tests/testthat/test-tools-cache.R

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

# LIBS
library(testthat)

# VARS
wd <- tempdir()

# RUNNING
context("Testing 'cache-tools'")
phylotaR:::cleanup(wd)
test_that("progress_init() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  phylotaR:::progress_init(wd = wd)
  expect_true(file.exists(file.path(wd, "cache", "progress.RData")))
})
phylotaR:::cleanup(wd)
test_that("progress_read() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  phylotaR:::progress_init(wd = wd)
  stg <- phylotaR:::progress_read(wd = wd)
  expect_true(stg == "taxise")
})
phylotaR:::cleanup(wd)
test_that("progress_save() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  phylotaR:::progress_init(wd = wd)
  phylotaR:::progress_save(wd = wd, stg = "taxise")
  expect_true(phylotaR:::progress_read(wd = wd) == "download")
  phylotaR:::progress_save(wd = wd, stg = "download")
  expect_true(phylotaR:::progress_read(wd = wd) == "cluster")
  phylotaR:::progress_save(wd = wd, stg = "cluster")
  expect_true(phylotaR:::progress_read(wd = wd) == "cluster2")
  phylotaR:::progress_save(wd = wd, stg = "cluster2")
  expect_true(is.na(phylotaR:::progress_read(wd = wd)))
})
phylotaR:::cleanup(wd)
test_that("progress_reset() works", {
  # create prgrss
  phylotaR:::cache_setup(ps = list("wd" = wd))
  phylotaR:::progress_init(wd = wd)
  phylotaR:::progress_save(wd = wd, stg = "taxise")
  phylotaR:::progress_save(wd = wd, stg = "download")
  phylotaR:::progress_save(wd = wd, stg = "cluster")
  phylotaR:::progress_save(wd = wd, stg = "cluster2")
  expect_true(is.na(phylotaR:::progress_read(wd = wd)))
  # reset
  phylotaR:::progress_reset(wd = wd, stg = "download")
  expect_true(phylotaR:::progress_read(wd = wd) == "download")
})
phylotaR:::cleanup(wd)
test_that("cache_setup() works", {
  ps <- list("alovelyparameter" = 1, "wd" = wd)
  phylotaR:::cache_setup(ps = ps)
  expect_true(file.exists(file.path(wd, "cache", "prmtrs.RData")))
  expect_error(phylotaR:::cache_setup(ps = ps))
})
phylotaR:::cleanup(wd)
test_that("parameters_load() works", {
  phylotaR:::cache_setup(ps = list("anotherlovelyparameter" = 1, "wd" = wd))
  ps <- phylotaR:::parameters_load(wd = wd)
  expect_true("anotherlovelyparameter" %in% names(ps))
})
phylotaR:::cleanup(wd)
test_that("cache_rm() works", {
  phylotaR:::cache_setup(ps = list("andfinally" = 1, "wd" = wd))
  phylotaR:::cache_rm(wd = wd)
  expect_false(file.exists(file.path(wd, "cache", "prmtrs.RData")))
})
phylotaR:::cleanup(wd)
test_that("obj_check() works", {
  expect_false(phylotaR:::obj_check(wd = wd, nm = "mylovelyobj"))
  phylotaR:::obj_save(
    wd = wd, nm = "mylovelyobj",
    obj = list("interestingthings")
  )
  expect_true(phylotaR:::obj_check(wd = wd, nm = "mylovelyobj"))
})
phylotaR:::cleanup(wd)
test_that("obj_save() works", {
  phylotaR:::obj_save(
    wd = wd, nm = "mylovelyobj",
    obj = list("interestingthings")
  )
  expect_true(file.exists(file.path(wd, "cache", "mylovelyobj.RData")))
})
phylotaR:::cleanup(wd)
test_that("obj_load() works", {
  expect_error(phylotaR:::obj_load(wd = wd, nm = "mylovelyobj"))
  phylotaR:::obj_save(
    wd = wd, nm = "mylovelyobj",
    obj = list("interestingthings")
  )
  obj <- phylotaR:::obj_load(wd = wd, nm = "mylovelyobj")
  expect_true(obj[[1]] == "interestingthings")
})
phylotaR:::cleanup(wd)
test_that("ncbicache_save() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  args <- list("term" = "unique_search_term", "db" = "nucleotide")
  fnm <- "search"
  obj <- "important_result"
  exptd <- file.path(wd, "cache", "ncbi", "search", "nucleotide", "1.RData")
  phylotaR:::ncbicache_save(fnm = fnm, args = args, wd = wd, obj = obj)
  expect_true(file.exists(exptd))
})
phylotaR:::cleanup(wd)
test_that("ncbicache_load() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  args <- list("term" = "unique_search_term", "db" = "nucleotide")
  fnm <- "search"
  obj <- "important_result"
  phylotaR:::ncbicache_save(fnm = fnm, args = args, wd = wd, obj = obj)
  res <- phylotaR:::ncbicache_load(fnm = fnm, args = args, wd = wd)
  expect_equal(obj, res)
})
phylotaR:::cleanup(wd)
test_that("blastcache_save() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  sids_1 <- c("1", "2", "3")
  sids_2 <- c("1", "2", "4")
  phylotaR:::blastcache_save(sids = sids_1, wd = wd, obj = "res_1")
  phylotaR:::blastcache_save(sids = sids_2, wd = wd, obj = "res_2")
  expect_true(file.exists(file.path(wd, "cache", "blast", "1.RData")))
  expect_true(file.exists(file.path(wd, "cache", "blast", "2.RData")))
  expect_false(file.exists(file.path(wd, "cache", "blast", "3.RData")))
})
phylotaR:::cleanup(wd)
test_that("blastcache_load() works", {
  phylotaR:::cache_setup(ps = list("wd" = wd))
  blst_rs <- data.frame("query.id" = as.character(c(1:5)), "subject.id" = "1")
  sids_1 <- c("1", "2", "3")
  sids_2 <- c("1", "2", "4")
  sids_3 <- c("1", "2", "5")
  sids_4 <- c("1", "2")
  phylotaR:::blastcache_save(sids = sids_1, wd = wd, obj = blst_rs[1:3, ])
  phylotaR:::blastcache_save(
    sids = sids_2, wd = wd,
    obj = blst_rs[c(1, 2, 4), ]
  )
  expect_true(nrow(phylotaR:::blastcache_load(sids = sids_1, wd = wd)) == 3)
  expect_true(nrow(phylotaR:::blastcache_load(sids = sids_2, wd = wd)) == 3)
  expect_null(phylotaR:::blastcache_load(sids = sids_3, wd = wd))
  # sqs 4 blast results are contained within sqs 1 and/or 2
  expect_true(nrow(phylotaR:::blastcache_load(sids = sids_4, wd = wd)) == 2)
})
phylotaR:::cleanup(wd)