tests/testthat/test_OlsSearch.R

In rols: An R interface to the Ontology Lookup Service

context("OlsSearch")

test_that("OlsSearch tgn", {
    tgn <- OlsSearch(q = "tgn",ontology = "GO")
    tgn <- olsSearch(tgn)
    
    tgnres <- structure(c("trans-Golgi network",
                          "clathrin coat of trans-Golgi network vesicle",
                          "Golgi to endosome transport",
                          "trans-Golgi network transport vesicle",
                          "trans-Golgi network transport vesicle membrane"),
                        .Names = c("GO:0005802", "GO:0030130",
                                   "GO:0006895", "GO:0030140", "GO:0012510"))

    expect_identical(sort(termLabel(as(tgn, "Terms"))),
                     sort(tgnres))
})


test_that("OlsSearch ESI", {

    esi2 <- OlsSearch(q = "ESI", ontology = "MS", rows = 28)
    esi1 <- OlsSearch(q = "ESI", ontology = "MS", exact = TRUE)

    esi1 <- olsSearch(esi1)
    esi2 <- olsSearch(esi2)
    
    expect_identical(esi1@numFound, 1L)
    expect_identical(esi2@numFound, 34L)
    expect_true(termId(as(esi1, "Terms")) %in% termId(as(esi2, "Terms")))
})


test_that("OlsSearch tgn 2", {
    tgngo <- OlsSearch("tgn","GO")
    tgngo <- olsSearch(allRows(tgngo))
    expect_equal(tgngo@numFound, 5L)
    
    tgn <- OlsSearch("tgn")
    tgn <- olsSearch(allRows(tgn))

    expect_true(all(tgngo@response[, "obo_id"] %in% tgn@response[, "obo_id"]))
})

test_that("OlsSearch show", 
    expect_null(show(OlsSearch(q = "cell", ontology = "GO"))))

test_that("OlsSearch rows", {
    res <- OlsSearch(q = "cell", ontology = "GO")
    expect_equal(res@rows, 20L)
    expect_equal(nrow(olsSearch(res)@response), 20L)

    res <- OlsSearch(q = "cell", ontology = "GO", rows = 32)
    expect_equal(nrow(olsSearch(res)@response), 32L)
    expect_equal(res@rows, 32L)
    expect_equal(res@rows, olsRows(res))
    
    olsRows(res) <- 108
    expect_equal(olsRows(res), 108L)
    expect_equal(nrow(olsSearch(res)@response), 108L)
    
    res <- allRows(res)
    expect_equal(olsRows(res), res@numFound)
    expect_equal(nrow(olsSearch(res)@response), res@numFound)   
})

test_that("OlsSearch coercion", {
    res <- OlsSearch(q = "plasma", ontology = "GO", rows = 32)
    res <- olsSearch(res)

    resdf <- as(res, "data.frame")
    expect_true(class(resdf) == "data.frame")

    resterms <- as(res, "Terms")
    expect_true(class(resterms) == "Terms")

    expect_identical(nrow(resdf), length(resterms))
    expect_equivalent(termId(resterms), resdf[, "obo_id"])
    expect_equivalent(termLabel(resterms), resdf[, "label"])
})