tests/testthat/test-io.R

context("test-io")

APPDIR <- "../apps"
DATADIR <- "../data"

APP <- file.path(APPDIR, "working")
DATA <- file.path(DATADIR, "working_1")

test_that("Read input as a data frame", {
    process <- fastgenomicsR::Process(app_dir=APP, data_dir=DATA)
    genes <- read.table(process@input$genes)
    cells <- read.table(process@input$cells)
    exprs <- read.table(process@input$some_input)
    expect_equal(colnames(cells), c("cell_id", "some_column", "batch_id"))
    expect_equal(colnames(genes), c("gene_id", "entrez_id", "some_column"))
    expect_equal(colnames(exprs), c("cell_id", "entrez_id", "expression"))
})

test_that("Read + write is a noop", {
    process <- fastgenomicsR::Process(app_dir=APP, data_dir=DATA)
    genes <- read.table(process@input$genes)
    cells <- read.table(process@input$cells)
    exprs <- read.table(process@input$some_input)
    write.table(genes, process@output$genes)
    write.table(cells, process@output$cells)
    write.table(exprs, process@output$some_output)
    expect_equal(readLines(process@input$genes@path), readLines(process@output$genes@path))
    expect_equal(readLines(process@input$cells@path), readLines(process@output$cells@path))
    expect_equal(readLines(process@input$some_input@path), readLines(process@output$some_output@path))
})
FASTGenomics/fastgenomicsR documentation built on June 26, 2019, 12:38 p.m.