tests/testthat/test_clinical.R

In Bioconductor/GenomicDataCommons: NIH / NCI Genomic Data Commons Access

test_that("clinical data is structured properly", {
    sizen <- 3
    case_ids <- cases() |> results(size=sizen) |> ids()
    clinical_data <- gdc_clinical(case_ids)
    # overview of clinical results
    expect_true(
        is(clinical_data, "GDCClinicalList")
    )
    expect_true(
        all(
            c("demographic", "diagnoses", "exposures", "follow_ups", "main")
            %in%
            names(clinical_data)
        )
    )
    
    expect_identical(
        vapply(clinical_data, nrow, integer(1L)),
        c(
            demographic = 3L, diagnoses = 2L, exposures = 0L,
            follow_ups = 0L, main = 3L
        )
    )
    expect_true(
        all(
            vapply(clinical_data, is.data.frame, logical(1L))
        )
    )
})