tests/testthat/test-class2tree.R

In taxize: Taxonomic Information from Around the Web

context("class2tree")

spnames <- c("Klattia flava", "Trollius sibiricus", "Arachis paraguariensis",
             "Tanacetum boreale", "Gentiana yakushimensis", "Sesamum schinzianum",
             "Pilea verrucosa", "Tibouchina striphnocalyx", "Lycium dasystemum",
             "Berkheya echinacea", "Androcymbium villosum",
             "Helianthus annuus", "Madia elegans", "Lupinus albicaulis",
             "Pinus lambertiana", "Haloarcula amylolytica JCM 13557",
             "Halomonas sp. 'Soap Lake #6'")

dupnames <- c("Mus musculus", "Escherichia coli",
              "Haloferax denitrificans", "Mus musculus")



test_that("internal functions of class2tree", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("class2tree_internal_fxns", {
    out <- classification(spnames, db = "ncbi", messages = FALSE)
  })
  
  rankList <- dt2df(lapply(out, get_rank), idcol = FALSE)
  expect_equal(nrow(rankList), 17)
  
  nameList <- dt2df(lapply(out, get_name), idcol = FALSE)
  expect_true(identical(colnames(nameList), colnames(rankList)))
  
  strainIndex <- grep("norank", rankList$X1)
  rankList$X1[strainIndex] <- "strain"
  nameList$X1[strainIndex] <- 
    gsub("norank_[[:digit:]]+", "strain", nameList$X1[strainIndex])
  expect_true(length(grep("norank", rankList$X1)) == 0)
  
  indexedRank <- rank_indexing(rankList)
  expect_true(tail(indexedRank, 1)$rank == "norank_131567")
  
  taxMatrix <- taxonomy_table_creator(nameList, rankList)
  expect_is(taxMatrix, "data.frame")
  expect_true(nrow(taxMatrix) == 17)
  
  # wrong indexing
  spnames <- c("Proteus mirabilis","Citrus sinensis","Cyanophora paradoxa")
  out <- classification(spnames, db = "ncbi", messages = FALSE)
  rankList <- dt2df(lapply(out, get_rank), idcol = FALSE)
  rankList[3,] <- c(
    "Cyanophora paradoxa","species","genus","family","superkingdom",
    "norank_131567","class",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
  )
  indexedRank <- rank_indexing(rankList)
  expect_true(
    indexedRank$index[indexedRank$rank == "kingdom"] <
      indexedRank$index[indexedRank$rank == "class"]
  )
})

test_that("class2tree returns the correct value and class", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("class2tree_classification_call", {
    out <- classification(spnames, db = "ncbi", messages = FALSE)
  })

  out <- out[!is.na(out)]
  tr <- class2tree(out)

  expect_identical(tr$names, names(out))

  expect_is(plot(tr), "list")
  expect_is(tr, "classtree")
  expect_is(tr$phylo, "phylo")
  expect_is(tr$classification, "data.frame")
  expect_is(tr$distmat, "dist")
  expect_is(tr$names, "character")
  expect_is(tr$phylo$node.label, "character")
  expect_equal(length(tr$phylo$node.label), tr$phylo$Nnode)
  expect_equal(
    anyDuplicated(gsub("\\.\\d+$", "", names(tr$classification))), 0)
})

test_that("class2tree will abort when input contains duplicate taxa", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("class2tree_classification_dup_call", {
    out <- classification(dupnames, db = "ncbi", messages = FALSE)
  })
  expect_error(class2tree(out),
    "Input list of classifications contains duplicates")
})