tests/testthat/test-tools-api.R

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

# LIBS
library(testthat)

# DATA
# error examples
failed_search_1 <- "Error in entrez_check(..."
failed_search_2 <- '<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n<!DOCTYPE eEfetchResult PUBLIC \"-//NLM//DTD efetch 20131226//EN\" \"https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20131226/efetch.dtd\">"\n<eFetchResult>"\n\t<ERROR>Unable to obtain query #1</ERROR>"\n</eFetchResult>"'
req <- list("x" = "An error occurred")
req$status_code <- 414
failed_search_3 <- try(rentrez:::entrez_check(req = req), silent = TRUE)
req$status_code <- 502
failed_search_4 <- try(rentrez:::entrez_check(req = req), silent = TRUE)

load(file.path(phylotaR:::datadir_get(subdir = "api"), "xml_timeout.rda"))
# real example: search tax
flpth <- file.path(
  phylotaR:::datadir_get(subdir = "api"),
  "entrez_search_tax.rda"
)
# trm <- 'txid10151[Subtree]'
# entrez_search_tax <- rentrez::entrez_search(db = 'taxonomy', retmax = 10,
#                                             term = trm)
# save(entrez_search_tax, file = flpth)
load(flpth)
# real example: search sids
flpth <- file.path(
  phylotaR:::datadir_get(subdir = "api"),
  "entrez_search_sid.rda"
)
# trm <- searchterm_gen(txid = '10151', ps = parameters(), direct = FALSE)
# entrez_search_sid <- rentrez::entrez_search(db = 'nucleotide', retmax = 0,
#                                             term = trm)
# save(entrez_search_sid, file = flpth)
load(flpth)
# real example: fetch sids
flpth <- file.path(
  phylotaR:::datadir_get(subdir = "api"),
  "entrez_fetch_sid.rda"
)
# trm <- phylotaR:::searchterm_gen(txid = '10151', ps = parameters(),
#                                  direct = FALSE)
# srch <- rentrez::entrez_search(db = 'nucleotide', retmax = 0, term = trm,
#                                use_history = TRUE)
# entrez_fetch_sid <- rentrez::entrez_fetch(db = 'nucleotide',
#                                           web_history = srch[['web_history']],
#                                           retmax = 1000L, rettype = 'acc',
#                                           retstart = 0L)
# save(entrez_fetch_sid, file = flpth)
load(flpth)
# real example: fetch seqs
flpth <- file.path(
  phylotaR:::datadir_get(subdir = "api"),
  "entrez_fetch_seqs.rda"
)
# ids <- sample(strsplit(entrez_fetch_sid, '\n')[[1]], 100)
# entrez_fetch_seqs <- rentrez::entrez_fetch(db = 'nucleotide', id = ids,
#                                            rettype = 'gb', retmode = 'text')
# save(entrez_fetch_seqs, file = flpth)
load(flpth)
wd <- tempdir()
ps <- parameters(wd = wd)
ps[["mxrtry"]] <- 2
ps[["wt_tms"]] <- c(0, 0)

# RUNNING
phylotaR:::cleanup(wd)
context("Testing 'tools-api'")
test_that("download_obj_check() works", {
  expect_true(phylotaR:::download_obj_check(entrez_search_tax))
  expect_true(phylotaR:::download_obj_check(entrez_search_sid))
  expect_true(phylotaR:::download_obj_check(entrez_fetch_sid))
  expect_true(phylotaR:::download_obj_check(entrez_fetch_seqs))
  expect_false(phylotaR:::download_obj_check(xml_tmout))
  expect_false(phylotaR:::download_obj_check(failed_search_1))
  expect_false(phylotaR:::download_obj_check(failed_search_2))
  expect_false(phylotaR:::download_obj_check(failed_search_3))
  expect_false(phylotaR:::download_obj_check(as.character(failed_search_3)))
  expect_false(phylotaR:::download_obj_check(failed_search_4))
  expect_false(phylotaR:::download_obj_check(as.character(failed_search_4)))
})
test_that("safely_connect(fnm = search) works", {
  phylotaR:::cache_setup(ps = ps)
  args <- list("term" = "ncbi search term", "db" = "nucleotide", "x")
  myfunc <- function(...) {
    print(...)
    return("NCBI record")
  }
  res <- phylotaR:::safely_connect(
    func = myfunc, args = args, fnm = "search",
    ps = ps
  )
  expect_true(res == "NCBI record")
  myfunc <- function(...) {
    print(...)
    stop()
  }
  args <- list("term" = "another ncbi search term", "db" = "nucleotide", "x")
  res <- phylotaR:::safely_connect(
    func = myfunc, args = args, fnm = "search",
    ps = ps
  )
  expect_null(res)
})
phylotaR:::cleanup(wd)
test_that("safely_connect(fnm = fetch) works", {
  phylotaR:::cache_setup(ps = ps)
  args <- list("id" = c(1, 2), "db" = "nucleotide", "x")
  myfunc <- function(...) {
    print(...)
    return("NCBI record")
  }
  res <- phylotaR:::safely_connect(
    func = myfunc, args = args, fnm = "fetch",
    ps = ps
  )
  expect_true(res == "NCBI record")
  myfunc <- function(...) {
    print(...)
    stop()
  }
  args <- list("id" = c(2, 3), "db" = "nucleotide", "x")
  res <- phylotaR:::safely_connect(
    func = myfunc, args = args, fnm = "fetch",
    ps = ps
  )
  expect_null(res)
})
phylotaR:::cleanup(wd)
test_that("batcher() works", {
  phylotaR:::cache_setup(ps = ps)
  res <- phylotaR:::batcher(ids = 1:10, func = function(ids, ps) {
    return(ids)
  }, ps, lvl = 1)
  expect_true(all(res == 1:10))
  res <- phylotaR:::batcher(ids = 1:1000, func = function(ids, ps) {
    return(ids)
  }, ps, lvl = 1)
  expect_true(all(res == 1:1000))
})
phylotaR:::cleanup(wd)