tests/testthat/test_report_generation.R

In countsimQC: Compare Characteristic Features of Count Data Sets

library(countsimQC)
context("Check report generation")

local({
  tempDir <- tempdir()
  data(countsimExample)
  x <- lapply(countsimExample, function(w) w[1:50, ])
  if (file.exists(file.path(tempDir, "report_from_test.Rmd"))) {
    file.remove(file.path(tempDir, "report_from_test.Rmd"))
  }
  if (file.exists(file.path(tempDir, "report_from_test.html"))) {
    file.remove(file.path(tempDir, "report_from_test.html"))
  }
  if (file.exists(file.path(tempDir, "report_from_test.pdf"))) {
    file.remove(file.path(tempDir, "report_from_test.pdf"))
  }
  if (file.exists(file.path(tempDir, "report_from_test_ggplots.rds"))) {
    file.remove(file.path(tempDir, "report_from_test_ggplots.rds"))
  }

  test_that("Input argument errors are recognized", {
    ## outputFormat
    expect_error(countsimQCReport(ddsList = x, outputFormat = "html",
                                  outputFile = "report_from_test.html",
                                  outputDir = tempDir, savePlots = TRUE))
    expect_error(countsimQCReport(ddsList = x, outputFormat = "html_document",
                                  outputFile = "report_from_test.pdf",
                                  outputDir = tempDir, savePlots = TRUE))
    ## ddsList
    expect_error(countsimQCReport(ddsList = x[[1]], outputFormat = "html_document",
                                  outputFile = "report_from_test.html",
                                  outputDir = tempDir, savePlots = TRUE))
    expect_error(countsimQCReport(ddsList = list(A = 1:3),
                                  outputFormat = "html_document",
                                  outputFile = "report_from_test.html",
                                  outputDir = tempDir, savePlots = TRUE))
    y <- x
    names(y) <- NULL
    expect_error(countsimQCReport(ddsList = y, outputFormat = "html_document",
                                  outputFile = "report_from_test.html",
                                  outputDir = tempDir, savePlots = TRUE))
    y <- x
    names(y) <- c("A", "A", "B")
    expect_error(countsimQCReport(ddsList = y, outputFormat = "html_document",
                                  outputFile = "report_from_test.html",
                                  outputDir = tempDir, savePlots = TRUE))

    ## rmd_template
    expect_error(countsimQCReport(ddsList = x, outputFormat = "html_document",
                                  outputFile = "report_from_test.html",
                                  outputDir = tempDir, savePlots = TRUE,
                                  rmdTemplate = "nonexistent.Rmd"))

    ## existing rmd output
    file.create(file.path(tempDir, "test_generated.Rmd"))
    expect_error(countsimQCReport(ddsList = x, outputFormat = "html_document",
                                  outputFile = "test_generated.html",
                                  outputDir = tempDir, savePlots = TRUE))
    file.remove(file.path(tempDir, "test_generated.Rmd"))

    ## existing plot output
    file.create(file.path(tempDir, "test_generated2_ggplots.rds"))
    expect_error(countsimQCReport(ddsList = x, outputFormat = "html_document",
                                  outputFile = "test_generated2.html",
                                  outputDir = tempDir, savePlots = TRUE,
                                  forceOverwrite = FALSE))
    file.remove(file.path(tempDir, "test_generated2_ggplots.rds"))
  })

  cqr <- countsimQCReport(ddsList = x, outputFormat = "html_document",
                          outputFile = "test_generated.html",
                          outputDir = tempDir, savePlots = TRUE,
                          description = NULL)
  expect_is(cqr, "character")
  expect_error(countsimQCReport(ddsList = x, outputFormat = NULL,
                                outputFile = "test_generated.html",
                                outputDir = tempDir, savePlots = TRUE,
                                forceOverwrite = FALSE))
  cqr <- countsimQCReport(ddsList = x, outputFormat = NULL,
                          outputFile = "test_generated.html",
                          outputDir = tempDir, savePlots = TRUE,
                          forceOverwrite = TRUE)
  expect_is(cqr, "character")
  generateIndividualPlots(
    ggplotsRds = file.path(tempDir, "test_generated_ggplots.rds"),
    device = "png",
    outputDir = tempDir, nDatasets = 3
  )


  if (file.exists(file.path(tempDir, "report_from_test.html"))) {
    file.remove(file.path(tempDir, "report_from_test.html"))
  }
  if (file.exists(file.path(tempDir, "report_from_test.pdf"))) {
    file.remove(file.path(tempDir, "report_from_test.pdf"))
  }
  if (file.exists(file.path(tempDir, "report_from_test_ggplots.rds"))) {
    file.remove(file.path(tempDir, "report_from_test_ggplots.rds"))
  }
})