tests/testthat/test-web-metadata.R

In recount: Explore and download data from the recount project

context("Website metadata")

test_that("Browse studies at SRA", {
    expect_equal(length(browse_study(c("ERP001942", "ERP009768"), FALSE)), 2)
    expect_equal(browse_study("ERP001942", FALSE), "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP001942")
})

test_that("Download studies", {
    expect_equal(download_study("ERP001942", download = FALSE), "http://duffel.rail.bio/recount/v2/ERP001942/rse_gene.Rdata")
    expect_equal(download_study("ERP001942", download = FALSE, version = 1), "http://duffel.rail.bio/recount/ERP001942/rse_gene.Rdata")
    expect_equal(download_study("ERP001942", type = "mean", download = FALSE), "http://duffel.rail.bio/recount/ERP001942/bw/mean_ERP001942.bw")
})


test_that("Finding abstracts", {
    expect_equal(
        abstract_search("Geuvadis consortium", id_only = TRUE),
        "ERP001942"
    )
    expect_equal(
        abstract_search("Geuvadis consortium"),
        recount_abstract[recount_abstract$project == "ERP001942", ]
    )
})