tests/testthat/test-getMetadata.R

In beadyallen/MGnifyR: R interface to EBI MGnify metagenomics resource

context("getMetadata")
test_that("getMetadata", {
    # Test that input check caches wrong arguments.
    mg <- MgnifyClient(useCache = FALSE)

    expect_error(getMetadata(1))
    expect_error(getMetadata("test"))
    expect_error(getMetadata(TRUE))

    expect_error(getMetadata(mg, accession = TRUE))
    expect_error(getMetadata(mg, accession = 1))
    expect_error(getMetadata(mg, accession = c(1, 2)))

    expect_error(getMetadata(mg, accession = "test", use.cache = NULL))
    expect_error(getMetadata(mg, accession = "test", use.cache = 1))
    expect_error(getMetadata(mg, accession = "test", use.cache = c(TRUE, FALSE)))

    expect_error(getMetadata(mg, accession = "test", show.messages = NULL))
    expect_error(getMetadata(mg, accession = "test", show.messages = 1))
    expect_error(getMetadata(mg, accession = "test", show.messages = c(TRUE, FALSE)))

    # Require internet access
    skip_if(httr::http_error("https://www.ebi.ac.uk/metagenomics/api/v1"))

    # Test that correct metadata is fetched based on certain accession ID.
    res <- getMetadata(mg, "MGYA00097621", show.messages = FALSE)
    expect_equal(nrow(res), 1)
    expect_true(ncol(res) > 1)
    expect_equal(rownames(res)[1] , "MGYA00097621")
    expect_equal(res$run_accession, "ERR1811651")
    
    # # To reduce the time used to build the package, these tests are commented
    # # When metadata is not found, should give a warning and the result should
    # # be empty tibble
    # expect_warning(res <- getMetadata(mg, "MGYS00005292", show.messages = FALSE))
    # expect_true(ncol(res) == 0 && nrow(res) == 0)
})