tests/testthat/test_defaultsAndClasses.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

context("Tests defaults and classes: 00defaults.R; 01classes.R; 02references.R")

test_that("Tests ezParam()", {
  globalParams = ezParam()
  expect_is(globalParams, "list")
  modifiedParam = ezParam(list(ram=7))
  expect_false(globalParams$ram == modifiedParam$ram)
})

test_that("Tests ezIsSpecified()", {
  is = ezIsSpecified("a")
  expect_is(is, "logical")
  isnt = ezIsSpecified("")
  expect_false(isnt)
  alsoisnt = ezIsSpecified(NULL)
  expect_false(alsoisnt)
  isnteither = ezIsSpecified(NA)
  expect_false(isnteither)
})

test_that("Tests ezFrame()", {
  frame = ezFrame(first=1:3, second=5, "with space"="text", row.names=letters[1:3])
  expect_is(frame, "data.frame")
})

test_that("Tests EzDataset", {
  param = list(dataRoot=system.file(package="ezRun", mustWork = TRUE))
  ds = EzDataset$new(file=system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE),
                     dataRoot=param$dataRoot)
  path = ds$getFullPaths("Read1")
  expect_is(ds,"EzDataset")
  expect_equal(ds$getNames(),c("wt_1","wt_2","mut_1","mut_2"))
  expect_is(ds$file,"character")
  expect_equal(ds$getLength(), 4)
  expect_equal(ds$getColumn("Read1"),c(wt_1="extdata/yeast_10k/wt_1_R1.fastq.gz",wt_2="extdata/yeast_10k/wt_2_R1.fastq.gz",
                                       mut_1="extdata/yeast_10k/mut_1_R1.fastq.gz",mut_2="extdata/yeast_10k/mut_2_R1.fastq.gz"))
  expect_is(ds$meta,"data.frame")
  expect_is(ds$columnHasTag("File"),"logical")
  expect_true(ds$columnHasTag("File")[2])
  expect_is(path,"character")
  expect_true(all(grepl("^/",path)))
  expect_equal(ds$subset("wt_1")$getLength(), 1)
})

test_that("Tests copying an EzDataset and the method setColumn", {
  ds = EzDataset$new(file=system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE))
  expect_is(ds,"EzDataset")
  ds2 = ds$copy()
  expect_is(ds2,"EzDataset")
  expect_equal(ds,ds2)
  ds$setColumn("Read1",1)
  expect_is(all.equal(ds,ds2,check.attributes=F),"character")
  expect_is(ds$meta[1,"Read1 [File]"],"numeric")
})

test_that("Tests EzApp", {
  ds = EzDataset$new(file=system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE))
  app = EzApp$new(runMethod=function(input, output, param){}, name="Test")
  expect_is(app,"EzApp")
  app2 = app$copy()
  expect_equal(app, app2)
  expect_is(app$runMethod,"function")
  expect_is(app$name,"character")
  expect_is(app$appDefaults,"data.frame")
  expect_null(app$run(input=ds, output=ds, param=list(process_mode="DATASET")))
})

test_that("Tests EzRef constructor", {
  refBuild = "Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Version-2013-03-18"
  ref = EzRef(param=ezParam(list(refBuild=refBuild)))
  expect_is(ref, "EzRef")
  expect_identical(ref["refBuild"], refBuild)
  expect_is(getOrganism(ref), "character")
})