testing 'stage1-tools'")
phylotaR:::cleanup(wd)
test_that("tax_download() works", {
example_res <- raw_recs[[sample(seq_along(raw_recs), 1)]]
ids <- unname(vapply(
X = XML::xmlToList(example_res), FUN = "[[",
FUN.VALUE = character(1), "TaxId"
))
res <- with_mock(
`phylotaR:::search_and_cache` = function(...) example_res,
phylotaR:::tax_download(ids = ids, ps = ps)
)
res <- vapply(
X = res, FUN = function(x) inherits(x, "TaxRec"),
FUN.VALUE = logical(1)
)
expect_true(all(res))
})
phylotaR:::cleanup(wd)
# # Example raw_txrecs ----
# search_obj <- rentrez::entrez_search(db = 'taxonomy', retmax = 0,
# term = 'txid2759[Subtree]',
# use_history = TRUE)
# # random 100 taxrecords
# retmaxes <- round(runif(n = 10, min = 1,
# max = search_obj[['count']]))
# raw_recs <- NULL
# for (i in retmaxes) {
# whobj <- search_obj[['web_history']]
# raw_rec <- rentrez::entrez_fetch(db = 'taxonomy',
# retstart = i, rettype = 'xml',
# web_history = whobj,
# retmax = sample(1:4, 1))
# raw_recs <- c(raw_recs, raw_rec)
# }
# otfl <- phylotaR:::datadir_get('raw_txrecs.rda')
# saveRDS(object = raw_recs, file = otfl)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.