tests/testthat/test-tools-entrez.R

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

# LIBS
library(testthat)

# DATA ----
wd <- tempdir()
ps <- parameters(wd = wd)
n <- integer(1)
# 9607

# STUBS ----
esearch_mock <- function(db, term, retmax, retstart, ...) {
  if (n == 0) {
    ids <- NULL
  } else {
    ids <- as.character(1:n)
  }
  res <- list("ids" = ids, "count" = n)
  class(res) <- "esearch"
  res
}
efetch_mock <- function(retmax, ...) {
  # when rettype == 'acc'
  paste0(rep("seqid1", retmax), collapse = "\n")
}

# RUNNING
phylotaR:::cleanup(wd)
context("Testing 'entrez-tools'")
test_that("searchterm_gen() works", {
  trm <- phylotaR:::searchterm_gen(txid = "9606", ps = ps, direct = FALSE)
  expect_true(is.character(trm))
  trm <- phylotaR:::searchterm_gen(txid = "9606", ps = ps, direct = TRUE)
  expect_true(is.character(trm))
})
test_that("seqs_count() works", {
  phylotaR:::cache_setup(ps = ps)
  res <- with_mock(
    `phylotaR:::safely_connect` = function(func, args, fnm, ps) {
      list("count" = args)
    },
    phylotaR:::sqs_count(txid = "9606", direct = FALSE, ps = ps)
  )
  expect_true(grepl(":exp", res[["term"]]))
  res <- with_mock(
    `phylotaR:::safely_connect` = function(func, args, fnm, ps) {
      list("count" = args)
    },
    phylotaR:::sqs_count(txid = "9606", direct = TRUE, ps = ps)
  )
  expect_true(grepl(":noexp", res[["term"]]))
})
phylotaR:::cleanup(wd)
test_that("txnds_count() works", {
  phylotaR:::cache_setup(ps = ps)
  res <- with_mock(
    `phylotaR:::safely_connect` = function(func, args, fnm, ps) {
      list("count" = args)
    },
    phylotaR:::txnds_count(txid = "9606", ps = ps)
  )
  expect_true(res[["term"]] == "txid9606[Subtree]")
})
phylotaR:::cleanup(wd)
test_that("sids_get() works", {
  phylotaR:::cleanup(wd)
  phylotaR:::cache_setup(ps = ps)
  n <<- 100
  res <- with_mock(
    `rentrez::entrez_search` = esearch_mock,
    `rentrez::entrez_fetch` = efetch_mock,
    phylotaR:::sids_get(txid = "9606", direct = FALSE, ps = ps)
  )
  expect_true(length(res) == n)
  phylotaR:::cleanup(wd)
  phylotaR:::cache_setup(ps = ps)
  n <<- 100
  res <- with_mock(
    `rentrez::entrez_search` = esearch_mock,
    `rentrez::entrez_fetch` = efetch_mock,
    phylotaR:::sids_get(
      txid = "9606", direct = FALSE, ps = ps, hrdmx = 20,
      retmax = 10
    )
  )
  expect_true(length(res) != n)
})
phylotaR:::cleanup(wd)