tests/testthat/test-misc.R

In recount: Explore and download data from the recount project

context("Misc")

test_that("Loading packages", {
    expect_equal(recount:::.load_check("recount"), NULL)
    expect_error(recount:::.load_check("somecrazyname"))
})

info <- geo_info("GSM836270")
chars <- data.frame(
    "cells" = "K562", "shrna.expression" = "no",
    "treatment" = "Puromycin", stringsAsFactors = FALSE
)
test_that("Geo info", {
    expect_equal(info, geo_info("GSM836270", TRUE))
    expect_equal(info$geo_accession, "GSM836270")
    expect_equal(find_geo("SRX110461"), "GSM836270")
    expect_equal(find_geo(""), NA)
    expect_equal(geo_characteristics(info), chars)
    expect_equal(geo_info(NA), NULL)
    expect_equal(colnames(geo_characteristics(geo_info("GSM359183"))), "characteristics")
    # expect_equal(geo_info('GSM1062236'), S4Vectors::DataFrame())
})

if (interactive()) {
    ## Open shiny app when running test in interactive mode.
    ## This will force the app to be available, which will then run the test
    ## successfully.
    ## If there is a better way to test this, please let me know!
    ## See thread at https://groups.google.com/forum/#!topic/shinyapps-users/ElMO_v1eurQ
    browseURL("https://jhubiostatistics.shinyapps.io/recount/")
    test_that("Shiny app is up", {
        expect_equal(
            RCurl::url.exists("https://jhubiostatistics.shinyapps.io/recount/"),
            TRUE
        )
    })
}